MICAIA^® Changelog

Version 1.4.0

- new annotation actions: fuse, subtract, convert to path, convert to polygon
- add convenience button for repeating the previous analysis (same area)
- [studio] new App: AI Authoring App
- [studio] new App: Annotation Metrics
  collects morphometric (area, perimeter, circularity, ...) as well as color attributes (e.g. mean intensity) for selected annotations and exports them into a CSV file. Can be used for measuring MFI (in FL scans) or for IHC Profiling
- [studio] Mask by Color App: support masking based on a fluorescence channel or an unmixed stain (e.g. DAB).
- [studio] FL Colocalization App: now supports adding annotations per marker or per marker-combination
- [studio] removed FL Cell Counting App. Use Case is covered by FL Colocalization App now
- [I/O] improved GeoJson import (support QuPath "cell annotations" with nucleus)
- better windowing of 16 bit FL slides for image analysis
- UI buttons are mostly disabled during an analysis
- Annotation classes sidebar has new option to show diagram with area [mm²] per class
- App configuration groupbox has convenience option to enable or disable auto-collapsing the groupbox when the analysis is done.
- switch AI backend to Onnx
- fix layout problems when UI is scaled to > 100%
- various bugfixes

- [I/O] new format: Olympus VSI (brightfield and fluorescence, 16 bit)
- [I/O] Akoya QPTIFF format: when available, name channels after biomarkers instead of dyes
- [I/O] Nanostring GeoMX: improve support for reading Nanostring GeoMX OME-TIFF
- new feature: Stain Estimation
- improved quality of live stain unmixing
- Save-As supports exporting ROI or FOV at custom resolution
- Save-As supports burning in annotations to create high-DPI images for journals
- [studio] new App: Spatial Clustering App
- [studio] IHC Cell Detection App

- supports custom stains other than default H-DAB
- new post-processing step: spatial clustering
- supports two modes how users can manually correct results: by setting an "ignore" class and the "load annotation" mode which loads existing cell annotations

- [studio] Cell-Cell Connections App:

- support selecting classes subset
- support constraining analysis to ROI or FoV
- report statistics not only for cell classes (one per marker combination) but also by marker

- [studio] FL Coloc App:

- use class naming scheme that remains stable accross runs
- report statistics not only for cell classes (one per marker combination) but also by marker

- [studio] colocalization scatter plots module: speed optimizations to make it work with high-plex scans with many channels
- faster startup: annotations from slides in workspace are not loaded directly at startup, but instead just in time when a slide is opened.
- cell annotation type (2 polygons: nucleus and membrane) can be saved and loaded
- support batch-deleting annotation class(es) in multiple slides
- new dialog/tool: add slide-shortcuts next to *.ano files
- new dialog/tool: retarget shortcuts in folders
 

• [I/O] new format: Zeiss CZI (brightfield and fluorescence, multiple scenes support)
• [I/O] new format: Hamamatsu NDPIS (mIF)
• [I/O] fix issue with opening certain Roche scans in *.bif format
• 16 bit rendering and 16 bit histogram (optionally force 8 bit to save memory)
• [studio] FL Colocalization App has new mode: segment nuclei and create cell outline by growing nucleus. Select for each marker whether they should be evaluated only in  the nucleus, only in the cytoplasm or in both zones.
  
• [studio] IHC Cell Detection App: redone from scratch. More options and better quality results. Support cytoplasmic/membrane markers such as T-cell markers CD3/CD4/CD8.
• [studio] FISH HER2/neu App: show additional diagrams / plots
  
• [studio] Mask-by-Color App: now also works with fluorescent slides
• [studio] Cell-Cell-Connection App: collect more statistics, incl. #bystanders by cell type and average distance by cell type
• new feature: Tiling App and Annotation-Image-Export App can now also create masks that can be used to train segmentation AI models
• new feature: force for annotations globally: filled or outline-only
• new feature: annotation classes can be tagged. Classes can be hidden or shown by tag.
• new feature: list annotations in column in "Slides" table view
• new feature: double-click viewer with hand-tool to zoom-in. Double-click again to zoom-out again.
  
• new feature: combine live stain unmixing with masking
• new feature: show annotation counts in slide pane (in table-view)
• new feature: export annotations from multiple selected slides into csv (via slide pane)
• highlight in "Slides" pane, which slides are currently opened
• add create/load preset buttons more prominently to classes sidebar
• make annotation actions (grow, scale, select, add margins...) accessible from popover in main toolbar
• new feature: add toolbar buttons to open previous / next slide in workspace
• new feature: fly to previous / next annotation in class
• bugfix: vertical coordinate offset in Aperio XML annotation export for slides with non-square pixels (e.g. 3DHistech P1000)
  
• various bugfixes

• MICAIA studio release
  
• [studio] new Apps: Mask by Color, Cell-based IHC Scoring, FL Cell Counting, FL Colocalization, FL Spot Counting, FL FISH HER2/neu Scoring, Cell-Cell Connections
• [studio] FL Colocalization Plots
• new free App: Foreground Detection
• Tile Export App: support only exporting tiles that contain foreground (tissue)
  
• improved pen tool: user can now release the mouse while drawing an annotation in order to to rest their finger or to navigate
  
• viewer supports stain-unmixing
  
• new "annotation class changer" tool. This brush changes all existing annotations it touches to the currently selected class.
  
• support Olympus VSI format (brightfield only)
  
• App configurations can now be saved as a prese
• support executing analysis batches from *.micbat file
  
• A set of classes including their names and styles can now be saved as a preset
  
• markup opacity can now be changed centrally for all classes at once
• the image layer can now be hidden in order to only show the markup
• added new more flexible window docking system
• when multiple slides are viewed side-by-side, their title is now visible in
  the tab title
  
• support reading annotations from *.mrxs slides
  
• when a Aperio XML markup file is located next to a slide and has the same base name, it will automatically be loaded
• redesigned the annotation class buttons so that it can be more easily selected
• bugfix: undo/redo not possible for changing an annotation's class
• bugfix: the current class was sometimes reset to the first class
• bugfix: slide was marked as having pending changes even when annotation layers were shown/hidden
  
• bugfix: auto-save file was used even when user answered "restore?" prompt with "no"
  
• various bugfixes and optimizations
   

• initial release of MICAIA^® lite