Release of v0.1.9

New

• added automatic path generation in the elastix app (great for 3d registration)
• simplified updating of modality names in the elastix app
• simplified updating preprocessing of all modalities in the elastix app
• added option to sort and recolor modalities in the elastix app
• added option to copy mask/crop to all modalities
• network viewer in the elastix app is now fully interactive
• modality colors are now assigned using non-clashing color algorithm

Changes

• improved layout of the dataset list dialog
• improved layout of the elastix app
• improved layout of the register app

Fixed

• fixed a bug where images were not transformed properly (sometimes...) in the elastix app
• fixed a bug where registration paths were not validated properly
• fixed a bug where the resolution wasn't being updated in the crop app
• fixed a bug where too many modalities were loaded into the viewer when check all were selected
• fixed a bug where you could end up with 'dangling' attachments
• fixed a bug where you could end up with 'dangling' registration nodes
• fixed a bug where image resolution was truncated (e.g., 0.1225 would become 0.123, which can lead to big errors!)
• fixed a bug when 'copying' mask/crop region in the elastix app
• fixed a bug where you could not drag images into the register app
• fixed a bug where network edges would disappear when zoom-in the plot
• fixed a bug where images were always overwritten when exporting

Release of v0.1.7

This is a fairly major release with a lot of improvements and changes

• there is a completely new dataset/channel selector - previously you had to use separate windows to select datasets, change which channels are selected and apply transformations - this now has been combined into one which should make it easier and more intuitive to use
• the elastix app now supports cropping so you no longer need to crop images before registration
• the elastix app can now handle multi scene CZIs properly (you must select one to perform registration)
• the elastix CLI has two new commands (accessible via image2image.exe elastix …) which enable export of complete transformation files (E.g. for hubmap submissions) and to apply said transformation to files
• the layout has been tweaked in places
• the writer is now much more efficient
• hundreds of bug fixes...

Release of v0.1.6a4

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).

Release of v0.1.6a0

This is alpha release to fix a couple of bugs.

Changed

• Improved export validation in the register app which let you save registration files without fixed/moving paths.
• Improved warnings when exporting registration files.

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.

Release of v0.1.5

General

• You can select multiple files when loading images.
• You can now drag-and-drop images into the app to load them this way.
• You can now drag-and-drop i2r/i2v/i2c etc files into the app.
• Improved loading of CZI images.
• Added new image2crop app to crop any microscopy image to smaller region (handy for Fusion of trying to cut-out regions that are of no interest).
• Added new czi2tiff app where you can convert CZI images into OME-TIFFs. If the CZI image has multiple scenes, each one will be exported as separate OME-TIFF file. (There will loss of metadata information!). You can edit information such as channel name and which channels to export by double-clicking on the table.
• Added support for reading in AutoIMS generated HDF5 files (includes centroids, supervised or unsupervised data) Export as image2image HDF5 file in AutoIMS
• Added statusbar to each app.
• You can now update the app directly from within the image2image app.
• Added step-by-step tutorials to each app.
• You can now create your own colormaps by clicking on the colormap button when editing image layer.
• Added support for qptiff (including qptiff.raw and qptiff.intermediate) file format.
• Select channels... is now searchable.

image2viewer app

• In the viewer app, you can now load GeoJSON files (e.g. from QuPath)
• In the viewer app, you can export masks from Shapes (e.g. from GeoJSON) (which you can provide as extra data in AutoIMS for supervised/unsupervised learning or other AutoIMS tasks!)
• Added copy to clipboard and save image to the image2viewer app so you can easily take a screenshot. Right-click on the button to have a couple more options.
• Added scalebar button in the statusbar.
• Improved layout of apps

image2register app

• In the register app you can now initialise moving image by rotation or flipping so that it’s easier and quicker to get good co-registration
• Added synchronised zoom to the register app (once you have more than 4 data points) - you can disable this in options.
• Added go to next and go to previous point keyboard shortcuts to quickly scroll through registration points.
• Added several shortcuts to make interaction faster.
• Added shortcuts button to open key of available shortcuts in the app.
• Improved the error calculation in image2register app (no more error = 0.00 since that’s very, very unlikely!)
• Improved error messaging in image2register app.

image2fusion app

• Improved performance of image2fusion app so it is (slightly) less memory hungry. If it’s still struggling, consider downsampling your image or cropping a portion of it using the image2crop app.

Changed

• Updated to use latest version of napari (v0.4.18)

Fixed

• Hundreds of bug fixes...
• Fixed a bug where you could not export registration data...

Breaking Changes

• Hopefully nothing? Please let me know if you notice anything doesn’t work as it used to.

First release

Version