Merge 2e833b8 into 4a3d153

vanvalenlab · May 22, 2020 · bfde073 · bfde073
2 parents 4a3d153 + 2e833b8
commit bfde073
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diff --git a/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p00_small.tif b/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p00_small.tif
diff --git a/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p01_small.tif b/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p01_small.tif
diff --git a/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p02_small.tif b/...uo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/journal_pcbi_1005177_s01_p02_small.tif
diff --git a/data/raw_data/dynamic/2d/fluo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/metadata b/data/raw_data/dynamic/2d/fluo/HEK293/Nuclear_H2B-mClover/journal_pcbi_1005177/metadata
@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "HEK293"],
+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
+		}
+	],
+	"EXP_ID" : ["journal_pcbi_1005177"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
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+	"METHODS" : [{
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+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
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diff --git a/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0010_Dapii.tif b/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0010_Dapii.tif
diff --git a/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0011_Dapii.tif b/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0011_Dapii.tif
diff --git a/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0012_Dapii.tif b/...a/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/20190514_A549_G07_0012_Dapii.tif
diff --git a/data/raw_data/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/metadata b/data/raw_data/static/2d/fluo/A549/Nuclear_Hoescht33342/20190514_EP01/metadata
@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "A549"],
+	"CHANNEL_MARKER" : [{
+		"0" : "Hoescht33342"
+		}
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+	"EXP_ID" : ["20190514_EP01"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "Caltech",
+		"COLLECTED_BY" : "Edward Pao",
+		"DATE_COLLECTED" : "05_14_2019",
+		"DOI" : ""
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+		"CULTURE" : "",
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diff --git a/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_0.tif b/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_0.tif
diff --git a/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_1.tif b/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_1.tif
diff --git a/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_2.tif b/...raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/20200116_DCIS_Point2304_crop_2.tif
diff --git a/data/raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/metadata b/data/raw_data/static/2d/mibi/DCIS/Nuclear_DNA/20200116_DCIS/metadata
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+{
+	"TYPE" : ["cell", "DCIS"],
+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
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+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
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+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Ti-E",
+		"CAMERA" : "Andor Neo 5.5",
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+		"NA": "",
+		"BINNING" : "2x2",
+		"PIXEL_SIZE" : "0.65um",
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+		"Y" : "512"
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+	"ONTOLOGY" : ["static","2d","mibi","nuclear"],
+	"METHODS" : [{
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+		"CULTURE" : "",
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diff --git a/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_0.tif b/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_0.tif
diff --git a/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_1.tif b/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_1.tif
diff --git a/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_2.tif b/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/Point2304_crop_2.tif
diff --git a/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/metadata b/data/raw_data/static/2d/mibi/DCIS/WholeCell_NaKATPase/20200116_DCIS/metadata
@@ -0,0 +1,39 @@
+{
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+	"CHANNEL_MARKER" : [{
+		"0" : "H2B-mClover"
+		}
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+	"EXP_ID" : ["20200116_DCIS"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "stanford",
+		"COLLECTED_BY" : "Takamasa Kudo",
+		"DATE_COLLECTED" : "11_13_2017",
+		"DOI" : " https://doi.org/10.1371/journal.pcbi.1005177"
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Ti-E",
+		"CAMERA" : "Andor Neo 5.5",
+		"MAGNIFICATION" : "20x",
+		"NA": "",
+		"BINNING" : "2x2",
+		"PIXEL_SIZE" : "0.65um",
+		"EXPOSURE_TIME" : "",
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+		}
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+		"Y" : "512"
+		}
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+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}
diff --git a/data/raw_data/static/3d/Phase/A549/20190514_EP01/20190514_A549_F07_0002_small.tif b/data/raw_data/static/3d/Phase/A549/20190514_EP01/20190514_A549_F07_0002_small.tif
diff --git a/data/raw_data/static/3d/Phase/A549/20190514_EP01/metadata b/data/raw_data/static/3d/Phase/A549/20190514_EP01/metadata
@@ -0,0 +1,39 @@
+{
+	"TYPE" : ["cell", "A549"],
+	"CHANNEL_MARKER" : [{
+		"0" : "Hoescht33342"
+		}
+	],
+	"EXP_ID" : ["20190514_EP01"],
+	"RAW_DATA_ORIGIN" : [{
+		"FACILITY" : "Caltech",
+		"COLLECTED_BY" : "Edward Pao",
+		"DATE_COLLECTED" : "05_14_2019",
+		"DOI" : ""
+		}
+	],
+	"IMAGING_PARAMETERS" : [{
+		"MICROSCOPE" : "Nikon Eclipse Ti-2",
+		"CAMERA" : "Prime 95B",
+		"MAGNIFICATION" : "20x",
+		"NA": "0.45",
+		"BINNING" : "1x1",
+		"PIXEL_SIZE" : "0.55um",
+		"EXPOSURE_TIME" : "25ms"
+		}
+	],
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+		"DIMENSIONS" : [{
+		"X" : "1608",
+		"Y" : "1608"
+		}
+	],
+	"ONTOLOGY" : ["static","2d","fluorescence", "nuclear"],
+	"METHODS" : [{
+		"SUBTYPE" : "",
+		"CULTURE" : "",
+		"LABELING" : "",
+		"IMAGING" : ""
+		}
+	]
+}
diff --git a/example_data/3D/FOV_0/Pos0_DAPIRegistered.tif b/example_data/3D/FOV_0/Pos0_DAPIRegistered.tif
diff --git a/example_data/multichannel/Training_Data_1/Point1/HH3.tif b/example_data/multichannel/Training_Data_1/Point1/HH3.tif
diff --git a/example_data/multichannel/Training_Data_1/Point1/Icon b/example_data/multichannel/Training_Data_1/Point1/Icon
diff --git a/example_data/multichannel/Training_Data_1/Point1/LaminAC.tif b/example_data/multichannel/Training_Data_1/Point1/LaminAC.tif
diff --git a/example_data/multichannel/Training_Data_1/Point1/NaK ATPase.tif b/example_data/multichannel/Training_Data_1/Point1/NaK ATPase.tif
diff --git a/example_data/multichannel/Training_Data_1/Point5/HH3.tif b/example_data/multichannel/Training_Data_1/Point5/HH3.tif
diff --git a/example_data/multichannel/Training_Data_1/Point5/LaminAC.tif b/example_data/multichannel/Training_Data_1/Point5/LaminAC.tif
diff --git a/example_data/multichannel/Training_Data_1/Point5/NaK ATPase.tif b/example_data/multichannel/Training_Data_1/Point5/NaK ATPase.tif
diff --git a/example_data/multichannel/Training_Data_1/Point9/HH3.tif b/example_data/multichannel/Training_Data_1/Point9/HH3.tif
diff --git a/example_data/multichannel/Training_Data_1/Point9/Icon b/example_data/multichannel/Training_Data_1/Point9/Icon
diff --git a/example_data/multichannel/Training_Data_1/Point9/LaminAC.tif b/example_data/multichannel/Training_Data_1/Point9/LaminAC.tif
diff --git a/example_data/multichannel/Training_Data_1/Point9/NaK ATPase.tif b/example_data/multichannel/Training_Data_1/Point9/NaK ATPase.tif
diff --git a/example_data/timelapse/HeLa_by_channel/FITC/img_000000000_FITC_001.png b/example_data/timelapse/HeLa_by_channel/FITC/img_000000000_FITC_001.png
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diff --git a/example_data/timelapse/HeLa_by_channel/FITC/img_000000002_FITC_001.png b/example_data/timelapse/HeLa_by_channel/FITC/img_000000002_FITC_001.png
diff --git a/example_data/timelapse/HeLa_by_channel/FITC/img_000000003_FITC_001.png b/example_data/timelapse/HeLa_by_channel/FITC/img_000000003_FITC_001.png
diff --git a/example_data/timelapse/HeLa_by_channel/FITC/img_000000004_FITC_001.png b/example_data/timelapse/HeLa_by_channel/FITC/img_000000004_FITC_001.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase0/img_000000000_Phase_000.png b/example_data/timelapse/HeLa_by_channel/phase0/img_000000000_Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase0/img_000000001_Phase_000.png b/example_data/timelapse/HeLa_by_channel/phase0/img_000000001_Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase0/img_000000002_Phase_000.png b/example_data/timelapse/HeLa_by_channel/phase0/img_000000002_Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase0/img_000000003_Phase_000.png b/example_data/timelapse/HeLa_by_channel/phase0/img_000000003_Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase0/img_000000004_Phase_000.png b/example_data/timelapse/HeLa_by_channel/phase0/img_000000004_Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase1/img_000000000_Phase_001.png b/example_data/timelapse/HeLa_by_channel/phase1/img_000000000_Phase_001.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase1/img_000000001_Phase_001.png b/example_data/timelapse/HeLa_by_channel/phase1/img_000000001_Phase_001.png
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diff --git a/example_data/timelapse/HeLa_by_channel/phase2/img_000000000_Phase_002.png b/example_data/timelapse/HeLa_by_channel/phase2/img_000000000_Phase_002.png
diff --git a/example_data/timelapse/HeLa_by_channel/phase2/img_000000001_Phase_002.png b/example_data/timelapse/HeLa_by_channel/phase2/img_000000001_Phase_002.png
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diff --git a/example_data/timelapse/HeLa_by_channel/phase2/img_000000004_Phase_002.png b/example_data/timelapse/HeLa_by_channel/phase2/img_000000004_Phase_002.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000000/FITC_001.png b/example_data/timelapse/HeLa_by_image/img_000000000/FITC_001.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000000/Phase_000.png b/example_data/timelapse/HeLa_by_image/img_000000000/Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000000/Phase_001.png b/example_data/timelapse/HeLa_by_image/img_000000000/Phase_001.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000000/Phase_002.png b/example_data/timelapse/HeLa_by_image/img_000000000/Phase_002.png
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diff --git a/example_data/timelapse/HeLa_by_image/img_000000001/Phase_000.png b/example_data/timelapse/HeLa_by_image/img_000000001/Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000001/Phase_001.png b/example_data/timelapse/HeLa_by_image/img_000000001/Phase_001.png
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diff --git a/example_data/timelapse/HeLa_by_image/img_000000002/Phase_000.png b/example_data/timelapse/HeLa_by_image/img_000000002/Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000002/Phase_001.png b/example_data/timelapse/HeLa_by_image/img_000000002/Phase_001.png
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diff --git a/example_data/timelapse/HeLa_by_image/img_000000003/Phase_000.png b/example_data/timelapse/HeLa_by_image/img_000000003/Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000003/Phase_001.png b/example_data/timelapse/HeLa_by_image/img_000000003/Phase_001.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000003/Phase_002.png b/example_data/timelapse/HeLa_by_image/img_000000003/Phase_002.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000004/FITC_001.png b/example_data/timelapse/HeLa_by_image/img_000000004/FITC_001.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000004/Phase_000.png b/example_data/timelapse/HeLa_by_image/img_000000004/Phase_000.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000004/Phase_001.png b/example_data/timelapse/HeLa_by_image/img_000000004/Phase_001.png
diff --git a/example_data/timelapse/HeLa_by_image/img_000000004/Phase_002.png b/example_data/timelapse/HeLa_by_image/img_000000004/Phase_002.png