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CHANGELOG.md

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Changelog

3.2.1

  • Add scalebar to capture
  • Add project tab with project settings

3.2.0.5

  • Fix MacOs X libvips issue with 90% jpeg compression
  • Make top menu collapsible in config
  • Add project list and description in upper corner (optional)

3.2.0.4

  • Run Docker container as non-root user
  • Allow marker size slider to be used with absolute scaling
  • Fix incorrect transforms of region points when image layer is flipped
  • Fix MacOS X libvps issue with percent value
  • Add new blend modes for marker rendering

3.2

  • Add annotation tools (in collaboration with Sanofi Digital R&D)
  • Move to WebGL rendering for regions
  • Refactor completely the region tab to better handle large number of items
  • Allow import of regions from multiple GeoJSON files
  • Add support for Geobuf (.pbf) region files
  • Add drag-and-drop opening of GeoJSON files
  • Add histogram button for analyzing individual regions
  • Make regions work in collection mode and with multiple image layers
  • Add marker outline and fill options in Advanced options
  • Increase number of barcodes that can be displayed for markers
  • Add validation of .tmap files (via tissuumaps-schema)
  • Move standalone installer from Python 3.8 to 3.11
  • Move to PySide6 instead of PyQt6
  • Add installers for MacOS X (.dmg) and Linux (.deb)
  • Update to OpenSeadragon 4.1.0
  • Add dzi support (opening as images directly)
  • Lots of minor fixes

3.1.1.6

  • Add a min-max filter to image layers for better contrast (@glbarlow)
  • Fix marker filtering
  • Update license from BSD-3 to MIT
  • Add collapsible sections in plugins
  • Minor fixes

3.1.1.5

  • Fix multiple images dropped on empty project
  • Change threading to allow higher priority to GUI than to server side
  • Add .tmap extension to all saved projects
  • Fix pie charts display update and colors
  • Add error message if update view fails

3.1.1.4

  • Fix bug of modal not hiding properly
  • Fix capture with scale of 1
  • Fix loading of AnnData files without X matrix
  • Add DEFAULT_PROJECT parameter for docker and server

3.1.1.3

  • Minor fixes

3.1.1.2

  • Make load of HDF5 data parallel
  • Add Colormaps and Channel splitting filters

3.1.1

  • Move to OpenSeadragon 4.0.0
  • Move docker to python-alpine for security reasons
  • Add sorting options of markers (applied automatically on AnnData observations)
  • Add zOrder parameter for draw order between datasets
  • Make Update View button always visible
  • Add colorbar canvas to png captures
  • Add flip and rotation of markers for each collection item
  • Add transformation inputs in Image Layers menu
  • Add background color input
  • Add gaussian marker shape
  • Fix flask deprecated function
  • Minor fixes

3.1.0.8

  • Fix chunk size for h5 files
  • Fix iPhone not loading markers with > 192 collection items

3.1.0.7

  • Critical fix for Mac OS (see row_major in WebGL2)

3.1.0.6

  • Minor fixes

3.1.0.5

  • Add flip and rotation of markers for each collection item
  • Add transformation inputs in Image Layers menu
  • Fix colormap with NaN values

3.1.0.4

  • Fix issue with slow rendering of web-gl using instancing
  • Hide colorbar on png captures when needed
  • Other minor fixes

3.1.0.3

  • Fix h5 autocomplete on iframes
  • Fix wrong marker index for color column when more than 100k markers
  • Add colorbar canvas to png captures
  • Small fixes

3.1.0.2

  • Fix crash on layer from a parent layer.
  • Change dropdown selection from Chosen to Select2 for faster loading.
  • Update docker to Alpine for security reasons.
  • Small fixes

3.1.0.1

  • Move docker to python-alpine for security reasons
  • Add sorting options of markers (applied automatically on AnnData observations)
  • Make Update View button always visible
  • Minor fixes

3.1

  • Adding HDF5 support on the client side
  • Adding AnnData support on the server side / GUI
  • Adding Network diagram visualization
  • Tabs now saved automatically even without buttons
  • Adding Plugin helpers in javascript
  • Many fixes on the interface
  • Move to PyQt6

3.0.10.4

  • Fix path issue on json loading from server

3.0.10.3

  • Reset all input dropdowns when new data selected

3.0.10.2

  • Add scale factor for coordinates of markers

3.0.10.1

  • Add optional offset (x, y) and scale properties to tmap.layers

3.0.10

  • Add collection mode (to display images next to each other with markers correctly placed)
  • IFrame mode (to hide navbar and make menu smaller when TissUUmaps is run inside an iFrame)

3.0.9.6

  • Add debug menu when running in debug mode, with debug access in javascript
  • Fix linux bugs with Qt displaying all blank
  • Fix empty columns in marker csv file

3.0.9.5

3.0.9.3

  • Go back to webGL 1 for compatibility issue with Safari 14
  • Fix missing .tissuumaps folder for recent files

3.0.9.1

  • Enable larger markers at high resolutiion (up to 1024x1024px)
  • Fix pinch to zoom center
  • Add code of conduct
  • Clean code and use ci (pre-commit)

3.0.9

  • Move to webgl2
  • Add Open Recent sub menu in File menu
  • Fix path for linux and mac in server mode
  • Minor fixes

3.0.8.9

  • Make it possible to update to newer version of plugins
  • Fully support --debug option in command line
  • Add tooltip title for piecharts
  • Add documentation https://tissuumaps.github.io/TissUUmaps-docs/
  • Fix marker picking when pixel ratio != 1
  • Other minor fixes and cleaning

3.0.8.5

  • Minor fixes.

3.0.8.4

  • Add tiling to viewport capture for higher resolution output
  • Increase resolution of markers on high resolution devices
  • Fix jumps on pan with mouse gesture (mobile)
  • Add fix for bright image canvas on Safari
  • Add an option to remove markers' outlines.

3.0.8.3

  • Fix png artifact in Firefox, by generating jpg tiles.

3.0.8.2

  • Add high resolution capture of viewport, up to 4096x4096 pixels.

3.0.8.1

  • Fix multiple dataset alignment when no background image

3.0.8

  • Fix black images generated by VIPS

  • Fix Linux and Mac open of captures

  • Auto save datasets as buttons when saving tmap projects

  • Add mpp (microns per pixel) option in tmap files, to add scale bar to viewer

  • Make region line thickness depend on zoom level

  • Add compatibility with JupyterLab

  • Add opacity per marker option

3.0.7

  • Add menu to load plugins through an update-site

3.0.6

  • Fix multiple plugins opening always last plugin
  • Move to OpenSeadragon 3.0.0
  • Add tooltip format in Advanced Settings
  • Add drag and drop to open CSV files and images
  • Add "Add layer" button for flask version
  • Add viewport capture

3.0.5

  • Move csv loading to Papa Parse streaming, to allow better memory management

3.0.4

  • Add filtering of markers

3.0

  • Add tissuumaps.jupyter module