Change Log - jeanollion/bacmman GitHub Wiki

Version 3.8.4

  • New Data Analysis tab with Jupyter Notebook library and Jupyter Notebook server (through docker)
  • Module parameters have been changed:
    • BoundingBox measurement is now more consistent with RelativePosition measurement (no retro-compatibility)
    • DiSTnet2D: regarding tracking > post-processing: range parameter is no longer under post-processing and is renamed 'post-processing range' (no retro-compatibility). Post-processing is now a list (retro-compatibility is ensured).

Version 3.8.3

  • Added DockerEngine for neural network prediction (in addition to TF2Engine). Requires Docker with GPU passthrough.

Version 3.8.2

  • Configuration library: configuration blocks keep track of their ID to facilitate update of configurations made of different blocks. See this page for more information.
  • Reduce memory footprint for pre-processing.

Version 3.8.1

  • Added feature: in track mode, ctrl + click displays a track and all connected tracks
  • Added feature for Kymographs: display next/previous tracks; this is useful to review kymographs that contains several layers of objects in the direction of the kymograph, in which track links would overlap. This is the case of large microchannels for instance. The minimal distance between links is controlled by the parameter: Misc > Interactive Image Options > Kymograph Options > Display Track Distance.
  • Improved memory management: videos that do not fit in memory can be processed, intermediate images will be automatically stored on the disk, in the folder of the database, and removed afterwards.

Version 3.8.0

  • Both Kymographs and Hyperstacks now use lazy-loading of images (meaning they load each slice when needed) which improves responsiveness.
  • Kymographs are now multichannel.
  • Kymographs are sliced: each slice correspond to several timepoints. The size of each slice in pixels is defined in the menu Misc > Interactive Image Options > Kymograph Options > Frame Overlap, which controls the number of timepoints on each slice. The Overlap between two successive slices is defined in the same menu.
  • added Views : draw a rectangle on an hyperstack, and before releasing the mouse, press shift+ctrl to generate a kymograph view or ctrl+alt to generate a hyperstack view of the current selection. v key synchronize ROI display between different views of the same parent track.
  • Added new database storage for segmented objects: ObjectBox (the previous one is called MapDB). For conversion use the menu Options > Database > Database Type . When using MapDB database it is not safe to perfom manual curation of a parent object class (e.g. microchannels) after segmentation and tracking have of a children (e.g. bacteria) class have been performed. The ObjectBox database removes this limitation, it is also faster for writing on disk.
  • Modified scrolling shortcut for different axis (Z-slices, time, channels, X, Y): see F1 table for shortcuts.
  • Added a new display mode for objects: all objects from all object classes are displayed with one color per object class (see F1 table for shortcuts).
  • A color for ROIs can be configured per each object class.

better late than never!!! updates are listed from January 2024 on