🔬 ImageJ Macros

My collection of macros for image processing in Fiji/ImageJ.

Stack wrangling

• ResaveStacks.ijm: Re-save (overwrite) stacks in a directory for fixing the calibration or contrast in batch.
• SplitTimepoints.ijm: Save individual timepoints of a large timelapse dataset to directory.
• CropSliceFromStack.ijm: Extract and crop a single slice from a stack saving the coordinates.

Timelapse or animation utilities

• SyncAndCombineStacks.ijm: Synchronize and combine two image stacks for pairing timelapse movies.
• ZStackProjectionMovie.ijm: Make an animation through a Z-stack with using a progressive projection.

Multi-channel tools

• EnhanceContrastForAllChannels.ijm: Quickly enhance the contrast of every channel in a stack.
• SaveAllChannelCombinations.ijm: Export all possible channel combinations to PNGs.

Image segmentation

• QuickMembraneSegmentation.ijm: Segment and label cells in a single image using MorphoLibJ.
• MembraneSegmentation.ijm: Segment cells in stack and generate watershed for downstream analyses.
• MembraneAnalyze.ijm: Analyze cell morphometry in stack outputting label maps for downstream visualization.
• MembraneVisualize.ijm: Visualize cell morphometry variables in stack by color-coding measurements.

Particle Image Velocimetry

• IterativePIVAdvancedBatch.ijm: Analyze particle image velocimetry in image stack.
• IterativePIVPlot.ijm: Plot vectors for PIV analysis of image stack.
• IterativePIVOverlay.ijm: Overlay PIV vectors on image stack.

Other

• MirrorFlyEmbryosTest.ijm: Test parameters for perfect roundness before mirroring fly embryo stacks.
• MirrorFlyEmbryosBatch.ijm: Mirror stacks of fly embryos in batch.