allencellmodeling/fish_morphology_code issues and pull requests

#66 - different readme for autocontrasted quilt package

Issue - State: closed - Opened by donovanr about 5 years ago

#65 - Data/scores and cotrasted images in quilt

Pull Request - State: closed - Opened by donovanr about 5 years ago

#64 - add test option

Pull Request - State: closed - Opened by donovanr about 5 years ago

#63 - function in data to distribute test dataset

Issue - State: closed - Opened by donovanr about 5 years ago

#62 - update dataset readme to new col names

Pull Request - State: closed - Opened by donovanr about 5 years ago

#61 - Data/scores and cotrasted images in quilt

Pull Request - State: closed - Opened by donovanr about 5 years ago

#60 - rename quilt_data cols

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment

#59 - rm channel from single seg output csv

Issue - State: closed - Opened by donovanr about 5 years ago

#58 - fix path

Pull Request - State: closed - Opened by donovanr about 5 years ago

#57 - add structure scores to quilt and add commit hash

Pull Request - State: closed - Opened by donovanr about 5 years ago

#56 - Bugfix/cellprofiler workflow

Pull Request - State: closed - Opened by tanyasg about 5 years ago - 1 comment

#55 - give github access to our s3 bucket to download data from quilt

Issue - State: closed - Opened by donovanr about 5 years ago

#54 - Tests/run ci on GitHub

Pull Request - State: closed - Opened by donovanr about 5 years ago

#53 - add instructions for dev install

Issue - State: closed - Opened by donovanr about 5 years ago

#52 - switch over to real pytset code

Issue - State: closed - Opened by donovanr about 5 years ago

#51 - data download -> readme + simpler bin script

Pull Request - State: closed - Opened by donovanr about 5 years ago - 1 comment

#50 - update readme to reference data in quilt

Issue - State: closed - Opened by donovanr about 5 years ago

#49 - update processing code to use data in quilt

Issue - State: closed - Opened by donovanr about 5 years ago

#48 - Data/add test data to quilt

Pull Request - State: closed - Opened by donovanr about 5 years ago

#47 - add 3d raw data to quilt

Issue - State: open - Opened by donovanr about 5 years ago
Labels: data release

#46 - add 2d raw data to quilt

Issue - State: closed - Opened by donovanr about 5 years ago

#45 - add 2d seg data to quilt

Issue - State: closed - Opened by donovanr about 5 years ago

#44 - test install and run on linux and mac

Issue - State: closed - Opened by donovanr about 5 years ago

#43 - add workflow files for builds / badges

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment

#42 - Reorg/cookiecutter init

Pull Request - State: closed - Opened by donovanr about 5 years ago

#41 - reorg into more trad python package

Pull Request - State: closed - Opened by donovanr about 5 years ago

#40 - move to cookie cutter template

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment
Labels: enhancement

#39 - use CellProfiler via python api

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment
Labels: enhancement

#38 - organize python code and cell profiler code together somehow

Issue - State: closed - Opened by donovanr about 5 years ago - 3 comments

#37 - add instructions for running code

Pull Request - State: closed - Opened by donovanr about 5 years ago

#36 - Bugfix/tiff output

Pull Request - State: closed - Opened by donovanr about 5 years ago

#35 - change format() class to fstrings

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#34 - continue channel dict move

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment

#33 - fix aicsimagio 3.0.1 bug, refactor kwarg handling

Pull Request - State: closed - Opened by donovanr about 5 years ago - 1 comment

#32 - aicsimageio v3.0.1 reads tiff in with channels as z dimension

Issue - State: closed - Opened by donovanr about 5 years ago - 2 comments
Labels: bug, help wanted

#31 - output tiff stacks rather than sets of single channel images

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment
Labels: bug, data

#30 - os.path -> pathlib + early exit for file not found

Pull Request - State: closed - Opened by donovanr about 5 years ago

#29 - update to scikit-image 0.16 when pip installable

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#28 - run crashes when file not found

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug, data

#27 - threadpool map parallelization of main loop

Pull Request - State: closed - Opened by donovanr about 5 years ago

#26 - parallelize loop over fields

Issue - State: closed - Opened by donovanr about 5 years ago - 2 comments
Labels: enhancement

#25 - parallelize cell_worker

Issue - State: closed - Opened by donovanr about 5 years ago - 3 comments
Labels: enhancement

#24 - rm index cols

Pull Request - State: closed - Opened by donovanr about 5 years ago

#23 - Data/input manifest

Pull Request - State: closed - Opened by donovanr about 5 years ago

#22 - add manifest of input raw images

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#21 - Doc/dev instructions

Pull Request - State: closed - Opened by donovanr about 5 years ago

#20 - add test for image normalization

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#19 - add dev / contrib setup instructions

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment
Labels: documentation

#18 - Do imagej auto contrast math in float64

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement, wontfix, numerical

#17 - Convert from os.path to pathlib

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement, good first issue

#16 - better case handling in stretch_utils.py

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#15 - Function refactor

Pull Request - State: closed - Opened by donovanr about 5 years ago - 2 comments
Labels: bug, enhancement

#14 - add option for switching auto contrast function

Issue - State: closed - Opened by donovanr about 5 years ago

#13 - add logging for settings used and files processed

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#12 - fix up stretch script to run using fire

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#11 - don't stretch brightfield the same as fluorescent channels

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#10 - script /functions for normalizing image fields pre segmentation

Issue - State: closed - Opened by donovanr about 5 years ago

#9 - add bash script to run cellprofiler on list of input files

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#8 - text-ish version of cellprofilers workflow to generate features from image data + segmentations

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#7 - add manifest of the locations of original image data + segmentations

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: bug

#6 - clean up structure annotations

Issue - State: closed - Opened by donovanr about 5 years ago - 1 comment
Labels: bug

#5 - added struct csv files and edited readme

Pull Request - State: closed - Opened by donovanr about 5 years ago

#4 - Stretch cleanup

Pull Request - State: closed - Opened by donovanr about 5 years ago - 1 comment

#3 - add simple normalization function

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#2 - refactor python code into run script and function files

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

#1 - clean up and comment image stretching code

Issue - State: closed - Opened by donovanr about 5 years ago
Labels: enhancement

GitHub / allencellmodeling/fish_morphology_code issues and pull requests