Development

Experimental protocol

Detailed procedures for preparing and imaging Caenorhabditis elegans phenotypes can be found at the following link: High-throughput image-based drug screening of Caenorhabditis elegans movement, development, and viability (Nature Protocol Exchange)

Configuration of the GUI

There are two CellProfiler pipelines that support analysis of development: C. elegans size and intensity (Cellpose) and C. elegans size. The first pipeline utilizes Cellpose for segementation of worms. The second pipeline uses generic image transformations for segmentation. wrmXpress ships with a Cellpose model that has been trained on thousands of images of drug-treated and untreated C. elegans throughout development. Both pipelines utilize a Worm Toolbox model to estimate morphological features from images. The first pipeline performs much better for mixed populations of worms but is much slower.

Custom worm models

Performance of both pipelines will vary based on the magnification used to take the images. If you are interested in training your own Cellpose model, please reach out to the wrmXpress developers.

In Pipeline Selection, choose CellProfiler and select the pipeline of choice (either C. elegans size and intensity (Cellpose) or C. elegans size). If using a pipeline that segments worms with a Cellpose model, select the appropriate model in the dropdown.

Expected input

Development data may be analyzed in the form of individual TIF images per frame (i.e., the TimePoint structure utilized by ImageXpress). See the Data Organization page for more details. The plate directory should have a single TimePoint with individual images for each well:

Development file structure

All experiments should include a single wavelength. Multisite images should be stitched according the ImageXpress + Multi Site instructions.

Validated species and stages

Caenorhabditis elegans

  • Larvae
  • Young adults
  • Gravid adults
  • Mixed stages

Example plates

  • 20220408-p01-MGC_1351: Caenorhabditis elegans mixed stages

Expected output

A CSV file with many columns of data generated by with CellProfiler's Worm Toolbox. If using Metadata, there will be an additional column for each provided metadata data frame.