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Fiji / ImageJ macros

These ImageJ macros pre-process raw timelapse movies before quantification. They were run with Fiji / ImageJ2 version 2.3.0/1.53q (build d544a3f481) and require the Bio-Formats importer (bundled with Fiji) plus, for colpoda_serieslabel_concatanate.ijm, the Series Labeler plugin.

Run a macro from Fiji via Plugins > Macros > Run... and select the .ijm file.

batch_framesubtraction.ijm

Prepares the Chlamydomonas swimming movies that feed the chlamy_swim_track.cppipe CellProfiler pipeline.

  • Inputs: When run, the macro prompts for an input directory, an output directory, and a file suffix (default .nd2). It recursively scans the input directory for movies matching the suffix. Input paths are expected to contain a raw folder; the path segment after raw/ is used to build matching output subfolders.
  • What it does: For each movie it scales by 0.5, computes a standard-deviation Z-projection (to visualize swim tracks), and performs frame subtraction (frame t minus frame t−11) starting at frame 12.
  • Outputs: Per input movie, creates STD/, subtract/, and frames/ subfolders in the output directory containing 8-bit TIFFs. The subtract/ TIFFs are the frame-subtracted images used as CellProfiler input.

colpoda_serieslabel_concatanate.ijm

A figure/movie-annotation helper for Colpoda timelapse series (used for presentation rather than as input to the analysis pipeline).

  • Inputs: Prompts for a directory and processes every .tif file in it.
  • What it does: Adds time labels (hours and seconds, using the Series Labeler plugin) and a scale bar to each stack.
  • Outputs: Saves an annotated copy of each image as <basename>concat.tif in the same directory.