The latest release of `toffy` introduces major updates to the watcher pipeline, removing duplicate data generation, re-extracting incomplete .bin files, and enabling startup without a run folder. It introduces mass proficient image extraction to address storage concerns from large .bin files, round 2 Rosetta for additional denoising, standardized curves and outlier capping for post-Rosetta normalization, and post-reorganization QC metrics to verify across TMAs. Additional features include improved tiled image stitching for TMA + tissue samples, FOV resolution QC checking, and standardized output folders on the D drive for MIBI computers.
🚀 Features
- Check for partially generated fovs camisowers ([416](https://github.com/angelolab/toffy/pull/416))
- Remove hanging `extracted_imgs_dir` reference in Rosetta notebook alex-l-kong ([413](https://github.com/angelolab/toffy/pull/413))
- QC Metrics - Save Longitudinal Transformed Metrics srivarra ([408](https://github.com/angelolab/toffy/pull/408))
- Ensure watcher can wait on run folder to appear alex-l-kong ([401](https://github.com/angelolab/toffy/pull/401))
- QC for TMAs and Control Samples srivarra ([358](https://github.com/angelolab/toffy/pull/358))
- FOV resolution check camisowers ([391](https://github.com/angelolab/toffy/pull/391))
- Adjust rosetta processing paths camisowers ([385](https://github.com/angelolab/toffy/pull/385))
- Tma and tiled run stitching camisowers ([382](https://github.com/angelolab/toffy/pull/382))
- Mass proficient extraction for NAS storage alex-l-kong ([342](https://github.com/angelolab/toffy/pull/342))
- Add Rosetta V2 processing functionality alex-l-kong ([319](https://github.com/angelolab/toffy/pull/319))
- Ensure runs below fovs\_per\_num threshold get skipped during Rosetta t… alex-l-kong ([406](https://github.com/angelolab/toffy/pull/406))
- Skip watcher callbacks for FOVs that already have data generated alex-l-kong ([394](https://github.com/angelolab/toffy/pull/394))
- Ensure incompletely extracted bin files get re-extracted alex-l-kong ([392](https://github.com/angelolab/toffy/pull/392))
- Turn off `combined.csv` file warnings for intermediate callbacks in watcher alex-l-kong ([393](https://github.com/angelolab/toffy/pull/393))
- Turn on y ticks for QC plots alex-l-kong ([386](https://github.com/angelolab/toffy/pull/386))
- Norm workflow alex-l-kong ([361](https://github.com/angelolab/toffy/pull/361))
- Cap normalization at 10X upper bound, and 1X lower bound alex-l-kong ([352](https://github.com/angelolab/toffy/pull/352))
- Add functionality to catch file renaming to watcher alex-l-kong ([359](https://github.com/angelolab/toffy/pull/359))
- Remove warning for .def.hist and .pro.hist files alex-l-kong ([381](https://github.com/angelolab/toffy/pull/381))
- Allow for image specified for flatfield correction to be empty cliu72 ([383](https://github.com/angelolab/toffy/pull/383))
🐛 Bug Fixes
- Fix rescale\_raw\_images error camisowers ([398](https://github.com/angelolab/toffy/pull/398))
- Ensure pulse heights file is named with `_` not `-` alex-l-kong ([412](https://github.com/angelolab/toffy/pull/412))
- Make sure watcher logging actually writes to file on CACs alex-l-kong ([390](https://github.com/angelolab/toffy/pull/390))
- Add a scale factor for `image_stitching.stitch_images` for Photoshop compatibility alex-l-kong ([374](https://github.com/angelolab/toffy/pull/374))
🧰 Maintenance
- Update environment.yml srivarra ([372](https://github.com/angelolab/toffy/pull/372))
alex-l-kong, camisowers, cliu72 and srivarra