Feat/v0.5 #575
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feat: containerized plate extraction and run with cwl.
…original intensities.
…-tool depends on segmentation/rt-cetsa-plate-extraction-tool
agerardin
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NHotaling,
Nicholas-Schaub and
hsidky
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liuji1031
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Jan 28, 2025
* feat: added plate extraction tool * feat: added intensity extraction tool * fix: plate extraction tool * fix: rt_cetsa intensity extraction tool. * fix: rt_cetsa intensity extraction * fix: rt_cetsa segmentation. * fix: intensity extraction. Filepattern provides lexicographic ordering. feat: containerized plate extraction and run with cwl. * feat: containerized and make intensity extraction runnable in a cwl workflow. * feat: save plate params when extracting plates. * dev: faster intensity extraction. * fix: cropped plate params. * fix: intensity extraction: fast implementation based on plate params. * fix: intensity extraction. Now extract a larger area to get close to original intensities. * dev: cleanup how segmentation mask is generated. * dev: replace tifffile by bfio. Stored roi_radius in plate_params. * dev: improve cli. Sorting now available from package methods. * feat: updated intensity extraction tool. * Bump version: 0.1.0 → 0.2.0-dev0 * feat: update extraction tool. * Bump version: 0.1.0 → 0.2.0-dev0 * fix: return extract signal df. optional temp in cwl * fix: package dependencies. * chore: cleanup before PR. * fix dependency on plate extraction to fix docker build. * chore: add dummy tests to pacify git actions. * fix: remove bfio and use tifffile for docker integration. * feat: process new rt_cetsa dataset. Preprocess with Median filter. * Bump version: 0.2.0-dev0 → 0.3.0-dev0 * feat: updated intensity extraction - temp extracted from filename. * Bump version: 0.2.0-dev0 → 0.3.0-dev0 * fix: intensity extraction now depends on segmentation 0.3.0-dev0 * feat: more robust wells detection. * Bump version: 0.3.0-dev0 → 0.4.0-dev0 * Bump version: 0.3.0-dev0 → 0.4.0-dev0 * fix: rt-cetsa-intensity-extraction-tool dependencies * fix: rt-cetsa-intensity-extraction-tool dependencies * fix: rt-cetsa-intensity-extraction-tool dependencies * fix: multi tool docker image : features/rt-cetsa-intensity-extraction-tool depends on segmentation/rt-cetsa-plate-extraction-tool * Bump version: 0.4.0-dev0 → 0.5.0-dev0 * fix: deleted tests for large local images. * Bump version: 0.4.0-dev0 → 0.5.0-dev0 * fix test spacing preventing git actions. --------- Co-authored-by: Najib Ishaq <najib_ishaq@zoho.com>
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RT_Cetsa latest and final updates.