Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / angelolab/toffy issues and pull requests

#479 - Bump `toffy` to 0.3.3

Pull Request - State: closed - Opened by alex-l-kong about 2 months ago

#478 - Fix mibi-bin-tools release to 0.2.14

Pull Request - State: closed - Opened by alex-l-kong about 2 months ago

#477 - Fix release issue inconsistency on PyPI

Pull Request - State: closed - Opened by alex-l-kong about 2 months ago

#476 - Release v0.2.3

Pull Request - State: closed - Opened by alex-l-kong about 2 months ago - 1 comment

#475 - Bump `mibi-bin-tools` to `0.2.14`

Pull Request - State: closed - Opened by alex-l-kong 2 months ago

#474 - Fix `incomplete_fov_check` to not require a channel named `Au`

Pull Request - State: open - Opened by alex-l-kong 2 months ago - 1 comment

#471 - Define Rosetta matrix for compensation on MIBIBlue slides

Issue - State: open - Opened by alex-l-kong 3 months ago
Labels: design_doc

#468 - `load_panel` should correct `Noodle` range in pre-defined `-toffy.csv` files

Issue - State: closed - Opened by alex-l-kong 4 months ago
Labels: enhancement

#465 - Script 3d sometimes tries to read the wrong json file

Issue - State: closed - Opened by dtebaykin 6 months ago - 1 comment
Labels: bug

#464 - Fix Noodle extraction range in convert_panel()

Pull Request - State: closed - Opened by camisowers 7 months ago
Labels: bug

#463 - Default extraction is only extracting noodle as 116.7-117

Issue - State: closed - Opened by cliu72 7 months ago
Labels: bug

#461 - Normalization notebook bug

Pull Request - State: closed - Opened by camisowers 10 months ago - 1 comment
Labels: bug

#460 - Bump commercial Rosetta matrix to v2

Pull Request - State: closed - Opened by alex-l-kong 10 months ago - 1 comment

#459 - Implement new JSON standard for MIBIScope Update

Pull Request - State: open - Opened by alex-l-kong 11 months ago

#458 - Adjust the batch effect QC notebook to average stats across all TMAs

Pull Request - State: closed - Opened by camisowers about 1 year ago - 1 comment
Labels: enhancement

#457 - Alpineer v0.1.12

Pull Request - State: open - Opened by camisowers about 1 year ago - 3 comments
Labels: dependencies

#456 - Prevent pulse_height_fit from throwing dtype warning with floats

Pull Request - State: closed - Opened by alex-l-kong about 1 year ago

#455 - Add support for MIBI runs acquired using autogain feature

Pull Request - State: closed - Opened by alex-l-kong about 1 year ago - 2 comments

#454 - Fix normalization documentation

Pull Request - State: closed - Opened by camisowers about 1 year ago - 1 comment
Labels: documentation

#453 - For autogain runs, add voltage plotting scheme

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 5 comments

#452 - Release `v0.2.2`

Pull Request - State: closed - Opened by srivarra over 1 year ago
Labels: dependencies

#451 - Fix rosetta comparison image output

Pull Request - State: closed - Opened by camisowers over 1 year ago - 1 comment
Labels: bug

#450 - `randomize_setting` in `QCControlMetrics.transformed_control_effects_data` does not randomize

Issue - State: closed - Opened by srivarra over 1 year ago - 1 comment
Labels: bug

#449 - Rosetta stitched images show black source row

Issue - State: closed - Opened by camisowers over 1 year ago
Labels: bug

#448 - MIT License

Pull Request - State: closed - Opened by srivarra over 1 year ago
Labels: documentation

#447 - MIT License

Issue - State: closed - Opened by srivarra over 1 year ago

#446 - Next Release v0.2.2

Issue - State: closed - Opened by srivarra over 1 year ago - 1 comment
Labels: enhancement

#445 - Notebook for extracting detector data for autogain testing.

Issue - State: closed - Opened by bryjcannon over 1 year ago - 2 comments
Labels: enhancement

#444 - Prevent mass column from adding during `rosetta.combine_compensation_files`

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago
Labels: bug

#443 - Ensure safe conversion of panel types during `modify_panel_ranges`

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: dependencies

#442 - Safer dtype handling for `panel_utils.modify_panel_ranges`

Issue - State: closed - Opened by alex-l-kong over 1 year ago
Labels: bug

#440 - Add scaling to rosetta source channel images

Pull Request - State: closed - Opened by camisowers over 1 year ago - 1 comment
Labels: bug

#439 - Rosetta image stitching error

Issue - State: closed - Opened by camisowers over 1 year ago
Labels: bug

#438 - QC TMA feature specification

Issue - State: open - Opened by camisowers over 1 year ago
Labels: bug

#437 - Add pre-commit to standardize toffy documentation

Pull Request - State: closed - Opened by camisowers over 1 year ago
Labels: documentation

#436 - Update pulse height generation to be compatible with `mibi-bin-tools==0.2.11`

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago
Labels: enhancement

#435 - Check for all run merge conflicts

Pull Request - State: closed - Opened by camisowers over 1 year ago
Labels: enhancement

#434 - Updated the `toffy` environment file

Pull Request - State: closed - Opened by srivarra over 1 year ago - 1 comment
Labels: dependencies

#433 - Update `environment.yml` to use the latest version of `toffy`

Issue - State: closed - Opened by srivarra over 1 year ago
Labels: bug, dependencies

#432 - Rosetta Round 2

Issue - State: open - Opened by HPiyadasa over 1 year ago
Labels: enhancement

#430 - Change logic to report all overlaps

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#429 - `jupyter_contrib_nbextensions` fix

Pull Request - State: closed - Opened by srivarra over 1 year ago
Labels: dependencies

#428 - Ensure low sensitivity normalization correction works with negative values too

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago
Labels: bug

#427 - Standardize indexing of over- and under-normalized channels in `normalize_fov`

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago
Labels: bug

#426 - Provide more robust round 1 -> round 2 copying

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: bug

#425 - Problem installing toffy_env and starting jupyter notebook

Issue - State: closed - Opened by srivarra over 1 year ago
Labels: dependencies

#424 - Toffy template 4a: compensate image data

Issue - State: closed - Opened by dtebaykin over 1 year ago
Labels: bug

#422 - Use updated round 2 Rosetta folder path spec

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: bug

#421 - Space optimization for tiled Rosetta images

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago
Labels: bug

#420 - Cite TSAI in tiling notebooks, deprecating them

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 2 comments
Labels: documentation

#419 - Partial FOVs clarification

Pull Request - State: closed - Opened by camisowers over 1 year ago
Labels: enhancement

#418 - Indicate incompatible normalization notebook with MIBIcontrol 1.8

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: documentation

#417 - Bump to v0.2.1

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago

#416 - Check for partially generated fovs

Pull Request - State: closed - Opened by camisowers over 1 year ago - 1 comment
Labels: enhancement

#415 - Helper function for scaling images

Pull Request - State: closed - Opened by camisowers over 1 year ago - 2 comments
Labels: enhancement

#414 - Add warning to normalization notebook

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#413 - Remove hanging `extracted_imgs_dir` reference in Rosetta notebook

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: enhancement

#412 - Ensure pulse heights file is named with `_` not `-`

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 2 comments

#411 - Automatically check for GitHub updates on the CACs

Issue - State: open - Opened by alex-l-kong over 1 year ago
Labels: enhancement

#410 - Check for missing fovs after run is complete

Pull Request - State: closed - Opened by camisowers over 1 year ago - 2 comments
Labels: enhancement

#409 - Add deprecation warning to notebooks 2

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#408 - QC Metrics - Save Longitudinal Transformed Metrics

Pull Request - State: closed - Opened by srivarra over 1 year ago
Labels: enhancement

#407 - Identify images partially extracted by watcher

Issue - State: closed - Opened by alex-l-kong over 1 year ago - 3 comments

#406 - Ensure runs below fovs_per_num threshold get skipped during Rosetta t…

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment

#405 - Add an option to save the transformed DataFrame as a `csv` for QC Longitudinal Metrics

Issue - State: closed - Opened by srivarra over 1 year ago
Labels: enhancement

#404 - Identify channels which would benefit from modified extraction range

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#403 - Add utility function for easy downscaling and upscaling of images

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#402 - Poor compression for rosetta stitched images

Issue - State: closed - Opened by ngreenwald over 1 year ago - 2 comments
Labels: bug

#401 - Ensure watcher can wait on run folder to appear

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment
Labels: enhancement

#400 - Check for partially generated FOVs

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#399 - Check for missing FOVs

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#398 - Fix rescale_raw_images error

Pull Request - State: closed - Opened by camisowers over 1 year ago
Labels: bug

#396 - Testing for macOS and Windows

Pull Request - State: open - Opened by srivarra over 1 year ago

#395 - Add tests for Windows and macOS

Issue - State: open - Opened by srivarra over 1 year ago
Labels: enhancement

#394 - Skip watcher callbacks for FOVs that already have data generated

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago

#393 - Turn off `combined.csv` file warnings for intermediate callbacks in watcher

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment

#392 - Ensure incompletely extracted bin files get re-extracted

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment

#391 - FOV resolution check

Pull Request - State: closed - Opened by camisowers over 1 year ago - 2 comments
Labels: enhancement

#390 - Make sure watcher logging actually writes to file on CACs

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment

#389 - Extracted images have weird artifact

Issue - State: closed - Opened by ngreenwald over 1 year ago - 1 comment
Labels: bug

#388 - Identify resolution per image

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#386 - Turn on y ticks for QC plots

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago - 1 comment

#385 - Adjust rosetta processing paths

Pull Request - State: closed - Opened by camisowers over 1 year ago - 1 comment
Labels: enhancement

#384 - Clean up watcher output

Issue - State: closed - Opened by ngreenwald over 1 year ago - 2 comments
Labels: enhancement

#383 - Allow for image specified for flatfield correction to be empty

Pull Request - State: closed - Opened by cliu72 over 1 year ago - 1 comment

#382 - Tma and tiled run stitching

Pull Request - State: closed - Opened by camisowers over 1 year ago
Labels: enhancement

#381 - Remove warning for .def.hist and .pro.hist files

Pull Request - State: closed - Opened by alex-l-kong over 1 year ago

#380 - Watcher doesn't execute run callbacks

Issue - State: closed - Opened by ngreenwald over 1 year ago - 2 comments
Labels: bug

#379 - Invalid file warnings in watcher

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: enhancement

#378 - qc_metrics plots don't have axis labels

Issue - State: closed - Opened by ngreenwald over 1 year ago
Labels: bug

#377 - Ensure watcher can run even if run folder not written to Data

Issue - State: closed - Opened by alex-l-kong over 1 year ago
Labels: enhancement

#376 - Add Powershell Scripts for Starting and updating the notebooks

Issue - State: open - Opened by srivarra over 1 year ago
Labels: enhancement