My collection of macros for image processing in Fiji/ImageJ.
- 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.
- SyncAndCombineStacks.ijm: Synchronize and combine two image stacks for pairing timelapse movies.
- CropSliceFromStack.ijm: Extract and crop a single slice from a stack saving the coordinates.
- MirrorFlyEmbryosTest.ijm: Test parameters for perfect roundness before mirroring fly embryo stacks.
- MirrorFlyEmbryosBatch.ijm: Mirror stacks of fly embryos in batch.
- 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.
- 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.
- EnhanceContrastForAllChannels.ijm: Quickly enhance the contrast of every channel in a stack.
- SaveAllChannelCombinations.ijm: Export all possible channel combinations to PNGs.