New plugin features

• File and series name filters now handle case sensitivity independently.
• Mac keyboard shortcuts now also use the command key

New module features

• Child and partner object count modules now have the option to have the measurements be fixed at the time they are first calculated, or be live (evaluated when accessed).

Other

• General bugfixes

New module features

• Numerical object filters (e.g. "Based on measurement") can now output summary and individual measurements with fixed names. This helps with downstream modules that rely on a known measurement name.
• Added visual outputs to some modules still missing them. All modules should now give a visual output (unless they don't make sense to).

Other

• Copy and paste (as well as equivalent operations) should now work on Mac using the command shortcut

New modules

• ScaleObjectSet module uniformly scales an entire object set. This is equivalent to the ScaleStack module. In addition to scaling by a specific factor, object sets can also be scaled to match a fixed size, existing object set size or image size. Scaled objects are stored as children of their respective input objects.

New module features

• SingleClassCluster now uses the Elki library for DBSCAN. This is much more performant than the previously-implemented Apache Commons Math version. Since this is a different implementation, results may differ slightly from the previous version.
• CalculateNearestNeighbour now assigns object partnerships between nearest neighbours

Other

• Fixed DeepImageJ and SAMJ dependency issues preventing GitHub Action from completing successfully.
• General bugfixes

New module features

• SetLookupTable can now accept RGB values to construct a new LUT

Other

• Bugfix for CreateSkeleton when exporting loops with multithreading enabled

New modules

• FitCircles uses ImageJ's built-in circle fitter to fit circles to 2D (or 3D projected) objects and add centroid and radius measurements to selected objects.

New module features

• ManuallyIdentifyObjects can now display selected objects on all slices and/or frames.
• Better memory handling for SAMJ modules.

Other

• General bugfixes.

New plugin features

• Overlays generated by MIA modules can be toggled on/off with F12 keyboard shortcut.

New modules

• UnwarpCentroids module uses sets of tracked object centroid coordinates to apply B-spline unwarping.

New module features

• Updated ApplyCellpose to work with the most recent version of PTBIOP wrapper. This also allows the latest Cellpose models (e.g. cpsam) to be used. PTBIOP can be installed directly from the ImageJ Updater again.
• ROIs can be selected in ManuallyIdentifyObjects by double-clicking on image
• ApplySegmentAnything now also accepts ROIs (not just point centroids) as inputs. When a ROI is provided, the full region is sent to Segment Anything.
• FocusStackLocal now ensures applied height map is within range of input stack.

Other

• Exported Excel files now record memory status of computer to help identify problems.
• Fixed environment installation in SAMJ modules.
• Updated variable names in Elastix modules to match latest versions of PTBIOP.
• General bugfixes.

New module features

• ManuallyIdentifyObjects can now remove regions from existing objects in an equivalent way to how they're added. With this, the interface of ManuallyIdentifyObjects has slightly changed.

New plugin features

• File browser is larger by default

Other

• General bugfixes

New module features

• CellposeDetection can now process 3D timepoints individually and reports current progress in MIA status bar

Other

• Changed function visibility in RunScript
• General bugfixes

New module features

• Classes can be automatically assigned in ManuallyIdentifyObjects
• ApplyDeepImageJ can convert images to RGB before processing

Other

• Fixed rendering of points in ManuallyIdentifyObjects
• General bug fixes.