diff --git a/docs/source/bio.rst b/docs/source/bio.rst index 5f3d686..01542c3 100644 --- a/docs/source/bio.rst +++ b/docs/source/bio.rst @@ -26,8 +26,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_bio" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_bio" This Table can be indexed mandatorily by Spot_ID. diff --git a/docs/source/cell.rst b/docs/source/cell.rst index 08457b3..9871113 100644 --- a/docs/source/cell.rst +++ b/docs/source/cell.rst @@ -24,8 +24,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_cell" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_cell" The header MUST include a detailed description of each optional columns used. diff --git a/docs/source/core.rst b/docs/source/core.rst index 58c5145..29936c2 100644 --- a/docs/source/core.rst +++ b/docs/source/core.rst @@ -55,8 +55,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_core" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_core" The header MUST contain a mandatory set of fields that describe the algorithm(s) that were used to identify and localize bright Spots and to diff --git a/docs/source/demultiplexing.rst b/docs/source/demultiplexing.rst index 8b07993..912e3f3 100644 --- a/docs/source/demultiplexing.rst +++ b/docs/source/demultiplexing.rst @@ -26,8 +26,8 @@ DNA spots detected with multiplexed barcodes File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_demultiplexing" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_demultiplexing" The header MUST contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. diff --git a/docs/source/examples/bio b/docs/source/examples/bio index 19ba65a..a32390a 100644 --- a/docs/source/examples/bio +++ b/docs/source/examples/bio @@ -1,10 +1,10 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_bio -##XYZ_unit=micron -#^NL_distance: -#^H4K27me3_distance: -#additional_tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell -##columns=(Spot_ID, NL_distance, H4K27me3_distance) +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_bio +##XYZ_Unit=micron +#^NL_Distance: +#^H4K27me3_Distance: +#Additional_Tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell +##Columns=(Spot_ID, NL_Distance, H4K27me3_Distance) 1, 1.345, 0.445 2, 1.245, 0.005 3, 1.005, 0.150 diff --git a/docs/source/examples/cell b/docs/source/examples/cell index dbca469..ccf1591 100644 --- a/docs/source/examples/cell +++ b/docs/source/examples/cell @@ -1,13 +1,13 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_cell -##XYZ_unit=micron -##Extra_Cell_ROI_type=Organoid -#^RNA_A_nr: the number of detected bright Spots corresponding to RNA transcript A detected in this Cell, see also RNA Spot Data table -#^RNA_B_nr: the number of detected bright Spots corresponding to RNA transcript B detected in this Cell, see also RNA Spot Data table -#^cell_cycle_state: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M. -#^cell_volume: the volume of this Cell expressed in micron^3. -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace -##columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_nr, RNA_B_nr, cell_cycle_state, cell_volume) +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_cell +##XYZ_Unit=micron +##Extra_Cell_ROI_Type=Organoid +#^RNA_A_Nr: the number of detected bright Spots corresponding to RNA transcript A detected in this Cell, see also RNA Spot Data table +#^RNA_B_Nr: the number of detected bright Spots corresponding to RNA transcript B detected in this Cell, see also RNA Spot Data table +#^Cell_Cycle_State: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M. +#^Cell_Volume: the volume of this Cell expressed in micron^3. +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace +##Columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_Nr, RNA_B_Nr, Cell_Cycle_State, Cell_Volume) 1, 1, 10, 22, 1041.5, 12354.24, G1, 13453 2, 1, 0, 11, 2041.3, 32234.24, G2, 35545 3, 2, 10, 33, 101.5, 12354.24, S, 10010 diff --git a/docs/source/examples/core b/docs/source/examples/core index b723990..a8da664 100644 --- a/docs/source/examples/core +++ b/docs/source/examples/core @@ -1,18 +1,18 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_core -##genome_assembly=GRCh38 -##XYZ_unit=micron +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_core +##Genome_Assembly=GRCh38 +##XYZ_Unit=micron #Software_Title: ChrTracer3 #Software_Type: SpotLoc+Tracing #Software_Authors: Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN #Software_Description: ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3. #Software_Repository: https://github.com/BoettigerLab/ORCA-public -#Software_PreferredCitationID: https://doi.org/10.1038/s41596-020-00478-x -#lab_name: Nobel -#experimenter_name: John Doe -#experimenter_contact: john.doe@email.com -#additional_tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell -##columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID) +#Software_Preferred_Citation_ID: https://doi.org/10.1038/s41596-020-00478-x +#Lab_Name: Nobel +#Experimenter_Name: John Doe +#Experimenter_Contact: john.doe@email.com +#Additional_Tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell +##Columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID) 1, 1, 14.43, 41.43, 1.23, chr1, 0001, 1000, 1 2, 1, 14.83, 41.83, 1.83, chr1, 1001, 2000, 1 3, 1, 15.83, 42.83, 1.33, chr1, 2001, 3000, 1 diff --git a/docs/source/examples/demultiplexing b/docs/source/examples/demultiplexing index d5c7827..0072190 100644 --- a/docs/source/examples/demultiplexing +++ b/docs/source/examples/demultiplexing @@ -1,21 +1,21 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_demultiplexing -##XYZ_unit=micron +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_demultiplexing +##XYZ_Unit=micron #Software_Title: ExampleLocalizationSoftware #Software_Type: SpotLoc #Software_Authors: Doe, J. #Software_Description: A pretty clear description #Software_Repository: https://github.com/repo_name_goes_here -#Software_PreferredCitationID: https://doi.org/doi_goes_here -#lab_name: Nobel -#experimenter_name: John Doe -#experimenter_contact: john.doe@email.com -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality +#Software_Preferred_Citation_ID: https://doi.org/doi_goes_here +#Lab_Name: Nobel +#Experimenter_Name: John Doe +#Experimenter_Contact: john.doe@email.com +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality #^Hyb: the labeling round in which this localization occurred #^Fluor: the fluorescent channel in which this localization was detected #^Brightness: the photon count for this localization event #^Fit_Quality: the quality of fit for this localization, on a relative scale of 0-1 -##columns=(Loc_ID, Spot_ID, X, Y, Z, Hyb, Fluor, Brightness, Fit_Quality) +##Columns=(Loc_ID, Spot_ID, X, Y, Z, Hyb, Fluor, Brightness, Fit_Quality) 1, 1, 2342, 2354, 545, 2, cy3, 1003, 0.83 2, 1, 2342, 2354, 545, 2, cy5, 2000, 0.93 3, 1, 2342, 2354, 545, 3, cy5, 1233, 0.85 diff --git a/docs/source/examples/extracell b/docs/source/examples/extracell index 43538b0..54c0d8d 100644 --- a/docs/source/examples/extracell +++ b/docs/source/examples/extracell @@ -1,12 +1,12 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_extracell -##XYZ_unit=micron -##Extra_Cell_ROI_type=Organoid -#^Cell_A_nr: the number of identified Cells of type A identified to belong to this extracellular ROI. -#^Cell_B_nr: the number of identified Cells of type B identified to belong to this extracellular ROI. -#^ROI_volume: the volume of this extracellular ROI expressed in micron^3. -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace -##columns=(Extra_Cell_ROI, Cell_A_nr, Cell_B_nr, ROI_volume) +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_extracell +##XYZ_Unit=micron +##Extra_Cell_ROI_Type=Organoid +#^Cell_A_Nr: the number of identified Cells of type A identified to belong to this extracellular ROI. +#^Cell_B_Nr: the number of identified Cells of type B identified to belong to this extracellular ROI. +#^ROI_Volume: the volume of this extracellular ROI expressed in micron^3. +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace +##Columns=(Extra_Cell_ROI, Cell_A_Nr, Cell_B_Nr, ROI_Volume) 1, 10, 22, 13453 2, 0, 11, 35545 3, 10, 33, 10010 diff --git a/docs/source/examples/mapping b/docs/source/examples/mapping index c4e0944..77ce9ff 100644 --- a/docs/source/examples/mapping +++ b/docs/source/examples/mapping @@ -1,13 +1,13 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_mapping -##XYZ_unit=micron -##intensity_unit=a.u. -##Sub_Cell_ROI_type=PML_body -##ROI_boundaries_format=(X1,Y1 X2,Y2 Xn,Yn) -#^ROI_volume: the volume of this ROI expressed in micron^3. -#^ROI_intensity: the integrated average signal intensity measured within the boundaries of this ROI, of the marker used to identify this nuclear feature. -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace -##columns=(Sub_Cell_ROI_ID, ROI_boundaries, ROI_volume, ROI_intensity) +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_mapping +##XYZ_Unit=micron +##Intensity_Unit=a.u. +##Sub_Cell_ROI_Type=PML_body +##ROI_Boundaries_Format=(X1,Y1 X2,Y2 Xn,Yn) +#^ROI_Volume: the volume of this ROI expressed in micron^3. +#^ROI_Intensity: the integrated average signal intensity measured within the boundaries of this ROI, of the marker used to identify this nuclear feature. +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace +##Columns=(Sub_Cell_ROI_ID, ROI_Boundaries, ROI_Volume, ROI_Intensity) 1, (0,0 1,2 3,5), 100, 1.00 2, (0,0 2,3 4,6), 48, 0.90 3, (0,0 3,2 7,5), 63, 0.67 diff --git a/docs/source/examples/quality b/docs/source/examples/quality index 17ddf6f..3caf61b 100644 --- a/docs/source/examples/quality +++ b/docs/source/examples/quality @@ -1,16 +1,16 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_quality -##XYZ_unit=micron -##intensity_unit=photonCount +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_quality +##XYZ_Unit=micron +##Intensity_Unit=photonCount #Software_Title: SpotQualityCheck #Software_Type: QualityControl #Software_Authors: John Doe et al. #Software_Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. #Software_Repository: https://eample.com -#Software_PreferredCitationID: https://doi.org/00000 -#lab_name: Nobel -#experimenter_name: John Doe -#experimenter_contact: john.doe@email.com +#Software_Preferred_Citation_ID: https://doi.org/00000 +#Lab_Name: Nobel +#Experimenter_Name: John Doe +#Experimenter_Contact: john.doe@email.com #^Channel_ID: A unique identifier that refers to the Channel that was used to image this Spot. #^Peak_Intensity: The signal intensity of the brightest pixel within a bright Spot (i.e. local maximum). #^Raw_X: the original fit x-position relative to the camera and objective, (prior to drift correction, chromatic correction, or conversion to stage coordinates). This is the appropriate coordinate system for correcting optical aberrations.  @@ -25,8 +25,8 @@ #^X_Loc_Precision: lower and upper bound of 95% confidence interval on X-position after fit #^Y_Loc_Precision: lower and upper bound of 95% confidence interval on Y-position after fit #^Z_Loc_Precision: lower and upper bound of 95% confidence interval on Z-position after fit -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell -##columns=(Spot_ID, Channel_ID, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision) +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell +##Columns=(Spot_ID, Channel_ID, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision) 1, 1, 100, 1.1, 1.05, 1.2, 0.1, 0.05, 0.2, 0.2, 0.2, 0.2, 0.01, 0.01, 0.01 2, 1, 200, 1.11, 1.055, 1.22, 0.11, 0.055, 0.22, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012 3, 2, 500, 1.12, 1.054, 1.21, 0.12, 0.054, 0.21, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012 diff --git a/docs/source/examples/rna b/docs/source/examples/rna index b4a7cf7..175daee 100644 --- a/docs/source/examples/rna +++ b/docs/source/examples/rna @@ -1,19 +1,19 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_rna -##genome_assembly=GRCh38 -##XYZ_unit=micron +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_rna +##Genome_Assembly=GRCh38 +##XYZ_Unit=micron ##Gene_ID_type=Ensemble_V38 #Software_Title: Xyz #Software_Type: SpotLoc #Software_Authors: Janet Doette #Software_Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum. #Software_Repository: https://xyz.com -#Software_PreferredCitationID: https://doi.org/xyz -#lab_name: Nobel -#experimenter_name: John Doe -#experimenter_contact: john.doe@email.com -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell -##columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Cell_ID) +#Software_Preferred_Citation_ID: https://doi.org/xyz +#Lab_Name: Nobel +#Experimenter_Name: John Doe +#Experimenter_Contact: john.doe@email.com +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell +##Columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Cell_ID) 1, 14.43, 41.43, 1.23, ACTB, ENSG00000075624, ENST00000646664.1, 1 2, 14.83, 41.83, 1.83, GAPDH, ENSG00000111640, ENST00000229239.10, 1 3, 15.83, 42.83, 1.33, MB, ENSG00000198125, ENST00000397326.7, 1 diff --git a/docs/source/examples/subcell b/docs/source/examples/subcell index 7ac8177..88d9376 100644 --- a/docs/source/examples/subcell +++ b/docs/source/examples/subcell @@ -1,12 +1,12 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_subcell -##XYZ_unit=micron -##intensity_unit=a.u. -##Sub_Cell_ROI_type=Nucleolus -#^ROI_volume: the volume of this ROI expressed in micron^3. +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_subcell +##XYZ_Unit=micron +##Intensity_Unit=a.u. +##Sub_Cell_ROI_Type=Nucleolus +#^ROI_Volume: the volume of this ROI expressed in micron^3. #^ROI_intensity: the integrated average signal intensity of the marker of interest as measured within the boundaries of this ROI. -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace -##columns=(Sub_Cell_ROI_ID, Cell_ID, ROI_volume, ROI_intensity) +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace +##Columns=(Sub_Cell_ROI_ID, Cell_ID, ROI_Volume, ROI_intensity) 1, 1, 1345, 3500 2, 1, 3554, 1500 3, 2, 1001, 2500 diff --git a/docs/source/examples/trace b/docs/source/examples/trace index 0dea2cd..ed3e47a 100644 --- a/docs/source/examples/trace +++ b/docs/source/examples/trace @@ -1,12 +1,12 @@ -##FOF-CT_version=v0.1 -##Table_namespace=4dn_FOF-CT_trace -##XYZ_unit=micron -##intensity_unit=a.u. -#^allele: This field records the Allele to which this Trace was mapped. This can be one of the following values: BL6, CAST. -#^RNA_A_intensity: This records the intensity of the nascent RNA A expression signal associated with this Trace. -#^NL_distance: This field records the distance of this Trace to the Nuclear Lamina. -#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_cell -##columns=(Trace_ID, allele, RNA_A_int, NL_distance) +##FOF-CT_Version=v0.1 +##Table_Namespace=4dn_FOF-CT_trace +##XYZ_Unit=micron +##Intensity_Unit=a.u. +#^Allele: This field records the Allele to which this Trace was mapped. This can be one of the following values: BL6, CAST. +#^RNA_A_Intensity: This records the intensity of the nascent RNA A expression signal associated with this Trace. +#^NL_Distance: This field records the distance of this Trace to the Nuclear Lamina. +#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_cell +##Columns=(Trace_ID, Allele, RNA_A_Intensity, NL_Distance) 1, BL6, 43253, 0.235 2, CAST, 40001, 0.563 3, BL6, 1000, 0.135 diff --git a/docs/source/extracell.rst b/docs/source/extracell.rst index 3833d1b..2c7b1ac 100644 --- a/docs/source/extracell.rst +++ b/docs/source/extracell.rst @@ -27,8 +27,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_extracell" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_extracell" The header MUST include a detailed description of each optional columns used. diff --git a/docs/source/format_overview.rst b/docs/source/format_overview.rst index 6a277e3..73b8a4e 100644 --- a/docs/source/format_overview.rst +++ b/docs/source/format_overview.rst @@ -25,56 +25,56 @@ File Header - Header lines are denoted by ``#``. In particular: - ``##`` denotes machine readable header lines. These lines must follow the - following format ``##Key1=Value1`` (e.g., ``##FOF-CT_version=v0.1``). + following format ``##Key_A=Value_1`` (e.g., ``##FOF-CT_Version=v0.1``). - ``#`` denotes human readable header lines. These lines should follow the - following format, ``#term: free text description`` (e.g., - ``#lab_name: name of the lab where the experiment was performed``). + following format, ``#Term_X: free text description`` (e.g., + ``#Lab_Name: name of the lab where the experiment was performed``). - ``#^`` denotes lines that define optional user specified columns. These lines provide the name of the column header and a description of the column content. Descriptions must be understandable and sufficient to ensure the interpretation and reproducibility of the results. These lines should - follow the following format ``#^term: free text description`` (e.g., - ``#^optional_column_1: optional column 1 description``). + follow the following format ``#^Term_X: free text description`` (e.g., + ``#^Optional_Column_1: optional column 1 description``). - Header names must use the underscore as a word separator (e.g., RNA_A_intensity). - The file header contains **required**, *conditionally-required*, and optional fields. - Conditionally-required fields are fields that are required when certains - conditions are met (e.g., *##intensity_unit=* is required any time an + conditions are met (e.g., *##Intensity_Unit=* is required any time an intensity metric is reported). - All tables have to contain a mandatory header section. Mandatory header lines (all tables) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -**##FOF-CT_version=** Data format version number. E.g. v0.2 +**##FOF-CT_Version=** Data format version number. E.g. v0.2 -**##XYZ_unit=** ​​The unit used to represent the XYZ location of bright +**##XYZ_Unit=** ​​The unit used to represent the XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problems with special, Greek symbols. Other allowed values are: nm, mm etc. -#lab_name: name of the lab where the experiment was performed +#Lab_Name: name of the lab where the experiment was performed -#experimenter_name: name of the person performing the experiment +#Experimenter_Name: name of the person performing the experiment -**#experimenter_contact:** email address of the person performing the +**#Experimenter_Contact:** email address of the person performing the experiment -**#description:** A free-text, description of the experiment and of the +**#Description:** A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. -**#additional_tables:** AddTable1, AddTable2, AddTableN +**#Additional_Tables:** AddTable1, AddTable2, AddTableN -**##columns=**\ (C1, C2, C3, Cn) +**##Columns=**\ (C1, C2, C3, Cn) Additional mandatory header lines (DNA spot/trace core and RNA tables) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In addition to all of the above, -**##genome_assembly=** Genome build. Note that the 4DN data portal only +**##Genome_Assembly=** Genome build. Note that the 4DN data portal only accepts GRCh38 for human and GRCm38 for mouse. **#Software_Title:** The name of the Software(s) that were used in this @@ -96,7 +96,7 @@ guarantee interpretation and reproducibility. **#Software_Repository:** The URL of any repository or archive where the Software executable release can be obtained. -**#Software_PreferredCitationID:** The Unique Identifier for the +**#Software_Preferred_Citation_ID:** The Unique Identifier for the preferred/primary publication describing this Software. Examples include Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,. diff --git a/docs/source/mapping.rst b/docs/source/mapping.rst index 4c01586..b3dd7d0 100644 --- a/docs/source/mapping.rst +++ b/docs/source/mapping.rst @@ -50,8 +50,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_mapping" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_mapping" The header MUST include a detailed description of each optional columns used. diff --git a/docs/source/quality.rst b/docs/source/quality.rst index c6eba21..a07525a 100644 --- a/docs/source/quality.rst +++ b/docs/source/quality.rst @@ -31,8 +31,8 @@ Spot fit quality File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_quality" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_quality" The header MUST contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. diff --git a/docs/source/rna.rst b/docs/source/rna.rst index 77fc3f5..4689a4a 100644 --- a/docs/source/rna.rst +++ b/docs/source/rna.rst @@ -50,8 +50,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_rna" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_rna" The header MUST contain a mandatory set of fields that describe the algorithm(s) that were used to identify and localize bright Spots. diff --git a/docs/source/subcell.rst b/docs/source/subcell.rst index 972592d..8430c5f 100644 --- a/docs/source/subcell.rst +++ b/docs/source/subcell.rst @@ -26,8 +26,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_subcell" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_subcell" The header MUST include a detailed description of each optional columns used. diff --git a/docs/source/tables/bio_columns.csv b/docs/source/tables/bio_columns.csv index 8236e88..553d020 100644 --- a/docs/source/tables/bio_columns.csv +++ b/docs/source/tables/bio_columns.csv @@ -1,5 +1,5 @@ Name,Description,Example,Conditional requirement conditions *Spot_ID*,A unique identifier for this bright Spot.,1, -optional_column_1:,,, -optional_column_2:,,, -optional_column_3:,,, \ No newline at end of file +Optional_Column_1:,,, +Optional_Column_2:,,, +Optional_Column_3:,,, diff --git a/docs/source/tables/bio_header.csv b/docs/source/tables/bio_header.csv index 5129bdd..ea50688 100644 --- a/docs/source/tables/bio_header.csv +++ b/docs/source/tables/bio_header.csv @@ -1,22 +1,22 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_bio, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_bio, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, *#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#Software_PreferredCitationID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", -*#Intensity_measurement_method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,,, -#^optional_column_2:,,, -#^optional_column_3:,,, -**##XYZ_unit=**,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +**#Software_Preferred_Citation_ID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", +*#Intensity_Measurement_Method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,,, +#^Optional_Column_2:,,, +#^Optional_Column_3:,,, +**##XYZ_Unit=**,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", diff --git a/docs/source/tables/cell_columns.csv b/docs/source/tables/cell_columns.csv index b64020e..791adbc 100644 --- a/docs/source/tables/cell_columns.csv +++ b/docs/source/tables/cell_columns.csv @@ -1,6 +1,6 @@ Name,Description,Example,Conditional requirement conditions **Cell_ID**,This fields reports the unique identifier for Region of Interest (ROI) that represent the boundaries of a Cell identified as part of this experiment. Note: this is used to connect individual Spots or Traces that are part of the same Cell.,1, *Extra_Cell_ROI_ID*,"In case multiple Cells are localized within a given extracellular structure (e.g., Tissue) Region of Interest (ROI), this fields reports the unique identifier that allows to identify such as ROI. Note: this is used to connect individual Cells that are part of the same extracellular ROI.",1,Conditional requirement: this column is mandatory if data in this table can be associated with an extracellular ROI identified as part of this experiment. -optional_column_1,,, -optional_column_2,,, -optional_column_3,,, \ No newline at end of file +Optional_Column_1,,, +Optional_Column_2,,, +Optional_Column_3,,, \ No newline at end of file diff --git a/docs/source/tables/cell_header.csv b/docs/source/tables/cell_header.csv index 57c4443..dfda5d0 100644 --- a/docs/source/tables/cell_header.csv +++ b/docs/source/tables/cell_header.csv @@ -1,23 +1,23 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_cell, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_cell, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, *#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -*#Software_PreferredCitationID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", -#Intensity_measurement_method,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,optional column 1 description,, -#^optional_column_2:,optional column 2 description,, -#^optional_column_3:,optional column 3 description,, -*##Extra_Cell_ROI_type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. -*##XYZ_unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +*#Software_Preferred_Citation_ID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", +#Intensity_Measurement_Method,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,optional column 1 description,, +#^Optional_Column_2:,optional column 2 description,, +#^Optional_Column_3:,optional column 3 description,, +*##Extra_Cell_ROI_Type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. +*##XYZ_Unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/core_header.csv b/docs/source/tables/core_header.csv index d6d26f3..929972d 100644 --- a/docs/source/tables/core_header.csv +++ b/docs/source/tables/core_header.csv @@ -1,17 +1,17 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_core, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_core, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, **#Software_Title:**,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3, **#Software_Type:**,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing, **#Software_Authors:**,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN", **#Software_Description:**,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.", **#Software_Repository:**,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public, -**#Software_PreferredCitationID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", -**##genome_assembly=**,Genome build. Note: the 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse.,GRCh38, -**##XYZ_unit=**,"The unit used to represent the XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problems with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +**#Software_Preferred_Citation_ID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", +**##Genome_Assembly=**,Genome build. Note: the 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse.,GRCh38, +**##XYZ_Unit=**,"The unit used to represent the XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problems with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/demultiplexing_columns.csv b/docs/source/tables/demultiplexing_columns.csv index 8456c6a..b832678 100644 --- a/docs/source/tables/demultiplexing_columns.csv +++ b/docs/source/tables/demultiplexing_columns.csv @@ -4,6 +4,6 @@ Name,Description,Example,Conditional requirement conditions **X**,The sub-pixel X coordinate of this Localization event.,, **Y**,The sub-pixel Y coordinate of this Localization event.,, **Z**,The sub-pixel Z coordinate of this Localization event.,, -#^optional_column_1:,,, -#^optional_column_2:,,, -#^optional_column_3:,,, \ No newline at end of file +#^Optional_Column_1:,,, +#^Optional_Column_2:,,, +#^Optional_Column_3:,,, \ No newline at end of file diff --git a/docs/source/tables/demultiplexing_header.csv b/docs/source/tables/demultiplexing_header.csv index 73db75f..4aa2fde 100644 --- a/docs/source/tables/demultiplexing_header.csv +++ b/docs/source/tables/demultiplexing_header.csv @@ -1,19 +1,19 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_demultiplexing, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_demultiplexing, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, *#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -*#Software_PreferredCitationID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", -*#Intensity_measurement_method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -*##XYZ_unit=*,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +*#Software_Preferred_Citation_ID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", +*#Intensity_Measurement_Method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +*##XYZ_Unit=*,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/extracell_columns.csv b/docs/source/tables/extracell_columns.csv index ccfc6c0..0ed1fe9 100644 --- a/docs/source/tables/extracell_columns.csv +++ b/docs/source/tables/extracell_columns.csv @@ -1,5 +1,5 @@ Name,Description,Example,Conditional requirement conditions **Extra_Cell_ROI_ID**,"This fields reports the unique identifier for an extracellular structure (e.g., Tissue, Organoid) Region of Interest (ROI) identified as part of this experiment. Note: this is used to connect individual Cells that are part of the same extracellular ROI.",1, -optional_column_1,,, -optional_column_2,,, -optional_column_3,,, \ No newline at end of file +Optional_Column_1,,, +Optional_Column_2,,, +Optional_Column_3,,, \ No newline at end of file diff --git a/docs/source/tables/extracell_header.csv b/docs/source/tables/extracell_header.csv index 3e57299..69d4c41 100644 --- a/docs/source/tables/extracell_header.csv +++ b/docs/source/tables/extracell_header.csv @@ -1,23 +1,23 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_extracell, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_extracell, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, *#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -*#Software_PreferredCitationID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", -*#Intensity_measurement_method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,optional column 1 description,, -#^optional_column_2:,optional column 2 description,, -#^optional_column_3:,optional column 3 description,, -*##Extra_Cell_ROI_type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. -*##XYZ_unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +*#Software_Preferred_Citation_ID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", +*#Intensity_Measurement_Method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,optional column 1 description,, +#^Optional_Column_2:,optional column 2 description,, +#^Optional_Column_3:,optional column 3 description,, +*##Extra_Cell_ROI_Type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. +*##XYZ_Unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/mapping_columns.csv b/docs/source/tables/mapping_columns.csv index a67e7c5..5f07e5f 100644 --- a/docs/source/tables/mapping_columns.csv +++ b/docs/source/tables/mapping_columns.csv @@ -2,6 +2,6 @@ Name,Description,Example,Conditional requirement conditions *Sub_Cell_ROI_ID*,"This fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a sub-cellular structure identified as part of this experiment. Note: this is used to connect all Spots, and Traces that belong to the same ROI.",1,Conditional requirement: This table must have at least one of the ID columns. Sub_Cell_ROI_ID MUST be reported if this table contains subcellular ROI data *Cell_ID*,This fields reports the unique identifier for Region of Interest (ROI) that represent the boundaries of a Cell identified as part of this experiment. Note: this is used to connect individual Spots or Traces that are part of the same Cell.,1,Conditional requirement: This table must have at least one of the ID columns. Cell_ID MUST be reported if this table contains Cell data *Extra_Cell_ROI_ID*,"This fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a extracellular structure (e.g., Tissue) identified as part of this experiment. Note: this is used to connect all Spots, and Traces that belong to the same ROI.",1,Conditional requirement: This table must have at least one of the ID columns. Extra_Cell_ROI_ID MUST be reported if this table contains extracellular ROI data. -optional_column_1,,, -optional_column_2,,, -optional_column_3,,, \ No newline at end of file +Optional_Column_1,,, +Optional_Column_2,,, +Optional_Column_3,,, \ No newline at end of file diff --git a/docs/source/tables/mapping_header.csv b/docs/source/tables/mapping_header.csv index 9c5c0f1..30a0b6c 100644 --- a/docs/source/tables/mapping_header.csv +++ b/docs/source/tables/mapping_header.csv @@ -1,25 +1,25 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_mapping, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_mapping, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, **#Software_Title:**,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3, **#Software_Type:**,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing, **#Software_Authors:**,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN", **#Software_Description:**,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.", **#Software_Repository:**,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public, -**#Software_PreferredCitationID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", -*#Intensity_measurement_method:*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,optional column 1 description,, -#^optional_column_2:,optional column 2 description,, -#^optional_column_3:,optional column 3 description,, -**##XYZ_unit=**,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -*##Sub_Cell_ROI_type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Nucleolus, NL, PML_body, Cajal_body, Chromosome_Domain, Other",Nucleolus,Conditional requirement: this MUST be reported in any Sub_Cell ROI is idenfied as part of this experiment. -*##Extra_Cell_ROI_type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. -**##ROI_boundaries_format=**,This field describes the format that is used to record the boundaries of the ROI in global coordinates. It is strongly recommended ot use the format defined by the OME Data Model to describe ROI (https://docs.openmicroscopy.org/ome-model/5.6.3/developers/roi.html).,"(X1,Y1, X2,Y2 Xn,Yn)", -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +**#Software_Preferred_Citation_ID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", +*#Intensity_Measurement_Method:*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,optional column 1 description,, +#^Optional_Column_2:,optional column 2 description,, +#^Optional_Column_3:,optional column 3 description,, +**##XYZ_Unit=**,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +*##Sub_Cell_ROI_Type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Nucleolus, NL, PML_body, Cajal_body, Chromosome_Domain, Other",Nucleolus,Conditional requirement: this MUST be reported in any Sub_Cell ROI is idenfied as part of this experiment. +*##Extra_Cell_ROI_Type=*,"This field records the type of extracellular structure ROIs used in this table represent. The value utilized should belong to this list: Tissue, Organoid, Other",Tissue,Conditional requirement: this MUST be reported in any Super_Cell ROI is idenfied as part of this experiment. +**##ROI_Boundaries_Format=**,This field describes the format that is used to record the boundaries of the ROI in global coordinates. It is strongly recommended ot use the format defined by the OME Data Model to describe ROI (https://docs.openmicroscopy.org/ome-model/5.6.3/developers/roi.html).,"(X1,Y1, X2,Y2 Xn,Yn)", +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", diff --git a/docs/source/tables/quality_columns.csv b/docs/source/tables/quality_columns.csv index 0f176a5..f8c42f4 100644 --- a/docs/source/tables/quality_columns.csv +++ b/docs/source/tables/quality_columns.csv @@ -1,8 +1,8 @@ Name,Description,Example,Conditional requirement conditions **Spot_ID**,A unique identifier for this bright Spot.,1, -conditionally_required_column_1:,,,one of the conditionally required columns desribed in the header -conditionally_required_column_2:,,,one of the conditionally required columns desribed in the header -conditionally_required_column_3:,,,one of the conditionally required columns desribed in the header -optional_column_1:,,, -optional_column_2:,,, -optional_column_3:,,, \ No newline at end of file +Conditionally_Required_Column_1:,,,one of the conditionally required columns desribed in the header +Conditionally_Required_Column_2:,,,one of the conditionally required columns desribed in the header +Conditionally_Required_Column_3:,,,one of the conditionally required columns desribed in the header +Optional_Column_1:,,, +Optional_Column_2:,,, +Optional_Column_3:,,, diff --git a/docs/source/tables/quality_header.csv b/docs/source/tables/quality_header.csv index 6ce6b9e..3e978dc 100644 --- a/docs/source/tables/quality_header.csv +++ b/docs/source/tables/quality_header.csv @@ -1,17 +1,17 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_quality, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_quality, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, **#Software_Title:**,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3, **#Software_Type:**,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing, **#Software_Authors:**,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN", **#Software_Description:**,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.", **#Software_Repository:**,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public, -**#Software_PreferredCitationID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", +**#Software_Preferred_Citation_ID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", *#Intensity_Measurement_Method:*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. **#^Channel_ID:**,A unique identifier that refers to the Channel that was used to image this Spot.,, **#^Fluorophore_ID:**,A unique identifier that refers to the Fluorophore whose Emission is utilized to detect this Spot.,, @@ -32,10 +32,10 @@ Name,Description,Example,Conditional requirement conditions #^X_Loc_Precision,"Metric used to quantify the Precision associated with the estimation of the X-axis localization of this bright Spot. Different methods might be used. The Cramer-Rao Lower and Upper Bounds methods is widely accepted, but it tends to overestimate the Precision value. Alternatively, the Thompson method, by which Precision is estimated to be proportional to Photon Count, can also be used even though this method highly overestimates the Precision. Whatever method is used, description of how this metric was computed and of the Software that was employed must be provided in the header of the table. Such description must contain enough details to allow interpretation and reproducibility.",, #^Y_Loc_Precision,"Metric used to quantify the Precision associated with the estimation of the Y-axis localization of this bright Spot. Different methods might be used. The Cramer-Rao Lower and Upper Bounds methods is widely accepted, but it tends to overestimate the Precision value. Alternatively, the Thompson method, by which Precision is estimated to be proportional to Photon Count, can also be used even though this method highly overestimates the Precision. Whatever method is used, description of how this metric was computed and of the Software that was employed must be provided in the header of the table. Such description must contain enough details to allow interpretation and reproducibility.",, #^Z_Loc_Precision,"Metric used to quantify the Precision associated with the estimation of the Z-axis localization of this bright Spot. Different methods might be used. The Cramer-Rao Lower and Upper Bounds methods is widely accepted, but it tends to overestimate the Precision value. Alternatively, the Thompson method, by which Precision is estimated to be proportional to Photon Count, can also be used even though this method highly overestimates the Precision. Whatever method is used, description of how this metric was computed and of the Software that was employed must be provided in the header of the table. Such description must contain enough details to allow interpretation and reproducibility.",, -#^optional_column_1:,,, -#^optional_column_2:,,, -#^optional_column_3:,,, -**##XYZ_unit=**,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", +#^Optional_Column_1:,,, +#^Optional_Column_2:,,, +#^Optional_Column_3:,,, +**##XYZ_Unit=**,"The unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", diff --git a/docs/source/tables/rna_header.csv b/docs/source/tables/rna_header.csv index f7e1004..81286cc 100644 --- a/docs/source/tables/rna_header.csv +++ b/docs/source/tables/rna_header.csv @@ -1,19 +1,19 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_rna, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_rna, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, **#Software_Title:**,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3, **#Software_Type:**,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing, **#Software_Authors:**,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN", **#Software_Description:**,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.", **#Software_Repository:**,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public, -**#Software_PreferredCitationID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, -#additional_tables:,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", -##genome_assembly=,Genome build. Note: the 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse.,GRCh38, +**#Software_Preferred_Citation_ID:**,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x, +#Additional_Tables:,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell", +##Genome_Assembly=,Genome build. Note: the 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse.,GRCh38, **##Gene_ID_type=**,The field used to report the type of unique ID used to identify the Gene encoding for the targeted RNA transcript.,Ensemble_V38, *##Transcript_ID_type=*,The field used to report the type of unique ID used to identify the targeted RNA transcript.,Ensemble_V38,Conditional requirement: this MUST be reported if multiple transcripts are associated with the same Gene_ID and the FISH probes are capable of distinguishing them. -**##XYZ_unit=**,"The unit used to represent XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +**##XYZ_Unit=**,"The unit used to represent XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron, +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/subcell_columns.csv b/docs/source/tables/subcell_columns.csv index e7e4682..cfd67b0 100644 --- a/docs/source/tables/subcell_columns.csv +++ b/docs/source/tables/subcell_columns.csv @@ -1,6 +1,6 @@ Name,Description,Example,Conditional requirement conditions **Sub_Cell_ROI_ID**,"This fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a sub-cellular structure identified as part of this experiment. Note: this is used to connect all Spots, and Traces that belong to the same ROI.",1, *Cell_ID*,This fields reports the unique identifier for Region of Interest (ROI) that represent the boundaries of a Cell identified as part of this experiment. Note: this is used to connect individual Spots or Traces that are part of the same Cell.,1,Conditional requirement: this column is mandatory if data in this table can be associated with a Cell identified as part of this experiment. -optional_column_1,,, -optional_column_2,,, -optional_column_3,,, \ No newline at end of file +Optional_Column_1,,, +Optional_Column_2,,, +Optional_Column_3,,, \ No newline at end of file diff --git a/docs/source/tables/subcell_header.csv b/docs/source/tables/subcell_header.csv index ee64160..600e061 100644 --- a/docs/source/tables/subcell_header.csv +++ b/docs/source/tables/subcell_header.csv @@ -1,23 +1,23 @@ Name,Description,Example,Conditional requirement conditions -**##FOF-CT_version=**,Version of the FOF format used in this case.,v0.1, -**##Table_namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_subcell, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -**#experimenter_contact:**,email address of the person performing the experiment.,john.doe@email.com, -**#description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +**##FOF-CT_Version=**,Version of the FOF format used in this case.,v0.1, +**##Table_Namespace=**,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_subcell, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +**#Experimenter_Contact:**,email address of the person performing the experiment.,john.doe@email.com, +**#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, *#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -*#Software_PreferredCitationID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -**#additional_tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", -*#Intensity_measurement_method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,optional column 1 description,, -#^optional_column_2:,optional column 2 description,, -#^optional_column_3:,optional column 3 description,, -**##Sub_Cell_ROI_type=**,"This field records the type of sub-cellular structure ROIs used in this table represent. The value utilized should belong to this list: Nucleolus, NL, PML_body, Cajal_body, Chromosome_Domain, Other",Nucleolus, -*##XYZ_unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. -*##time_unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -*##intensity_unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -**##columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +*#Software_Preferred_Citation_ID:*,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +**#Additional_Tables:**,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace", +*#Intensity_Measurement_Method*,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,optional column 1 description,, +#^Optional_Column_2:,optional column 2 description,, +#^Optional_Column_3:,optional column 3 description,, +**##Sub_Cell_ROI_Type=**,"This field records the type of sub-cellular structure ROIs used in this table represent. The value utilized should belong to this list: Nucleolus, NL, PML_body, Cajal_body, Chromosome_Domain, Other",Nucleolus, +*##XYZ_Unit=*,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. +*##Time_Unit=*,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +*##Intensity_Unit=*,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +**##Columns=**,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/tables/trace_columns.csv b/docs/source/tables/trace_columns.csv index f538e7d..aa984bf 100644 --- a/docs/source/tables/trace_columns.csv +++ b/docs/source/tables/trace_columns.csv @@ -1,5 +1,5 @@ Name,Description,Example,Conditional requirement conditions Trace_ID,This field reports the unique identifier for a DNA Trace identified as part of this experiment. Note: this is used to connect data in this table with a given Trace as recorded in the corresponding DNA-Spot/Trace Data core table.,1, -optional_column_1,,, -optional_column_2,,, -optional_column_3,,, \ No newline at end of file +Optional_Column_1,,, +Optional_Column_2,,, +Optional_Column_3,,, \ No newline at end of file diff --git a/docs/source/tables/trace_header.csv b/docs/source/tables/trace_header.csv index 517cc50..0633ccb 100644 --- a/docs/source/tables/trace_header.csv +++ b/docs/source/tables/trace_header.csv @@ -1,22 +1,22 @@ Name,Description,Example,Conditional requirement conditions -##FOF-CT_version=,Version of the FOF format used in this case.,v0.1, -##Table_namespace=,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_trace, -#lab_name:,name of the lab where the experiment was performed.,Nobel, -#experimenter_name:,name of the person performing the experiment.,John Doe, -#experimenter_contact:,email address of the person performing the experiment.,john.doe@email.com, -#description:,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, +##FOF-CT_Version=,Version of the FOF format used in this case.,v0.1, +##Table_Namespace=,Identifier for this type of table. Value must be as in the example.,4dn_FOF-CT_trace, +#Lab_Name:,name of the lab where the experiment was performed.,Nobel, +#Experimenter_Name:,name of the person performing the experiment.,John Doe, +#Experimenter_Contact:,email address of the person performing the experiment.,john.doe@email.com, +#Description:,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",, #Software_Title:,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,ChrTracer3,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. #Software_Type:,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",SpotLoc+Tracing,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. #Software_Authors:,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.","Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. #Software_Description:,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.","ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.",Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. #Software_Repository:,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/BoettigerLab/ORCA-public,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -#Software_PreferredCitationID:,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. -#additional_tables:,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_cell", -#Intensity_measurement_method,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -#^optional_column_1:,optional column 1 description,, -#^optional_column_2:,optional column 2 description,, -#^optional_column_3:,optional column 3 description,, -##XYZ_unit=,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. -##time_unit=,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. -##intensity_unit=,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. -##columns=,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file +#Software_Preferred_Citation_ID:,"The Unique Identifier for the preferred/primary publication describing this Software. Examples include, Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.",https://doi.org/10.1038/s41596-020-00478-x,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table. +#Additional_Tables:,list of the additional tables being submitted. Note: use a comma to separate each table name from the next.,"4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_cell", +#Intensity_Measurement_Method,"If relevant, the method that was used to performed intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted in Photon conunts.",Spot centroid intensity.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +#^Optional_Column_1:,optional column 1 description,, +#^Optional_Column_2:,optional column 2 description,, +#^Optional_Column_3:,optional column 3 description,, +##XYZ_Unit=,"If relevant, the unit used to represent XYZ locations or distances in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc.",micron,Conditional requirement: this MUST be reported if any locations metrics are reported. +##Time_Unit=,"If relevant, the unit used to represent a time interval. Note: use 'sec' for seconds, 'msec' for milliseconds, 'min' for minutes, and 'hr' for hours.",sec,Conditional requirement: this MUST be reported if any time metrics are reported. +##Intensity_Unit=,"If relevant, the unit used to represent intensity measurements.",a.u.,Conditional requirement: this MUST be reported if any intensity metrics are reported. +##Columns=,list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next.,"(Spot_ID, X, Y, Z)", \ No newline at end of file diff --git a/docs/source/trace.rst b/docs/source/trace.rst index ceb591a..ac03583 100644 --- a/docs/source/trace.rst +++ b/docs/source/trace.rst @@ -18,8 +18,8 @@ Example File Header ----------- -- The first line in the header is always "##FOF-CT_version=vX.X" -- The second line in the header is always "##Table_namespace=4dn_FOF-CT_trace" +- The first line in the header is always "##FOF-CT_Version=vX.X" +- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_trace" The header MUST include a detailed description of each optional columns used.