MIKAIA^® Changelog

- improved annotation rendering performance at presence of hundreds of thousands of annotations
- Tissue Detection has improved TMA dearraying and can take user hints (grid size & location of cores in corners)
- [studio] new App: "HE Cell AI"
- [studio] new App: "Cellular Neighborhood App"
- [studio] FL Cell Analysis App:
    - add AI-based nuclei and membrane segmentation options
        - scatter plot shows intermediate results during computation of T-SNE or UMAP. Computation can be aborted prematurely.
        - scatter plot supports animated morphing of points between the cells' spatial and feature space coordinates
- [studio] IHC Cell Detection App:
   - add AI-based segmentation options for nuclear, cytoplasmic or membrane markers
    - restructure configuration controls
- [studio] AI Author App and Colon Tissue AI App:
    - make shape adaptiveness of superpixels configurable
- [studio] AI Author App:
    - store settings inside *.ai file
- [studio] all apps:
    - omit group separator in numbers in exported csv files.
    - make decimal separator configurable
- [studio] HE Cell Detection App now uses an AI to detect and segment cells
    Renaming it to "HE Cell AI (Detection only)" to avoid confusion with the new "HE Cell AI" app (which additionally identifies cell types)
- [studio] Cell-Cell-Connections App now recognizes when cells from different ROIs ("Divide by ROI") have the same expression/type
- [studio] Mask by Color App:
     - support various modes on how fluorescence black and white levels are determined (content adaptive or fixed across entire batch)
     - bugfix: accuracy [um/px] not restored properly for some slides
- I/O: support sparse DICOMs where a resolution level is split across multiple files
- I/O: support manually specifying um/px resolution also for tiled BigTiffs
- "Subtract" annotations now shows dialog where sets A and B can be selected.
- new feature: "subtract annotations from tissue"
- new feature: start *.micbat batch analysis file via command-line. MIKAIA closes automatically when batch is done.
- CUDA device (or CPU) used to run AI is now selectable 
- decimal separator in exported CSV files is configurable
- bugfix: polygons with holes were not exported correctly to GeoJson (for QuPath) or Aperio XML.
- bugfix: restore slide-label-visible state properly after restart
- bugfix: class changer brush should not act when user forces panning with CTRL key
- bugfix: autosave files were not always deleted properly

- allow full text filtering of annotation class list
- allow toggling visibility of multiple classes via multi-selection
- Tissue Detection supports creating ROIs per TMA core (TMA de-arraying) or per tissue particle
- I/O: support (3DHistech) DICOM files that do not have a file extension
- [studio] new App: "Crypt AI App"
- [studio] new App: "Colon Tissue Cartography App"
- [studio] FL Cell Analysis App:
   - now supports grouping detected cells by ROIs.
      This way, cell statistics can be quantified separately per ROI.
   - improved segmentation quality for high resolution scans (0,3 µm/px and higher)
   - improve support for analysis of 8 bit FL scans with low intensity
   - redesigned layout of diagrams and tables in "results" panel
- support rotating annotations
- support clipping a set of annotations with other annotations
- improvement accuracy of how concentric margins are generated
- improve speed and UI responsiveness when Apps (e.g. FL Cell Analysis App or
   Cell-Cell-Connections App) create many classes
- bugfix: clipping annotations with holes in "Tissue" class did not work
- bugfix: polygon simplification for very large polygons, e.g. the "Tissue" contours
   was often too aggressive.
- bugfix: when an annotation tool was selected, it was not possible to interact with
   yellow annotation edit handles

- add extra "Are you sure?" prompt before batch-deleting annotation classes from multiple slides and saving them in-place
- bugfix: "annotation already exists" when deleting both a class group and its child classes
- bugfix: axis attribute selection dropdown for scatter plots not shown
- speed up creation of distance margins
- add "create margins for all annotations in current class" button
- fix regression: Annotation classes were no longer visible in workspace table view
- workspace table view: add new column that shows number of z-planes
- [studio] Mask by Color App:

- improve accuracy of generated masks
- when using a different class label and unless the configuration is otherwise identical, the mask created in the previous run is no longer removed, but now left in place to facilitate creation of overlapping masks for separate targets.

- [studio] IHC Cell Detection App bugfix: when assigning cells to ROIs and scan areas, cells outside any ROIs were assigned into a global "other" class instead of a "rest of scan area" specific class
 

- rename MICAIA to MIKAIA
- [I/O] support opening brightfield DICOM-WSI slides
- open loading annotations from *.ano file via drag&drop on already opened slide
- annotation classes can now be grouped in UI
- new annotation action: intersect
- new batch-operation: apply color histogram settings to other slides
- new batch-operation: create margins to all selected annotations in other slides
- annotations are now associated with a z-plane. The viewer by default shows only annotations from the currently visible z-plane.
- [studio] new App: "Plug in your own AI App". This is a REST API that allows users to plug in their own AI scripts as an App into MIKAIA.
- [studio] IHC Cell Detection App: support grouping cells by scan area and by ROI
- [studio] AI Author: new training annotation inspector lists all training slides/classes/annotations for a selected AI model and creates T-SNE plot
- [studio] Mask-by-Color App:

- support grouping masks by scan area and by ROI
- tiled analysis at higher resolution
- honor "Ignore" class
- bugfix: when analyzing a ROI, it analyzed the bounding box. Now it analyzes the true (non-rectangular) ROI

- [studio] rename FL Colocalization App to FL Cell Analysis App
- [studio] FL Cell Analysis App:

- it can now be select for 16 bit FL slides which signal range is analyzed
- it can now be selected which z-planes are analyzed. Cells' z attributes are listed in exported CSV file

- add convenience buttons in viewer's corners for opening the label photo or minimap
- Annotation-to-Image-Export App: support applying user color histogram
- sort slides in work space alphabetically
- histogram control's y-axis is not logarithmic. Trim markers are auto-set.
- Annotation-to-Image Export App

- bugfix: minimum required intersection was not honored
- bugfix: selected class was not restored in batch analysis
 

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 MIKAIA lite