The next generation of antiparasitics will likely be discovered through high-content and high-throughput screening using automated microscopy. As the amount of antiparasitic drug screening data swells at a rapid pace, researchers need to keep up by also developing analytical tools that can quickly and reliably analyze these data. A variety of proprietary and open-source software exists for these approaches, but none that are oriented towards images of worms (whether parasitic or free-living). We developed wrmXpress to fill this software gap.
wrmXpress has been used in screens to identify compounds with microfilaricidal and macrofilaricidal effects, characterize structure-activity relationships of drug classes against schistosomes, and assess the effects of cholinergic compounds on worm feeding. It has already been used to analyze dozens of terabytes worth of data.
The next generation of wrmXpress will include a graphical user interface for more widespread and inclusive use, include modules for new phenotypic endpoints, and incorporate deep learning into image analysis. Our collaboration with the Zamanian Lab seeks to push the field forward and provide a flexible, intuitive software that is used by diverse labs and companies around the world.
Relevant publications
Track wrmXpress updates
Title | Created At | Description | Merged At | PR Number | Related Github Creator | State | Updated At |
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March 20, 2024 8:03 PM (UTC) | March 20, 2024 8:03 PM (UTC) | 19 | March 20, 2024 8:03 PM (UTC) | ||||
September 23, 2022 2:38 PM (UTC) | Incorporates #5 and #7 | September 23, 2022 2:40 PM (UTC) | 16 | September 23, 2022 2:40 PM (UTC) | |||
August 2, 2022 6:09 PM (UTC) | Supports images from \_S. mansoni\_ (2X) with or without adults in the well and \_Brugia\_ spp. (4X, tiled 2x2) without adults in the well. Binary diagnostic image is written to thumbnails. Fixes #13 | August 2, 2022 6:11 PM (UTC) | 14 | August 2, 2022 6:11 PM (UTC) | |||
July 29, 2022 2:06 PM (UTC) | July 29, 2022 2:07 PM (UTC) | 12 | July 29, 2022 2:07 PM (UTC) | ||||
July 28, 2022 5:07 PM (UTC) | Fixes #9 | July 28, 2022 5:08 PM (UTC) | 10 | July 28, 2022 5:08 PM (UTC) | |||
January 19, 2022 9:29 PM (UTC) | The \`species\` parameter is now incorporated in select modules. \`species == 'Sma'\` will adjust the segment and thumbnail modules. | January 19, 2022 9:29 PM (UTC) | 1 | January 19, 2022 9:29 PM (UTC) | |||
January 26, 2022 8:07 PM (UTC) | CP pipelines now use annotated training data and the XGBoost library to classify each straightened worm (single worm, multiple worms, partial worm, or debris). Predictions are added as columns to \`{plate}\_tidy.csv\` output data and can be used in downstream analyses. | January 26, 2022 8:07 PM (UTC) | 3 | January 26, 2022 8:07 PM (UTC) |