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Release of v0.1.6a4

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@lukasz-migas lukasz-migas released this 10 May 13:12
· 10 commits to main since this release
v0.1.6a4
71a310f

Featured

  • Added new merge2image app which let's you combine multiple OME-TIFFs into a single OME-TIFF (images must be co-registered, have same pixel spacing and shape image shape).

New

  • In the viewer and crop app, RGB images (PAS, HE, etc) will now be loaded as single RGB image rather than being split into individual channels. You can disable this behaviour in the More options... dialog.
  • The czi2tiff app has been renamed to image2tiff and now enable conversion of many image formats to OME-TIFF.
  • In the image2tiff app, you can now define the tile size and modify resolution (be cautions - should only be used if you know what you are doing).
  • In the image2tiff app, you can now merge multiple channels together (e.g. to create a better marker for cell boundary recognition). Just click on the row, click on the Merge... button and select channels to merge.
  • In the viewer and register app, you will be able to quickly iterate through images to select only the channels that matter in your visualisation.
  • You can launch any app from the other apps via the Menu -> Apps -> ... menu option.
  • You can now perform version check via Help -> Check for updates....
  • You can now export any loaded image as a OME-TIFF. Simply click on the More options... > <save icon>. This can be particularly useful if you've extracted ion images for a TDF/TSF raw files.
  • You can now quickly toggle between synchronize views in the register app by clicking on S key on your keyboard.
  • You can now create your own mask in the viewer app which can be used by AutoIMS.
  • You can now load shape layers (e.g. polygons from Xenium in CSV format). You can now also select how they should be displayed - as polygon (slow) or path (fast). If there are a lot of shapes, path is the better choice!
  • You can now load point layers (e.g. nuclei markers from Xenium in CSV format).
  • When loading Bruker .d files, it is now possible to load specific ROI rather than the entire dataset (necessary when registering multi-ROI images that will be split in AutoIMS!).
  • You can now drag-n-drop configuration files (e.g. i2r.json, i2v.json, etc...) in all windows and they will be opened appropriately.
  • You can now drag-n-drop i2r config into the image2viewer app and it will load the transformation data in the background.

Changed

  • Improved export validation in the register app which let you save registration files without fixed/moving paths.
  • Improved warnings when exporting registration files.
  • Improved layout of the image2register app.
  • Improved layout of the launcher app.
  • Improvements to layout and behaviour of few visual components.
  • Incremented schema version of image2register app to include the reader_kws parameter.
  • Updated and improved style.

Fixed

  • Fixed a bug which prevented from reading in files without fixed/moving paths (so you couldn't edit them...).
  • Fixed a bug which prevented deleting selected points if some of the points have already been deleted.
  • Fixed a bug which could happen if you opened Orient moving image... before there were any images opened.
  • Fixed a bug which would prevent proper zoom synchronisation between fixed and moving images in the register app.
  • Many bug fixes that are not worth mentioning...
  • Fixed a bug where CZI image would take a lot of HDD space, even if they were closed.

Known issues (to be fixed in the future)

  • image2crop - polygon masks should zero-out anything outside of the mask but within the boundary of the mask.
  • image2register/image2viewer when loading Bruker .d file that has multiple ROIs and specific ROI is selected, extraction of ion images will not be possible due to limitation in the imzy library (will be fixed in the full release).
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