MIKAIA^® Changelog

• [studio] IHC Cell Detection App
  • bugfix: randomly occuring crash when using XXL AI model
• [studio] FL Cell Analysis App
  • bugfix: randomly occuring crash when using XXL AI model
• [studio] HE Cell AI App
  • improve speed
  • prevent that UI stalls when selecting a margin annotation that intersects with thousands of cell annotations (intersection test takes long)
     

• [studio] IHC Cell Detection App
  •   in exported CSV, decide list and order of class columns in an image-independent way, so that in a batch analysis, all slides have the same columns  
  •   fix inconsistent behavior: when "verbose annotations" and automatic-intensity
  •   threshold options are enabled, some false-positives cells were put in a ROI-specific class and others in a ROI-independent class.
• [studio] Grid Analysis App
  •   bugfix: when using a metric that requires two classes, "annotation already exists" error occurred
• [studio] FL Cell Analysis App         
  •    software freezes during CSV export for high-plex scans when no cell type map is configured and each marker-permutation is treated as a cell type in CSV, add per-class rows
  •    bugfix: scatter plot showed mean expression intensities, even when top-x%   intensity mode was selected for a marker.
• [studio] Proximity Analysis App
  •   support to compute distance to closest object in each (instead of any) targetclass
  •   add additional diagram that shows the mean distances
• annotation class side panel: add option to show only entries for classes that

• when no slide is opened, the entire black viewer background now accepts a drag&drop
• [studio] IHC Cell Detection App
  • support subcellular analysis via "estimate membrane by expanding nucleus" or "estimate nucleus by shrinking membrane" options. It can then be selected which cell compartment is used to determining the cell's positivity.
  • add table of filtered cells (false positive filters, too small, too large) in results panel.
  • additional result diagram (horizontal stacked bar chart) for illustrating relative distribution of pos. vs. neg. cells (or grades)
  • replace optional "min required positive area" constraint with new option where the mean intensity in the top x% is computed. This option is also available, when the auto-intensity threshold is enabled.  
  • improve structure of CSV export
• [studio] FL Cell Analysis App
  • replace optional "min required positive area" constraint with new option where the mean intensity in the top x% is computed. This option is also available, when the auto-intensity threshold is enabled.
  • increase internal computation accuracy for >8 bits images.
  • also measure intensities of disabled markers
  • include channel color for channel-specific attributes in in annotatation attribute table
  • improve structure of CSV export
  • bugfix: absolute required intensity of markers is computed based on integer value, not based on fractional value.
  • bugfix: when nuclei+membrane mode is selected, the used threshold is stated in the wrong column of the exported CSV spreadsheed
  • bugfix: crash when "find smaller/larger objects" advanced option is enabled  
•  [studio] Proximity Analysis App
  • bugfix: crash during CSV export when no single path was found during the analysis
• [studio] H&E Colon Cell AI App
  • bugfix: random crash when a "Divide by ROI" class is selected.
• [studio] Crypt AI App
  • when grading is enabled, occasionally the algorithm got stuck in an infinite loop
• redesigned and improvied app config preset menu.
• check if annotation that serves as analysis ROI is from a class that is selected in the app's config's "Divide by ROI" list. Complain if that is the case.
• improve how cells in tile overlap regions are resolved. The chance that adjacent cells, especially those where the nucleus was expanded, overlap is reduced significantly
• when importing annotations file and classes with same name already exist, let user select if annotations should be merged or assigned to new classes with "(imported)" class name suffix.
• I/O: support Versa SVS files
• bugfix: crash when rotating viewer by pressing SHIFT+arrow
• bugfix: color histogram button "Apply to all selected slides" remains disabled even though multiple slides are selected for a batch analysis.
• bugfix: "ignore jpgs" only takes effect for imported directories, but not for their subdirectories
• bugfix: when a very large slide is opened and the user is prompted to compute resolution levels, the resulting new slide lacks the original native resolution level
• bugfix: when exporting annotations to *.ano file, deleted annotations were also written out (flagged as "deleted"). Now they are skipped.
• bugfix: for annotations of type "polygon", the bounding box instead of the true shape acted as a click zone

• annotations of classes without a fill color are now selected by clicking on their outline. This way it is possible to select an annotation that is obscured by another annotation.
• [studio] FL Cell Analysis App
  • in membrane+nuclei mode where AI yields cells' outer contour, additionally delineate the cells' nuclei.
  • req. intensity parameter changed from integer 1-100 to float 0.0 - 100.0 to facilitate more finely grained threshold steps. 
• [studio] IHC Cell Detection App
  • bugfix: limit number of points in scatter plot so that it does not freeze the UI
  • additional filter for unspecifically stained cells.
• Tissue Detection App
  • bugfix: crash when opening new slide while the AI input preview dialog is opened 
• Tile Export App
  • make changes to facilitate export of annotations as a rasterized mask image, e.g. for import into MACS iQ View. Cell nuclei and membrane contours can be exported into separate masks.
• slide info popover: use vertical splitter layout, so that more space can be assigned to any of the tables
• "Results" section in image analysis sidebar: add undock and export buttons.
• bugfix: in v2.3.1 version number in window title read "2.3.0" instead of "2.3.1"
• bugfix: crash when clicking "info" button that shows table with class tags, when at least one tag has a space in the name.
• bugfix: crash when open multiple slides side by side, then closing a viewer (except last one) and then opening an additional new slide
• bugfix: when the application UI scale is changed, the center buttons in the main tool bar did not correctly adjust their icon size.  
• bugfix: files in workspace folders were not recognized when their file extension was not lower case.

• [studio] FL Cell Analysis App
• new feature: in membrane+nuclei AI segmentation mode, support selecting multiple channels. Then these will be merged and jointly presented as a cytoplasmic/membrane marker to the segmentation AI.
• new feature: allow changing the image scale in order to detect smaller or larger cell-like objects such as Glomeruli
• [studio] IHC Cell Detection App
• new feature: allow changing the image scale in order to detect smaller or larger cell-like object
• when a large slide without downscaled resolution levels is opened, warn the user and offer to generate a new slide that includes resolution levels.
• bugfix: crash when opening multiple side-by-side viewers and then closing a viewer
• bugfix: crash in IHC Cell Detection App or FL Cell Analysis App when assign a cell to a ROI or scan area in combination with activated auto-threshold option

•  Tissue Detection App 
  •  improve cache lookup. When a tissue annotation has been manually edited, then use the existing annotation instead of re-using a previously computed mask from the cache
• [studio] IHC Cell Detection
  • new improved AI models (custom trained CellPose3 and CellPose4)
  • parameter "average cell size in µm" no longer required. Removed the control.
  • new feature: "Preview AI input" shows dialog that displays the pre-processed images as they are fed to the segmentation AI. This simplifies finding good pre-processing parameters.
  • new feature: automatically find threshold for determining marker positivity
  • when grading is enabled, the H-score is computed
  • new parameter: marker or counter-stain channels can be individually boosted or dimmed to improve cell segmentation results for very dim or very strong stains
  • change class naming scheme, when cells are grouped by ROI, from "ROI: class" to "class (ROI)" for consistency with other Apps
• [studio] FL Cell Analysis
  •  new improved AI models (custom trained CellPose3 and CellPose4)
  •  parameter "average cell size in µm" no longer required. Removed the control.
  •  new feature: automatically find threshold for determining marker positivity
  •  new dialog previews image channels and helps find levels and thresholds   
  •  allow to manually configure levels per channel   
  •  add buttons to toggle visibility of channels   
  •  don't compute MFI for disabled channels anymore to save time.
  •  in cell type map, allow configuring alternative rules (OR-combinations)
  •  constraint about required positive area in a cell can now be enabled selectively per channel
•  [studio] Mask by Color App:
  •  (FL slides only) new dialog previews image channels and helps find levels and thresholds. 
  •  (FL slides only) allow to manually configure levels per channel
  •  automatic threshold finding for FL channels or unmixed stains
  •  when only a single FL channel is selected, include the channel name in the created mask and use the complementary stain color for better contrast
• [studio] HE Cell AI
  • speed up rendering of generated annotations. They are now of type "Cell annotation" instead of "path" annotation
• [studio] Cellular Neighborhood App
  • make k-means clustering optional. When disabled, only radius-analysis is performed.
  • new horizontal stacked bar diagram that shows relative cell composition per neighborhood type
  • new diagram that shows cell composition by distance per cell type and ROI
    
•  [studio] Plug-in your own AI (REST/Python API)
  • add "tissue detection" to configuration panel
  • fix: annotations split into multiple parts using the eraser tool were not correctly transferred to the plugin
  • fix: communication with plugin was very slow when executed as a separate App in the MIKAIA app center ("show in app center")
  • new API command: plugin can set caption and subcaption of results panel
  • new API command: plugin can specify and new class'es group name and tags   
    
• [studio] Cell Cell Connections App
  • values computed for bystander analysis did not handle connections between cells of same type correctly (these values now count twice)
  • in result panel, replace matrix table with a prettier and more interactive 2d heatmap
•  [studio] Annotation Metrics App
  • dditionally compute and visualize diameters of annotations
• Tile Export App
  • new feature: when slide has more than 8 bits, export tiles as 16 bit png
  • new feature: add button to compute size in pixels for selected annotation
  • for multiplex slides, export each channel separately
  • bugfix: width and height of generated masks was swapped
•  Annotation to Image Export App   
  • new feature: when slide has more than 8 bits, export tiles as 16 bit png
  • for multiplex slides, export each channel separately
• Tissue Detection App
  • add levels control to configure which FL channels shall be analyzed and what black and white levels to use
•  new fallback renderer: when Desktop OpenGL is not available (e.g. on Windows Server or headless Windows), fallback to GLES/ANGLE for better compatibility
•  new feature for computing diameter of shapes
•  when importing external annotations from a file, show options for adding additional offsets, scaling or class name prefix/suffix. This mitigates compatibility issues between different viewers that either respect or ignore the slide origin coordinate.
•  when importing external annotations from a file, show options for centering the annotations in the currently visible field of view. This way, annotation files can serve as shape libraries.
•  mask annotations: do not enable blur by default
•  cell annotations: decrease diameter of points that are drawn at low zoom,when many annotations are visible
•  While an annotation tool is active, allow selecting other annotations by pressing the SHIFT key
•  support editing fluorescence channel names
•  pressing shift key while editing a rectangle annotation forces a square
•  when drawing a new annotation, deselect the current annotation in case its size text box is in the way
•  support grow/shrink also when more than one annotation is selected.
• I/O: support SCN files with fluorescence image
• I/O: for TIFF based formats, the "origin" metadata is now honored
• I/O: the *.multifile.csv format which ties together multiple files into a slide, can now address a fluorescence source file's individual channels
• support converting mask annotations to polygons or paths
• bugfix: toggling between current annotation tool and hand-tool by pressing the "." key did not always work. Sometimes, a text area was created instead.
• bugfix: size text box missing while new annotations are created
• bugfix: annotation not painted correctly anymore after it has been temporarily dragged outside the visible field of view
• bugfix: crash when drawing new annotation to class that is currently hidden
• bugfix: when burning-in annotations while exporting image, for some complex paths ugly connecting lines between parts of the path were introduced
• bugfix: colocalization plot only computed first 10 diagrams and then stopped  

• support opening multi-file scans (e.g. one tiff per FL channel) by grouping files using a *.multifile or *.multifile.csv file (documented in manual)
• UI: add in-line explanations in many places
• Workspace
  • speed up loading of slides
  • mproved and faster handling and loading of flat (non-pyramidal) images in workspace  
  • move filter options into separate menu button
  •  add colored border to search box as reminder that a filter is still active
• [studio] new App: Grid Analysis
• [studio] new App: Proximity Analysis
• [studio] improve selection of duplicate cells in tile overlap regions. Prevent that cut-off cells are selected (FL Cell Analysis App, IHC Cell Detection App, H&E Cell AI App)
• [studio] Cellular Neighborhood App: 
  • collect separate statistics by ROI and scan area
  • support neighborhood by radius instead of or in addition to k-nearest neighbor.
• [studio] Plug-in your own AI (REST/Python API)              
  • support new annotation type: masks
  • 2 new API commands for creating a CSV and for showing a diagram
• [studio] IHC Cell Detection App
  • fix: in exported CSV, class labels of "verbose" classes absent
  • fix: in exported CSV, in "class" rows,  wrong cell count reported for "Divide by  ROI" classes
• fix: in exported CSV, "class" rows now sorted alphabetically to ensure stable column order
• [studio] Annotation Metrics App
  • fix: crash when creating color histogram for very large annotations
  • name color channels and include threshold in exported CSV
  • treat class names case-insensitively
• [studio] Tile Export App 
  • new option: min. intersection with "Tissue" annotation
• [studio] Tile Export App & Annotation Image Export App 
  • treat class names case-insensitively
  • fix: ensure that color mapping for grey level masks remains stable for batch, where slides do not have identical class sets
  • fix: painting priority of classes was not reliably honored
• fix: occasional crash in batch analysis after one or more previous jobs have failed
• fix: textures not correctly released by viewer or single-tile WSIs or flat images. This caused, that occasionally, images were not displayed.
• fix: when converting an annotation to type "Path", the original annotation was not removed.
• fix: play button for starting morph animations in scatter plots initially absent before plot is resized
• fix: AI Author rejected flat images because it did not correctly recognize them as images of type "Brightfield"

- to speed up the startup, skip loading slides from workspace folders that contain a lot of slides. The user can later manually trigger that these slides are loaded.
- add option that workspace folders are not restored at next start.
- change behavior: now, when a slide is closed, the annotations are always unloaded. (before they were only unloaded, when the slide contained a lot of annotations)
- new feature: reload slide from folder
- bugfix: when annotations that were created by an App were changed in the same program run, then the "*" (changes pending) status was not set for the slide.
- bugfix: in slide workspace table view, the # annotations in the annotation class columns sometimes were not updated correctly
- add dropdown menu to "Create new Annotation Class" button. Add dialog for manually creating TMA core annotations. Also support slides with multiple TMA grids.
- support batch-renaming annotation class and group names in current slide
- [studio] AI Author:

- bugfix: crash when last AI model from dropdown list was removed
- do not throw error when a slide has no new training annotations. Instead print info text in the result panel
- add new action "reset training"
- prompt "are you sure?" before deleting a model

- [studio] IHC Cell Detection App:

- bugfix: hotspot search not working when no ROIs were selected

- [studio] FL Cell Analysis:

- do not reset dynamic range settings when loading a new slide
- restore possibility to analyze a specific z-plane
- use deterministic color scheme
- bugfix: tissue detection was performed even when option was deselected

- [studio] Mask by Color App:

- allow selecting which z-plane shall be analyzed

- Tile Export App:

- bugfix: when exporting large tiles, sometimes the export dead-locked

- annotation renderer: hide texts for automatically generated annotations when the text size exceeds the annotation size (at low zoom levels)
 

- 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