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CellProfiler pipelines

These pipelines segment and track cells in the pre-processed timelapse images and export per-cell measurements. They were run with CellProfiler version 5.

To run a pipeline: open CellProfiler, choose File > Open Project... (or drag the .cppipe onto the window), drag the input images into the Images module file list, set the Default Output Folder, and click Analyze Images.

chlamy_swim_track.cppipe

Tracks swimming Chlamydomonas reinhardtii and produces the measurements used by the R analysis.

  • Inputs: The frame-subtracted 8-bit TIFFs produced by code/FIJI/batch_framesubtraction.ijm (the macro's subtract/ output). The pipeline's NamesAndTypes rule selects files whose path/name contains subtract. Metadata (Sample, Well, hour) is extracted from the folder/file names, so keep the macro's output folder structure intact.
  • What it does: rescales intensity, identifies primary objects (cells), tracks objects across frames (TrackObjects), and saves overlay/label images.
  • Outputs: Exports comma-delimited per-object measurement tables to the Default Output Folder with the prefix measurements_. The cells table is measurements_Cells.csv — this is the file the R notebook reads (archived gzip-compressed as measurements_Cells.csv.gz on Zenodo, DOI 10.5281/zenodo.6999004).

colpoda_segment_cells.cppipe

Segments Colpoda steinii cells (used for the Colpoda datasets rather than the Chlamydomonas swim-track analysis).

  • Inputs: Color/RGB images of Colpoda; metadata (including chamber) is extracted from file names.
  • What it does: converts color channels to grayscale, identifies primary objects, overlays outlines, and measures object size/shape.
  • Outputs: Exports object measurements to the Default Output Folder (filename prefix microchamber) and saves outline/overlay images.