Phenotypic differences between interfertile Chlamydomonas species- measurements, Cellprofiler

This repository contains 2D morphology measurements from timelapse microscopy data of two interfertile Chlamydomonas algal species. The protocol to generate this data is described in the associated publication, "Phenotypic differences between interfertile Chlamydomonas species", and summarized here. Cells were collected from agar plates and suspended in water, then left to sit overnight to encourage gamete formation. During this time, non-motile cells settled, allowing for the enrichment of motile cells in the supernatant. These enriched cells were then loaded onto agar microchambers (100 micron diameter and 40 micron depth) for imaging. We collected videos on a Nikon Ti2-E microscope equipped with a Photometrics Kinetix digital scMos camera. We performed differential interference contrast (DIC) imaging using a Plan Apo 10× 0.45 Air objective. We collected videos with a 5.1 ms exposure with acquisition every 50 ms for three minutes. We placed a red light filter [IR longpass, 610 nm (ThorLabs)] in the light path to maintain swimming behavior of cells. The procedure was standardized and repeated four times to ensure consistency. Measurements collected with Cellprofiler of timelapse data of C. reinhardtii or C. smithii cells in agar microchamber wells are shared here.
Reference
Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile Chlamydomonas species
Notes
Directory and subdirectories containing csv files of measurements of algal cells segmented from images.Directory structure: experiments_csv/{experiment}/{video_length}/objects/{species}/{microchamber AKA "pool ID"}/measurements/measurementschlamy.csv
"Cr" indicates Chlamydomonas reinhardtii
"Cs" indicates Chlamydomonas smithii