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Update to ORIGAMI-ANALYSE (1.0.4)
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@lukasz-migas lukasz-migas released this 03 Nov 15:00
· 165 commits to master since this release
1.0.4
b48575c

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

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