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

#375 - Add fallback protection to Rosetta pipeline

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

#374 - Add a scale factor for `image_stitching.stitch_images` for Photoshop compatibility

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

#373 - Revert "Add method to combine compensation matrices for Rosetta V2"

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

#372 - Update environment.yml

Pull Request - State: closed - Opened by srivarra almost 2 years ago
Labels: dependencies

#371 - Next Release - v0.1.3

Pull Request - State: closed - Opened by srivarra almost 2 years ago - 1 comment
Labels: dependencies

#370 - GitHub Actions - CI Updates

Pull Request - State: closed - Opened by srivarra almost 2 years ago
Labels: enhancement

#369 - GitHub Actions Updates and Extended Python Versions

Issue - State: closed - Opened by srivarra almost 2 years ago
Labels: enhancement

#368 - toffy and alpineer version conflicts

Issue - State: closed - Opened by camisowers almost 2 years ago
Labels: bug

#367 - Update normalization notebook to work with automatic voltage updates

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 2 comments
Labels: enhancement

#366 - Add method to combine compensation matrices for Rosetta V2

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 2 comments

#365 - Clarify documentation for round 2 compensation

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 1 comment

#364 - Additively add multiple compensation matrices together for round 2 Rosetta

Issue - State: open - Opened by alex-l-kong almost 2 years ago - 3 comments
Labels: design_doc

#363 - Refresh intermediate callback plotting on each new FOV

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 2 comments
Labels: bug

#362 - TMA-wide QC Tissue Ranks

Issue - State: closed - Opened by srivarra almost 2 years ago
Labels: enhancement

#361 - Norm workflow

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 5 comments

#360 - Multiple tile stitching

Pull Request - State: closed - Opened by camisowers almost 2 years ago - 1 comment
Labels: enhancement

#359 - Add functionality to catch file renaming to watcher

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 6 comments

#358 - QC for TMAs and Control Samples

Pull Request - State: closed - Opened by srivarra almost 2 years ago - 4 comments
Labels: enhancement

#357 - Change name of stitched_images folder

Issue - State: closed - Opened by ngreenwald almost 2 years ago
Labels: enhancement

#356 - Fix median pulse height chart drawn by `visualize_mph`

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago
Labels: bug

#355 - create_stitched_images callback produces tiffs that are incompatible with photoshop

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 3 comments
Labels: bug

#354 - Added conda-forge channel to `environment.yml`

Pull Request - State: closed - Opened by srivarra almost 2 years ago - 4 comments
Labels: bug

#353 - conda environment fails to build

Issue - State: closed - Opened by bryjcannon almost 2 years ago - 3 comments
Labels: bug

#352 - Cap normalization at 10X upper bound, and 1X lower bound

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 1 comment

#351 - Increase stitching flexibility for multiple tiled regions

Issue - State: closed - Opened by camisowers almost 2 years ago - 5 comments
Labels: design_doc

#350 - Watcher freezes randomly

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 4 comments
Labels: bug

#349 - Add pre-commit hooks for Jupyter notebooks

Issue - State: open - Opened by alex-l-kong almost 2 years ago
Labels: enhancement

#348 - Remove duplicate plots in notebook for intermediate callbacks

Issue - State: closed - Opened by ngreenwald almost 2 years ago
Labels: enhancement

#347 - Potential memory leak in watcher

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 1 comment
Labels: bug

#346 - Allow watcher to skip previously processed files

Issue - State: closed - Opened by ngreenwald almost 2 years ago
Labels: enhancement

#345 - Add a pre-commit hook for docstrings

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 1 comment
Labels: enhancement

#344 - Update tuning curve process for normalization

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 8 comments
Labels: design_doc

#343 - Update `axes_size` to `axes_font_size` in `3c` notebook

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 1 comment
Labels: bug

#342 - Mass proficient extraction for NAS storage

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 18 comments

#341 - Fix brew install command for pre-commit

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago
Labels: documentation

#340 - Print out FOV name in compensation notebook

Issue - State: closed - Opened by camisowers almost 2 years ago
Labels: enhancement

#339 - Ensure watcher picks up final `.bin` files and not temp `.bin.{hash}` files

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 2 comments
Labels: bug

#337 - Additional empty plot being drawn for MPH visualization

Issue - State: closed - Opened by alex-l-kong almost 2 years ago
Labels: bug

#336 - `axes_size` should be `axes_font_size` in `3c_generate_qc_metrics.ipynb`

Issue - State: closed - Opened by alex-l-kong almost 2 years ago
Labels: bug

#334 - Missing import in extraction notebook

Pull Request - State: closed - Opened by camisowers almost 2 years ago - 3 comments
Labels: bug

#333 - Update README.md

Pull Request - State: closed - Opened by ngreenwald almost 2 years ago
Labels: documentation

#332 - Adapt stitching for multiple tiled regions in a single run

Issue - State: closed - Opened by camisowers almost 2 years ago - 5 comments
Labels: enhancement

#331 - Tiled stitching produces incorrect image with the new mibi tiler

Issue - State: closed - Opened by camisowers almost 2 years ago - 1 comment
Labels: bug

#330 - Flexible Requirements

Pull Request - State: closed - Opened by srivarra almost 2 years ago
Labels: enhancement

#329 - Don't display warning if the watcher discovers a temp file

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 1 comment
Labels: bug

#328 - GitHub Actions

Pull Request - State: closed - Opened by srivarra almost 2 years ago - 1 comment
Labels: enhancement

#327 - Extract proficient data to account for NAS bin file deletion

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 8 comments
Labels: design_doc

#326 - Ensure normalization doesn't happen for all-zero pulse height channels

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 2 comments
Labels: bug

#325 - Default normalization curves

Issue - State: closed - Opened by ngreenwald almost 2 years ago
Labels: enhancement

#324 - Add min/max values for normalization

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 2 comments
Labels: enhancement

#323 - Remove MIBItracker tests

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago
Labels: bug

#322 - NAS-friendly extraction

Issue - State: closed - Opened by ngreenwald almost 2 years ago - 3 comments
Labels: enhancement

#321 - Add QC check to track intensity as a function of run acquisition order

Issue - State: closed - Opened by ngreenwald almost 2 years ago
Labels: enhancement

#320 - MIBItracker API download tests failing

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 2 comments
Labels: bug

#319 - Add Rosetta V2 processing functionality

Pull Request - State: closed - Opened by alex-l-kong almost 2 years ago - 7 comments

#318 - Allow users to run subsequent rounds of Rosetta for specific channels

Issue - State: closed - Opened by alex-l-kong almost 2 years ago - 7 comments
Labels: design_doc

#317 - Indicate or move tuning curve generation to normalize notebook

Issue - State: closed - Opened by HPiyadasa almost 2 years ago - 2 comments
Labels: enhancement

#316 - check_detector_voltage function when voltage is 0

Issue - State: closed - Opened by HPiyadasa about 2 years ago - 1 comment
Labels: bug

#315 - 4a notebook - skip over previously compensated runs

Issue - State: closed - Opened by HPiyadasa about 2 years ago - 3 comments
Labels: enhancement

#314 - `start_watcher` won't process "missed" FOVs if MIBI run interrupted

Issue - State: closed - Opened by alex-l-kong about 2 years ago - 1 comment
Labels: bug

#313 - Add ability to override run callbacks to process per FOV

Pull Request - State: closed - Opened by alex-l-kong about 2 years ago - 4 comments
Labels: enhancement

#311 - Add option to execute certain run callbacks per FOV

Issue - State: closed - Opened by alex-l-kong about 2 years ago - 4 comments
Labels: design_doc

#308 - 4b normalization produces images with negative expression values

Issue - State: closed - Opened by HPiyadasa about 2 years ago - 3 comments
Labels: bug

#307 - 4b, Normalization script sometimes produces an error when smoothing outliers

Issue - State: closed - Opened by dtebaykin about 2 years ago - 9 comments
Labels: bug

#306 - 3a Monitor run notebook does not plot until the end of run

Issue - State: closed - Opened by HPiyadasa about 2 years ago - 3 comments
Labels: enhancement

#305 - `ipympl` is not pinned properly.

Issue - State: closed - Opened by srivarra about 2 years ago
Labels: dependencies

#304 - Marker Intensity vs. Image Location Analysis Script

Issue - State: open - Opened by srivarra about 2 years ago - 3 comments
Labels: enhancement

#300 - Update Rosetta test directory setup

Pull Request - State: closed - Opened by alex-l-kong about 2 years ago - 4 comments
Labels: enhancement

#299 - Issue with ffc_masses argument in rosetta.compensate_image_data

Issue - State: closed - Opened by efrancis28 about 2 years ago
Labels: bug

#297 - Conda Environment - scikit-learn & seaborn

Pull Request - State: closed - Opened by srivarra about 2 years ago - 1 comment
Labels: dependencies

#296 - Toffy miniconda does not install scikit-learn

Issue - State: closed - Opened by dtebaykin about 2 years ago - 1 comment
Labels: dependencies

#295 - Substituted Ark imports with TMI in the Jupyter Notebooks

Pull Request - State: closed - Opened by srivarra about 2 years ago - 1 comment
Labels: dependencies

#294 - Fix Ark / TMI imports in the Notebooks

Issue - State: closed - Opened by srivarra about 2 years ago
Labels: dependencies

#293 - Make sure Rosetta converts images to `float` prior to running

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

#292 - Load images in as `float32` prior to compensation

Issue - State: closed - Opened by alex-l-kong about 2 years ago
Labels: bug

#291 - Rework Rosetta directory structure to support subsequent rounds of compensation

Issue - State: closed - Opened by alex-l-kong about 2 years ago - 1 comment
Labels: design_doc

#290 - Skip empty json files in voltage check

Pull Request - State: closed - Opened by camisowers about 2 years ago
Labels: bug

#289 - Skip empty jsons in voltage check

Issue - State: closed - Opened by camisowers about 2 years ago
Labels: bug

#286 - Adding TMI

Pull Request - State: closed - Opened by srivarra about 2 years ago
Labels: dependencies

#285 - Tiled stitching for toffy

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

#284 - add tmi to environment.yml

Pull Request - State: closed - Opened by camisowers over 2 years ago
Labels: dependencies

#283 - Add tmi to environment.yml

Issue - State: closed - Opened by camisowers over 2 years ago
Labels: dependencies

#282 - Image Utils in TMI

Pull Request - State: closed - Opened by srivarra over 2 years ago
Labels: dependencies

#281 - Next Release - v0.1.1

Pull Request - State: closed - Opened by srivarra over 2 years ago - 3 comments
Labels: dependencies

#280 - Compressed Tiff Files

Pull Request - State: closed - Opened by srivarra over 2 years ago - 1 comment
Labels: enhancement

#279 - Create toffy-native functionality for stitching images

Issue - State: closed - Opened by ngreenwald over 2 years ago
Labels: design_doc

#278 - Add link in notebooks for the ark tiled Image Stitching script

Pull Request - State: closed - Opened by camisowers over 2 years ago - 3 comments
Labels: documentation

#277 - Plot marker intensity as a function of image location

Issue - State: closed - Opened by ngreenwald over 2 years ago
Labels: enhancement

#276 - Link to image stitching code

Issue - State: closed - Opened by ngreenwald over 2 years ago

#271 - Make sure loading in convert_panel happens in utf-8

Pull Request - State: closed - Opened by alex-l-kong over 2 years ago
Labels: bug

#270 - Use compressed tifs by default

Issue - State: closed - Opened by ngreenwald over 2 years ago
Labels: enhancement

#269 - Fix extraction logic for run with a single fov crash

Pull Request - State: closed - Opened by camisowers over 2 years ago
Labels: bug

#268 - bin_extraction logic fails for run crash during first FOV

Issue - State: closed - Opened by camisowers over 2 years ago
Labels: bug

#267 - Toffy Setup Video Fix

Pull Request - State: closed - Opened by srivarra over 2 years ago
Labels: documentation

#265 - Update toffy with new `ark` release

Issue - State: closed - Opened by ngreenwald over 2 years ago
Labels: dependencies

#246 - Error creating toffy env

Issue - State: closed - Opened by ngreenwald over 2 years ago
Labels: documentation

#218 - Duplicate Notebook bug

Issue - State: closed - Opened by benoberlton over 2 years ago - 8 comments
Labels: bug

#208 - Enforce consistent type hinting throughout toffy

Issue - State: closed - Opened by alex-l-kong over 2 years ago - 1 comment
Labels: enhancement