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@lukasz-migas lukasz-migas released this Aug 28, 2019

Minor version bump to prevent erroneous update message.

Next version will be v2.0.0.0 which will pack a lot of new features, improvements and fixes.

Assets 3

@lukasz-migas lukasz-migas released this Jan 10, 2019 · 16 commits to master since this release

What changed in ORIGAMIANALYSE

Documentation

Added Added online documentation

Added Added several new videos to the YouTube playlist

Document Tree

Fixed Fixed typo: spectrun -> spectrum (grr)

Fixed When loading mzml/mgf files, the individual scans will no longer be shown in the document tree as it caused some major issues. If you would like to see the individual spectra, please double-click on the header 'Tandem Mass Spectra'

Fixed Fixed a problem when trying to plot waterfall plot from the Document Tree menu

Improved When loading any data into the INTERACTIVE document, you will be asked whether data should be duplicated, merged or duplicated

Improved When plotting a waterfall plot, data will be checked to ensure its not too big (e.g. not too many rows). If the value is above the threshold (set to 500), you will be asked if you would like to continue

Main window

Added Added new menu: Plugins. This menu will hold all future mini-applications

Added Umder the menu Plot settings I've added a couple new options that allow modification of plot extra plot parameters.

Improved The help pages (Help -> Help pages -> ...) have now been replaced with links to the new documentation (opens in the browser). Where no documentation exists yet, old pages will be shown. Also available online

Annotations

Added you can now also easily 'duplicate/multiply' annotations. Action -> Multiply annotations... this will result in a copy of the selected annotation(s) with slight difference in the min-value (so they can be distinguished from its parent)

Added Text annotations can now be added to other plots (scatter, v-bar, h-bar, waterfall, multi-line/overlay). To added annotations, find it in the Document Tree, right-click on it and you should be presented with option Show annotations panel.... Then you can simply follow the standard annotations protocol. See here for more information

Added Annotations parameters can now be easily modified as they can be dragged on the plot. If an annotation is shown on your plot, you can simply drag it around in the plot area and once you let-go, new settings (e.g. position) will be updated in the ORIGAMI document.

Fixed font size, weight and rotation will now be aplied when adding labels

Fixed auto-label generator will now also create labels based purely on the charge state

Fixed annotation parameters (e.g. size, weight, rotation) will be respected when replotting from the Document Tree

Interactive panel

Added Made big progres in terms of copying/applying styles for plot elements. When you
double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'.

Added certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset.

Added Scatter plots that are created from datasets loaded through text files with added metadata can be enhanced with weblinks/URLs. See the example for more information.

Fixed fixed sorting in the list (especilaly when using the 'Show selected' option) Lists are sorted using 'natural sorting' from now on, meaning they should be more logically sorted.

Fixed fixed the show/hide table elements when you right-click on the table headers

Improved Colorbars:

  • added loads of new settings users can control
  • better behaviour when adding colorbars to plots

Changed removed tools/toolset from ORIGAMI - the new system of copy/apply style should work much better

Improved I've realised that using 'coffeescript' for widget exportation was a big mistake as it takes ~10x+ longer to compile that script than pure JavaScript. Adding widgets will be a lot faster from now on (a couple haven't been ported to JS yet).

Plots

Improved Improved color handling in violin and waterfall plots. The line color (edge) and shade/fill-under can be independently controlled now.

UVPD processing ⭐️

Added Added new plug that allows analysis and processing of UVPD datasets that were acquired with laser being constantly switched on/off. This is a user-specific plugin that will most likely have no use for anyone else apart from some Barran group members. To activate, click on the Menu -> Plugins -> UVPD processing window....

Tandem MS panel

Added You can now load .mzML files (haven't figured out how to add .mzIdentML files to them yet...)

Added MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial.

Added Added two new options in the Action menu which permit improved population of the table by either excluding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options.

Added You can see what PTMs have been included in the scan by clicking on the Modifications list

Improved Scans that have multiple identification information will be separated into separae instances in the table (e.g. look at the column ID #)

Improved Fragment generator can now handle PTMs (at least those that have kept the mass information)

Improved Improved the way scans are loaded (faster and actually works...)

Improved Improved the way butterfly plots are shown. A horizontal line will be drawn from now on (at y=0)

Improved Added several new customisation parameters that permit better data visualisation. These are found under Action -> Customise...

Fixed When selecting frag-all option, appropriate checkboxes will be ticked from now on

Fixed Fixed fragment generator to stop overriding fragments with same name (e.g. y1+ was equal y_H2Ox11+...)

Other data -> Annotated data

Added Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots

Changed Changed the poorly selected name of 'Other data' to 'Annotated data'

Figures

Updated MS/MS panel

MSMS

MS/MS customisation window

MSMS

Annotated MS/MS mass spectrum with automatically generated arrows

MSMS

Interactive data customisation window

Interactive

Interactive copy style

Interactive

Animation

Interactive adjustment of labels

Interactive

Mailing list

If you would like to be added to the ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk or visit ORIGAMI documentation website.

How to update

A lot has changed in this version so the only way to update is to download the package and unpack it somewhere else on your PC. I've tried really hard not to break too many things :)

Many thanks,
Lukasz

Assets 4

@lukasz-migas lukasz-migas released this Nov 5, 2018 · 86 commits to master since this release

What changed in ORIGAMIANALYSE:

Note 

Again, this was meant to be a small-ish update but turned into a fairly significant revamp of ORIGAMI. Because of this, I have upgraded it to version 1.2.0.3.

General:

[IMPROVED]: The underlying codebase of ORIGAMI has been improved to make it more readable and more responsive

[IMPROVED]: Item font color will be automatically adjusted to ensure best contrast from the background color in various lists in the GUI

[CHANGED]: Modification of the table elements is now available by Right-clicking on the column name

[CHANGED]: Logging of events was temporarily disabled as it appears to be causing some issues. I haven't been able to figure out why it crashes the program (yet).

Tandem MS [NEW]:

[NEW]: Added support to load .mgf and .mzIdentML file formats to visualise tandem mass spectrometry results. Menu -> Open open-source files... to load .mgf files. You can then annotate the tandem MS with peptide fragments. See Figure 1 for example.

Interactive panel:

[NEW]: Started adding support for individual modification of parameters for interactive plots (double-clicking on an item in the list)

[NEW]: Interactive documents can now be visualised without access to internet. Just check the "Add offline support" checkbox

[NEW]: Annotated mass spectra will now include label + arrow (if available)

[IMPROVED]: Legends now work with markers and shaded areas

[FIXED]: Issue that prevent exporting interactive documents with legends has been removed

[FIXED]: Issue that prevent proper showing of toolbar has been removed

Peaklist panel:

[NEW]: Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)

[NEW]: Added 'Overlay automatically' check tool (Peaklist -> Toolbar -> Overlay...)

[IMPROVED]: Added a lot of new shortcuts for easier plotting

Text file panel:

[NEW]: Added 'Extract automatically' check tool (Peaklist -> Toolbar -> Extract...)

[NEW]: Added 'Show chromatogram' and 'Show mobiligram' for each viewed file (Right-click -> Select appropriate)

[IMPROVED]: Added a lot of new shortcuts for easier plotting

[FIXED]: Removed an issue that prevented loading certain text files

[FIXED]: Removed an issue that would incorrectly remove documents from the text file list

Multiple MS files panel:

[NEW]: The average mass spectrum can be re-binned/re-processed based on new parameters (Process -> Average mass spectra (current document))

[IMPROVED]: Item font color will be automatically adjusted to ensure best contrast from the background color

[IMPROVED]: Average mass spectrum will be automatically re-binned/re-processed when an item is added or deleted

[FIXED]: Removed an issue that prevented typing-in numerical values in the 'variable' colument when using laptop keyboards. I have only ever encountered this issue once... Let me know if it still occurs!

Document tree:

[NEW]: Double-clicking on the document header will now clear all plots and show the most basic plots for that document (e.g. MS, DT, RT, etc). You can also do this by Right-click -> Refresh document.

[NEW]: You can now change the x-/y-axis labels for chromatograms and mobiligrams. Right-click on the item and slect 'Change x/y-axis to...'. These changes will be taken into account when extracting data from the chromatogram/mobiligram windows

[IMPROVED]: Significant improvements to the right-click menus (most notably for UniDec/Annotations)

Plots panel

[NEW]: Some images can now be rotated by 90 degrees (mainly 2D)

[IMPROVED]: Significant improvements to the right-click menus.

[IMPROVED]: Wheel-zoom in the X-dimensions has been improved (works like on maps now)

Data extraction:

[NEW]: You can now extract mass spectra from the '2D' panel. Hold CTRL on your keyboard and drag the mouse in the plot area. Only works when standard plot is shown (e.g. Drift time (bins) vs Scans/Time)

[IMPROVED]: All data extraction will be carried out in a temporary_data folder (found in the ORIGAMI directory). This should fix any issues where data was being extracted from network drives and should keep your HDDs a  little bit tidier. All files will be deleted at the end of the session.

[IMPROVED]: Data extraction in the DT, RT, DT/MS panels now takes into account the plot labels/units.

[IMPROVED]: Extracted mass spectra extracted in the DT and RT windows will be now shown in an area beneath the extraction plot (for convenience)

MS annotations:

[NEW]: Peaks can now be annotated with an arrow (also available when exporting in an interactive format)

[NEW]: Added new customisation parameters window where you can change your visualisation preferences. Action -> Customise other settings...

[IMPROVED]: Selection of a peak in the MS window using the mouse (Annotating: On) will automatically try to determine the charge state based on the peaks isotopic distribution. You can change the error tolerance in Action -> Customise other settings -> Charge prediction value (default: 0.05).

UniDec settings:

[NEW]: Plots can now be customised using settings editor. (Settings: UniDec -> Customise plots...)

[NEW]: You can switch between tabbed view where each plot is in a separate tab OR continuous view where all plots are available on the same page (Customise plots... -> Panel view)

[IMPROVED]: Deconvolution is now done in a multi-threaded mode. Should stop program from hanging

[IMPROVED]: All deconvolution results will be now stored in a temporary_data folder (found in ORIGAMI directory). This should keep your HDDs a little bit tidier. All files will be deleted at the end of the session.

MS comparison:

[NEW]: You can now assign your own label to the plot.

[IMPROVED]: You can now compare ALL available mass spectra and not just those that were hidden under 'Mass Spectra' tag. (This includes: Mass Spectra, Mass Spectrum, Mass Spectrum (processed)). To open comparison panel: Menu -> View -> Open MS comparison panel...)

Peak detection:

[IMPROVED]: Works in multi-threaded mode. Should stop program from hanging.

Figures:

Tandem MS editor

Annotated butterfly tandem mass spectrum

Annotated mass spectrum

Updated UniDec panel

Mailing list

If you would like to be added to a ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk

How to update

Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.2.0.3.zip file, unpack it somewhere on your PC and it should work out of the box. :)

As you might notice, the size of the directory increased quite a bit, it is about 1 Gb when unpacked.

Many thanks,

Lukasz

Assets 4
Nov 5, 2018
Update ORIGAMI_ANALYSE/update_info.md
Pre-release

@lukasz-migas lukasz-migas released this Aug 10, 2018 · 98 commits to master since this release

What changed in ORIGAMIANALYSE :

Note 

This was meant to be a mini-update but it has spaned over several weeks and includes a fairly significant revamp of the Interactive output panel (with loads new features), addition of many new plot types, cleaner interface (in some places), bug fixes and more.

I have changed the way I compile ORIGAMI (switched from obsolete py2exe to pyinstaller) which increased the size of the directry (~2x) and made it less organised but it should result in better support. Overall, you should see similar performance and not notice the change.

New in v1.1.2:

  • Added several new plotting methods:
    • Waterfall overlay
    • Violin
    • Scatter
    • Bar plot
  • The document type (Type: Interactive) now supports addition of "Other..." data type. This is fairly versatile and can include any of the following: line, multi-line, scatter, vertical-bar, horizontal-bar, grid-line, waterfall, grid-line and grid-scatter and is mostly aimed at enabling exporting of more complex (and not necessarily MS related datasets) in an interactive format. To take advantage of its full potential I made a repository where you can see example files, but it basically requires specification of some meta-data (i.e. title, x/y-axis labels etc) and addition of data. You can learn more about it by going to Menu -> Help -> Help pages -> Learn more: Other datasets (shortcut F1+9). Check out the example files here. I've also included a couple example files in folder 'example_files/other_data'.
  • Added new "Annotation" panel that enables you add annotations to mass spectra (i.e. charge state, protein name, any description). To enable it, plot the mass spectrum and right-click in the Documents Tree and select -> Add/Show annotations (shown below). You can learn more about it going to Menu -> Help pages -> Learn more: Annotating mass spectra (shortcut F1+8)
  • Added a proper version checker that will check whether new version of ORIGAMI is available online at each start of the program.
  • General changes to the Interactive Output panel:
    • Tried to reorganise several components to make it look less cluttered.
    • Added several new parameters that you can change
    • All generated plots can now benefit from using 'custom JavaScript' widgets and events. Events are currently limited to 'double-click in plot area will zoom-out' whereas widgets are much more versatile and include addition of buttons, sliders, toggles, radio buttons and few others. These can control the size of the labels, level of zoom, transparency or position of legend and many others. These are enabled by default and can be turned off in the Interactive Panel -> Annotations -> Add custom JS events/scripts when available. Addition of custom JS events/widgets slows down generation of interactive plots as these have to be compiled to JS. Note: First time you try this you will most likely be greeted with an error message. Follow the instructions there to solve it.
    • Expanded the list of available plots.
    • Interactive plots can be exprted in multi-threaded mode now, enabling you to do other tasks while they are being exported. Note: If you close the output window, the export process will stop.
  • Overlay plots will not be added to overlay document by default. You first must toggle "Add overlay plots to document" in the menus of individual overlay panels.

Improvements in v1.1.2:

  • Loads of small improvements in the Interactive output pane
  • Improved and extended list of available labels
  • Reorganised the Plot parameters panel
  • Some of the plot parameter options will take an immediate effected without the need to replot the data. Some will not!
  • General improvements to the Peak fitting/finding in the Processing panel.
  • General improvements to the Mass spectrum processing the Processing panel.
  • Usually at start of the program, ORIGAMI looks for Driftscope on your PC. If it doesn't find it, it usually notifies you of it. You can disable this behaviour now.
  • Configuration files are not saved automatically. You can disable this by going to Plot settings -> Extra -> Auto-save settings to off.
  • Added two new color palettes (cividis - colorblind friendly and winter)
  • Rearranged the UniDec panel and improved error messges.
  • Added label position optimisation (can be disabled if you don't like the results).

 Fixes in v1.1.2:

  • Many fixes that should improve the general usability and reliability of the analysis software
  • Fixed an issue where the colorbar wasn't displaying correct values
  • Fixed issues with the waterfall plots.
  • Fixed an issue which occurs when the size of the screen is not optimal. I've tested the software on screens with severan screen dimensions (1980x1080, 1680x1050, 1600x900, 1366x768, 1280x102 and 1280x800) and its looks pretty good.  I would recommend using a decent sized screen for using ORIGAMI.

 

 

Waterfall overlay:

Violin:

Scatter:

Bar plot

Waterfall plot with JavaScript widgets

Annotations panel

Planned features:

  • Interactive panel:
    • I don't like the current positiong of various settings and how they are actively enabled/disable upon selection in the list. I intend to add a separate window where when you double-click on an item it will open and you will only see relevant settings.
    • Widgets are awesome but still require a lot of work. A couple of really cool widgets I intend to add are toggles for colorblind mode, data selection dropdowns, comparison tools etc
    • I would like to add a number of neat plots, including circos-style plot for XL-MS, HDX-style grid plots etc
  • Plots:
    • I have a couple of ideas for new plot types, especially for RMSD-type plots
  • Main program:
    • Speed-up certain operations
    • Improve GUI
    • Add support for other vendor files. I intend to use multiplierz + other open-source libraries
  • Help pages:
    • Improve the text + add more examples
  • Videos:
    • Record a couple of videos showing various features + usage

 

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

Video tutorials:

A couple of videos is available on YouTube. Will try to add more in future.

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Mailing list

If you would like to be added to a ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk

How to update

Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.1.2.zip file, unpack it somewhere on your PC and it should work out of the box. :)

As you might notice, the size of the directory increased quite a bit, it is about 1 Gb when unpacked.

Many thanks,

Lukasz

Assets 3

@lukasz-migas lukasz-migas released this Jun 19, 2018 · 116 commits to master since this release

What changed in ORIGAMIANALYSE :

Note 

This is a major update, predominantly focusing on adding support for deconvolution of mass spectra using UniDec and introducing several new plotting options while also improving the Interactive Output documents.

New in v1.1.1:

  • Added support for UniDec deconvolution in ORIGAMI.
    • You can easily load MS and deconvolute using the well-established UniDec's Bayesian deconvolution algorithm
    • ORIGAMI generates nearly identical plots to those of UniDec
    • All deconvolution results can be exported in a HTML format
    • The results obtained in ORIGAMI are identical to those of UniDec
    • All results can be saved in text format for viewing elsewhere
    • If you use this feature, please ensure to cite UniDec in your research!
  • Can now export RGB plots in Interactive Format
  • Added overlay method (Waterfall) for mass spectra, exportable in HTML format
    • Enables comparison of multiple mass spectra (from same or different files)
    • Comparison of UniDec results
    • First you have to add mass spectra to the Multiple files panel (right-click on the Mass Spectra heading in the Documents panel and select Add spectra to multiple files panel)
  • Added two new overlay methods (Grid (2->1) and Grid (n x n)), both are exportable in HTML format
    • The Grid (2->1) method allows viewing RMSD plot alongside its individual components
    • The Grid (n x n) allows viewing up to 16 species simultaneously
  • Added Drag'n'Drop support for multiple data types
    • .raw files will be assumed to in an ORIGAMI format (it is compatible will all data processing tools)
    • .raw files dropped in the Multiple Files panel will be added to currently opened MANUAL document, if none present it will create a new one
    • .txt/.csv/.tab files are also supported. ORIGAMI will perform a test to see if its in a 2D IM-MS or MS format
  • Added visualisation of MS using a waterfall-like plot
    • Right-click on Mass Spectra in the document window --> Select Show mass spectra (waterfall). You can change waterfall settings in the Waterfall settings panel
    • By default it will try to sort files based on energy, if not available it will sort it by name
  • Added
  • Added color palette option in the Settings -> General panel
  • Added new document type (INTERACTIVE) which allows loading of MS, RT, DT and 2D datasets independent of the vendor (text format of course!). All of these can be exported in a HTML format
    • To add data to INTERACTIVE document, right-click on the document in the Documents panel and select one of Add ... options
    • If you would like to compare mass spectra, right-click on the item (Mass Spectra) and select option Add spectra to multiple files panel.
    • If you would like to compare 2D heatmaps, right-click on the item (Drift time (2D, EIC) and select option Add to text file table

Improvements in v1.1.1:

  • Interactive documents will now contain a watermark
  • Small improvements to the hover tool in the HTML viewer
  • small twaks to the 1D plots
  • Fixed an issue with the waterfall plots (incorrect ordering of the plot lines)
  • When extracting peaks in the MS window, ORIGAMI will try to determine the charge state automatically by examining the isotopic pattern
  • Binning is no longer the default method of linearizing data. Added multiple other methods that are better at that (some are quite slow)
  • Significant improvements to the way images and text output is saved

 Fixes in v1.1.1:

  • Many fixes that should improve the general usability and reliability of the analysis software
  • Minor problems when analysing multiple MassLynx files simultaneously
  • A couple of small issues when loading Linear DT files
  • Removed a bug that broke ORIGAMI when you tried removing all documents from the Documents panel

 Known issues:

  • The DT-IMS panel still lacks a lot of functions
  • The CCS panel is quite clunky and not intuitive - needs a revamp!
  • When zooming-in and the mouse cursor goes outside of the plot axes, the zoom tools get locked-up - kind of annoying

Preview Interactive documents

Analysis of p27-FL IDP protein using UniDec deconvolution engine

Visualisation of multiple 2D datasets simultaneously

Example images:

Unidec in ORIGAMI

UniDec GIF

Grid (2->1) overlay method

Grid (2->1)

Grid (n x n) overlay method

Grid (n x n)

MS waterfall method

MS Waterfall

MS Waterfall 2

MS comparison view

MS comparison viewer

Customise plots panel

Customise plots

 

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

Video tutorials:

A couple of videos is available on YouTube. Will try to add more in future.

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Mailing list

If you would like to be added to a ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk

How to update

Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.1.1.zip file, unpack it somewhere on your PC and it should work out of the box. :)

As you might notice, the size of the directory increased quite a bit, it is about 500 Mb when unpacked.

 

Many thanks,

Lukasz

Assets 3
Pre-release

@lukasz-migas lukasz-migas released this Apr 6, 2018 · 135 commits to master since this release

What changed in ORIGAMIANALYSE :

Note 

This is a major update (hence version upgrade to 1.1.0) so none of the previous pickle files will work. I intend to move to hdf5 in future to ensure this sort of problem doesn't persist, but for the time being please hang on. This version incorporates major changes to the user interface with many improvements added to ensure better plotting capabilities and more consistent behaviour. 

Fixes in v1.1.0:

  • Many fixes that should improve the general usability and reliability of the analysis software
  • Minor problems when analysing multiple MassLynx files simultaneously

Improvements in v1.1.0:

  • Changed the entire layout of the user interface. It is a lot cleaner looking (in my opinion, of course..) and should hopefully make for a better analysis experience. The whole design is based on having multiple little windows open that allow simultaneous tweaking of the plot parameters, data processing and data extraction
  • Many of the plotting functions have been improved and you might notice some speed-ups!
  • Changed the way you modify ion or text file parameters. You can simply double-click on any item in the Peaklist or Text file list panels for quick editing options
  • Added lots of shortcuts to speed analysis
  • Significantly improved the way charge states are detected for high-resolution mass spectra
  • Legends are now draggable (not pickable, yet..)

New in v1.1.0:

  • Added new 'RGB' format in the overlay methods. It simply allows you to plot more than two species simultaneously.
  • Added quickly accessible links to request new features + report any bugs.
  • You can now easily save and interact with the logging window - very useful if you would like to send me any bug reports!
  • Added lots of little convenience tools in the Overlay panels. 
  • You can now export NEARLY all plot types in an interactive format. The two exceptions are 3D plots and RGB plots. These are coming... (slowly!)
  • Added compare MS module where you can select mass spectra from different collision voltages and directly compare how they relate to one another

Known issues:

  • The DT-IMS panel still lacks a lot of functions
  • The CCS panel is quite clunky and not intuitive - needs a revamp!
  • When zooming-in and the mouse cursor goes outside of the plot axes, the zoom tools get locked-up - kind of annoying

 

Example images:

Updated main window

Main window

RGB Overlay

Overlay RGB

Overlay mobiligram

Overlay 1D

Compare mass spectra

Compare mass spectra

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

Video tutorials:

A couple of videos is available on YouTube. Will try to add more in future.

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Mailing list

If you would like to be added to a ORIGAMI mailing list where you will be notified of new releases, please contact lukasz.migas@manchester.ac.uk

How to update

Since the whole package was revamped, the only way to update ORIGAMI is to download the ORIGAMI_ANALYSE_v1.1.0.zip file, unpack it somewhere on your PC and it should work out of the box. :)

As you might notice, the size of the directory increased quite a bit, it is about 500 Mb when unpacked.

 

Many thanks,

Lukasz

Assets 3

@lukasz-migas lukasz-migas released this Nov 29, 2017 · 144 commits to master since this release

What changed in ORIGAMIANALYSE :

Note 

This will be the last update for a little while (unless I find a big bug that needs fixing) as I need to focus on some other work for a couple of weeks. Let me know if you spot anything that I might have not.

Fixes in v1.0.5:

  • [CRITICAL] Fixed an issue when you tried processing 2D datasets (i.e. smoothing or normalizing).
  • Fixed an issue where you could not open more than one manual CIU document
  • Fixed an issue where you could not assign name or any header/footer information to items in the Interactive Panel

Improvements in v1.0.5:

  • Changed a couple of labels and layout in the GUI
  • The file list will now be automatically sorted by energy (and document name) when dealing with manual CIU datasets

New in v1.0.5: 

  • Added  support for colorbars in the Interactive Panel (hidden under Interactive Panel --> Properties --> Colorbar properties)
  • Added better controls for adjusting figure and border controls in Interactive Panel
  • You can open the User Guide internally as PDF (wow!)

Known issues:

  • The DT-IMS panel still lacks a lot of functions
  • The 3D plot can be improved a lot, just need a bit of time to tinker!
  • The GUI needs some restructuring
  • When zooming-in and the mouse cursor goes outside of the plot axes, the zoom tools get locked-up - kind of annoying

CHANGES

Annoyingly, as I was working on this version I have updated a couple of the packages ORIGAMI relies on, meaning that some previously saved documents might not open... It is rather regretful! The ones affected would be those including links to 'Multiple MassLynx files' or 'CCS calibration files' as they contain a certain data structure that has changed. I will try to prevent that from happening in the future...

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

Video tutorials:

A couple of videos is available on YouTube. Will try to add more in future.

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Documentation

Small changes have been made to the guide, although it still lacks description for all features. I will try to get it up to date in the next couple of weeks (months?).

How to update

Because of the package changes, to update ORIGAMI, you will have to download the ORIGAMI_ANALYSE_v1.0.5.zip file, unpack it somewhere on your PC and you should be good to go! :-) 

As you might notice, the size of the directory increased quite a bit, it is about 500 Mb when unpacked.

 

Thanks,

Lukasz

Assets 5

@lukasz-migas lukasz-migas released this Nov 3, 2017 · 158 commits to master since this release

What changed in ORIGAMIANALYSE :

Note 

This will be the last update for a little while (unless I find a big bug that needs fixing) as I need to focus on some other work for a couple of weeks. Let me know if you spot anything that I might have not.

Fixes in v1.0.4:

  • [CRITICAL] Fixed issues found when trying to analyse multiple files simultaneously
    • would not let you show data
    • you could not select data from the table
    • you could not load data (path issues)
  • Slight improvements to the 2D plot. Previously pixel positions were slightly off.
  • Fixed a couple of problems in the zoom function.
  • Fixed an issue where adjusting the colormap intensities did nothing. 
  • Improved the data extraction tools.
  • Rearranged a couple of labels in the graphical interface
  • Fixed an issue where you could not export certain datasets to file

New in v1.0.4: 

  • you can now extract MS from a selected region in the RT (retention time) window. Just hold CTRL and drag with your mouse in the plot area.
  • you can now assign charge state from multiple places (Document tree, Peak list or Document Information Panel). Charge states will be modified for each data type
  • Significant changes to the zoom function:
    • Added mouse wheel support - just hover over a plot and use the mouse wheel to either zoom-in or zoom-out. If you hold SHIFT key while doing this, will adjust the Y-axis.
    • Hold SHIFT and double-click in the plot area will reset the Y-axis to the default values.
    • Hold CTRL and double-click in the plot area will reset the X-axis to the default values.
  • If you load an ORIGAMIMS style file, a new plot type of MS vs DT is added.
    • The plot resolution is controlled by the MS/DT bin size in the Extract Parameters.
    • You can extract RT data by holding CTRL and selecting an area in the MS vs DT plot area (extracting data for specific mass spectrum and drift time area).
  • You can assign charge state and transparency in batch mode for selected items in the Peak list. (Peak list --> Annotate... --> Assign ...)
  • You can use DELETE key to remove items or documents from the Document Tree
  • The status bar has been improved.
    • Field 1 shows the X, Y coordinates, Δx when extracting (hold CTRL) or z and molecular weight when measuring (hold ALT)
    • Field 2 shows the MS range (for loaded file)
    • Field 3 shows the MSMS value for mass selected ion
    • Field 4 shows current action/error or warning
    • Field 5 shows current action/error/warning or extraction range (hold CTRL)
    • Field 6 shows current zoom function (Wheel X, Wheel Y, Add data, Measure)
  • Significant changes to the Interactive Output panel.
    • The whole interface was rearranged. All parameters are contained within Properties tab
    • You can assign different set of tools for individual plots
    • Better filtering (based on plot type and document name)
  • Upon opening the program, ORIGAMI will check for any updates to the software.
  • You can export multiple mass spectra to single file (if they have been binned!) or separate files
  • Added new shortcut to save CSV data (ALT+V)
  • New function to open more than one ORIGAMI-style file (shortcut CTRL+SHIFT+Q)
  • You can now either enable or disable logging messages to file
  • [experimental] You can try to automatically assign charge states to high-resolution data (i.e. small molecules where isotopes are easily separated). This function is not always correct, so please check!
  • [experimental] added multi-threading to several functions to prevent the GUI from hanging during time-consuming tasks (i.e. opening files, extracting data, saving figures or saving data). These are currently being tested and might occasionally cause errors. If so, you can disable Threading from Properties tab --> General parameters --> Threading

Known issues:

  • The DT-IMS panel still lacks a lot of functions
  • The 3D plot can be improved a lot, just need a bit of time to tinker!
  • The GUI needs some restructuring
  • When zooming-in and the mouse cursor goes outside of the plot axes, the zoom tools get locked-up - kind of annoying

CHANGES

Annoyingly, as I was working on this version I have updated a couple of the packages ORIGAMI relies on, meaning that some previously saved documents might not open... It is rather regretful! The ones affected would be those including links to 'Multiple MassLynx files' or 'CCS calibration files' as they contain a certain data structure that has changed. I will try to prevent that from happening in the future...

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

Video tutorials:

A couple of videos is available on YouTube. Will try to add more in future.

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Documentation

Small changes have been made to the guide, although it still lacks description for all features. I will try to get it up to date in the next couple of weeks (months?).

How to update

Because of the package changes, to update ORIGAMI, you will have to download the ORIGAMI_ANALYSE_v1.0.4.zip file, unpack it somewhere on your PC and you should be good to go! :-) 

 

Thanks,

Lukasz

Assets 5

@lukasz-migas lukasz-migas released this Oct 11, 2017 · 158 commits to master since this release

What changed in ORIGAMIANALYSE :

Fixes in v1.0.3:

  • changed an incorrect label in GUI (Threshold -> Fit plot)
  • when applying protein label in the Document Information Panel, the molecular weight value was not properly set
  • the 1D DT label incorrectly said 'Drift time(bins)' - replaced it with 'Drift time (bins)'
  • a couple of changes to menus - removed several spelling mistakes (probably put new ones in!)

New in v1.0.3: 

  • added a couple of new shortcuts:
    • Alt+X will now zoom-in on the ion of interest (if the selected item has x-axis label)
    • Alt+Z will now show charge assignment window for a selected item
  • you can now change the x-axis labels for 1D data
  • if your processing settings are incorrect (i.e. threshold too low/high, smoothing issues), you will be notified of them via dialog box
  • you can now change the document path in the Documents Information Panel
  • added option to clear all plots (Menu --> Window --> Clear all plots)
  • you can now measure the distance between MS peaks by holding Shift on your keyboard and dragging. You can see the deltaX value in the bottom left corner in the status bar. If you release the Shift key before you release the left-mouse key, the plot will be zoomed-in on.

Known issues:

  • The DT-IMS panel still lacks a lot of functions
  • The 3D plot can be improved a lot, just need a bit of time to tinker!
  • The GUI needs some restructuring
  • When zooming-in and the mouse cursor goes outside of the plot axes, the zoom tools get locked-up - kind of annoying

ORIGAMI-MS:

There have been no changes to ORIGAMIMS, so please download it from release 1.0.1.

 Video tutorials:

Released first video about how to setup ORIGAMIMS and ORIGAMIANALYSE! A couple more are coming in the next few days from the same YouTube channel. 

ORIGAMI-MS: Setup Guide

ORIGAMI-ANALYSE: Analysis of ORIGAMI-MS files

Documentation

Have been pre-occupied with other things so haven't updated any of the guides. Sorry!

How to update

If you already have ORIGAMI on your PC, then all you have to do is download the updateFilesOnly_ORIGAMI_ANALYSE_v1.0.3.zip file, extract it and copy the contents to the ORIGAMIANALYSE folder. 

If you do not, just download the ORIGAMI_ANALYSE_v1.0.3.zip, unpack it somewhere on your PC and you are good to go! :)

 Thanks,

Lukasz

 

Assets 5
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