v0.2.1

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)
• Remove hanging extracted_imgs_dir reference in Rosetta notebook @alex-l-kong (#413)
• QC Metrics - Save Longitudinal Transformed Metrics @srivarra (#408)
• Ensure watcher can wait on run folder to appear @alex-l-kong (#401)
• QC for TMAs and Control Samples @srivarra (#358)
• FOV resolution check @camisowers (#391)
• Adjust rosetta processing paths @camisowers (#385)
• Tma and tiled run stitching @camisowers (#382)
• Mass proficient extraction for NAS storage @alex-l-kong (#342)
• Add Rosetta V2 processing functionality @alex-l-kong (#319)
• Ensure runs below fovs_per_num threshold get skipped during Rosetta t… @alex-l-kong (#406)
• Skip watcher callbacks for FOVs that already have data generated @alex-l-kong (#394)
• Ensure incompletely extracted bin files get re-extracted @alex-l-kong (#392)
• Turn off combined.csv file warnings for intermediate callbacks in watcher @alex-l-kong (#393)
• Turn on y ticks for QC plots @alex-l-kong (#386)
• Norm workflow @alex-l-kong (#361)
• Cap normalization at 10X upper bound, and 1X lower bound @alex-l-kong (#352)
• Add functionality to catch file renaming to watcher @alex-l-kong (#359)
• Remove warning for .def.hist and .pro.hist files @alex-l-kong (#381)
• Allow for image specified for flatfield correction to be empty @cliu72 (#383)

🐛 Bug Fixes

• Fix rescale_raw_images error @camisowers (#398)
• Ensure pulse heights file is named with _ not - @alex-l-kong (#412)
• Make sure watcher logging actually writes to file on CACs @alex-l-kong (#390)
• Add a scale factor for image_stitching.stitch_images for Photoshop compatibility @alex-l-kong (#374)

🧰 Maintenance

• Update environment.yml @srivarra (#372)
  @alex-l-kong, @camisowers, @cliu72 and @srivarra