Phenotypic differences between interfertile Chlamydomonas species- measurements, Cellprofiler

<p>This repository contains 2D morphology measurements from timelapse microscopy data of two interfertile <i>Chlamydomonas</i> algal species. The protocol to generate this data is described in the associated publication, <a href="https://doi.org/10.57844/arcadia-35f0-3e16">"Phenotypic differences between interfertile <i>Chlamydomonas</i> species"</a>, 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 <i>C. reinhardtii </i>or C<i>. smithii </i>cells in agar microchamber wells are shared here.</p><h4>Reference</h4><p><a href="https://doi.org/10.57844/arcadia-35f0-3e16">Essock-Burns T, Garcia III G, MacQuarrie CD, Mets DG, York R. (2023). Phenotypic differences between interfertile <i>Chlamydomonas </i>species</a></p><h4>Notes</h4><p>Directory and subdirectories containing csv files of measurements of algal cells segmented from images.<br><br>Directory structure: experiments_csv/{experiment}/{video_length}/objects/{species}/{microchamber AKA "pool ID"}/measurements/measurementschlamy.csv</p><p>"Cr" indicates <i>Chlamydomonas reinhardtii</i></p><p>"Cs" indicates <i>Chlamydomonas smithii</i></p>