5.13p - April 3, 2024

  • Allow co-localization study for XYShape/ShapePlot...
  • Fix an issue in Contour Roi (triggered in nucleoid detection)
  • Fix an issue in ShapePlot (Only the categories of the last group were taken into account)
  • Add a new version of CombineStack
  • Fix a few issues in Charts
  • Fix the offset issue for overlay
  • Upgrade XYShape/ShapePlot to display Curved Shaped bacteria
  • Fix a few issues in Chain detection
  • Add SuperPlots & ShapeProportionPlot
  • Fix Criteria Error
  • Add a way to edit Features in the Editing Interface
  • Improve SuperPlots
  • Fix a few issues in Tree display (Profiles)
  • Add a way to rescue old version of Results
  • Add a way to export cell boundaries as a binary mask or a label map
  • Add a way to export Shape as Relative Polygon coordinates
  • Add the DeepIJThresholding option for segmentation
  • Add a way to generate demograph with more than one profile
  • Fix an issue with DeepImagej
  • Upgrade ResultJ in order to accept special characters in criteria
  • Fix an issue in the experiment editor : features a now updated
  • Fix an issue in the user defined Mask management
  • Upgrade Fiber detection
  • Implement the template detection ooption
  • Make MJ compatible with the latest version of DeepImageJ 2.15
  • Fix an issue in Criteria
  • Fix an issue in the experiment editor : features were not updated correctly
  • Add Event detection in TimeParticle
  • Add a way to apply a filter (opening) on the mask used for the background measurement
  • Add the distance on the boundary in PolarCoordinate
  • Add a way to compute averaged local background
  • Fix an issue about image resolution
  • Fix an issue in contact detection
  • Fix an issue in ContourShape
  • Add a way to manually add feature using line drawer
  • Fix an issue in ContourShape (2)
  • Fix an issue in Geometry
  • Fix an display issue during initialization
  • Add MicrobeJ_m to call microbeJ using a macro
  • Add a way to bin category values from the graph interface
  • Add constriction ratio in shape descriptors
  • Fix a few issues with subcellular representation (2/2)
  • Add signal variation analysis
  • Add plugin BackGround Correction
  • Fix a few issues in Graph

5.13p (13) - beta - July 12, 2024

  • Upgrade label mask utilization and add a wrapper to use omnipose as new segmentation method
  • Allow Features tracking and analysis
  • Fix an issue in ShapePlot
  • Upgrade XYStatErrorRenderer
  • Upgrade MSD
  • Upgrade Omnipose & CombineStack
  • Add CellPose as a new segmentation method
  • Add a way to use RGB images as input Images
  • Add ParticleJ a "simplified" version of MicrobeJ
  • Upgrade Cellpose & omnipose interface in order to choose the channel ou RGB channel
  • Add a way to generate the mask using omnipose & cellpose from the MJ interface
  • Add a way to select if the manually drawn particle can fusion or not with existing particles
  • Big upgrade of Association/RelativePosition in order to facilitate angle determination for Features (Warning : may cause a compatibility issue)
  • Add a way to compute the correlation between a theoretical cytoplasmic signal and the signal of each channel
  • Fix an issue in the particle trackin algorithm

How to Install MicrobeJ

  • Locate the ImageJ or Fiji Folder:
    • On Windows...
    • On MacOSX...
  • Download MicrobeJ_.jar into the "ImageJ\plugins\" or "Fiji.app\plugins\" folder.
  • For ImageJ, you must also download and drop bioformatspackage.jar into the "ImageJ\plugins\" folder.
  • Restart ImageJ or Fiji.
  • Select 'MicrobeJ' in the Plugins menu.

Older Versions of MicrobeJ

Sources