vanvalenlab/caliban-toolbox issues and pull requests

#123 - Migrate CI/CD from TravisCI to GitHub Actions

Pull Request - State: closed - Opened by willgraf about 4 years ago

#122 - crop_multichannel_data fails when crop_size is None

Issue - State: open - Opened by geneva-miller over 4 years ago - 1 comment
Labels: bug

#121 - Add option to split by number of images

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#120 - Adding batch-size to dataset_splitter

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#119 - Reference to undefined variable in example notebook

Issue - State: open - Opened by jowch over 4 years ago - 2 comments

#118 - Balanced datasets

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#117 - DatasetSplitter

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 2 comments

#116 - Add label QC to pipeline

Issue - State: open - Opened by ngreenwald over 4 years ago

#115 - DatasetBuilder and DatasetBenchmarker

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 6 comments

#114 - Anolytics pipeline

Pull Request - State: open - Opened by ngreenwald over 4 years ago

#113 - resize individual images within NPZ

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 1 comment

#112 - update image adjustment widgets

Issue - State: open - Opened by geneva-miller over 4 years ago

#111 - add support for multiple labels

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 3 comments

#110 - streamline postprocessing workflow

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#109 - Update example notebook

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#108 - Save compressed NPZs

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 6 comments

#107 - typo in notebook leads to incorrect npzs saved

Issue - State: closed - Opened by geneva-miller over 4 years ago

#106 - compute_crop_indices returns values as np.float64

Issue - State: closed - Opened by geneva-miller over 4 years ago
Labels: bug

#105 - Reduce default file/image sizes

Issue - State: open - Opened by ngreenwald over 4 years ago

#104 - Mock figure8 and aws functions for testing

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 4 comments

#103 - aws_functions bug

Issue - State: closed - Opened by geneva-miller over 4 years ago - 2 comments
Labels: bug

#102 - Paramterize input and output buckets

Issue - State: open - Opened by willgraf over 4 years ago
Labels: enhancement

#101 - AWS uploaded files have public-read ACL

Issue - State: open - Opened by willgraf over 4 years ago - 1 comment

#100 - Post-processing for labels

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 2 comments
Labels: wip

#99 - Create NPZ file for training

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 3 comments
Labels: wip

#98 - Catch missing files

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 1 comment

#97 - Validate inputs for cropping

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#96 - Set job name

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 4 comments

#95 - gridlines overlay doesn't work for non-square images

Issue - State: open - Opened by ngreenwald over 4 years ago
Labels: bug

#94 - Error checking in data loader

Issue - State: open - Opened by epao111 over 4 years ago

#93 - Validate URLs for F8 upload

Issue - State: open - Opened by ngreenwald over 4 years ago

#92 - Aws helper functions

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#91 - Specify number of crops

Pull Request - State: closed - Opened by ngreenwald over 4 years ago

#90 - allow multiple npz key names

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 3 comments

#89 - Update README.md

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 4 comments

#88 - update example data

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 4 comments

#87 - Feature requests for data loader

Issue - State: open - Opened by ngreenwald over 4 years ago - 1 comment

#86 - Patch data loader for single-frame ("Static") 2D data

Pull Request - State: closed - Opened by ngreenwald over 4 years ago - 1 comment

#85 - Data loader

Pull Request - State: closed - Opened by MekWarrior over 4 years ago
Labels: enhancement

#84 - Multi-stage jobs

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 4 comments

#83 - Pipeline automation and metadata tracking

Pull Request - State: open - Opened by ngreenwald almost 5 years ago - 1 comment
Labels: wip

#82 - clarify crop indices calculations

Issue - State: closed - Opened by geneva-miller almost 5 years ago

#81 - Better organizing of utils functions

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 3 comments

#80 - Identify which additional code can be removed

Issue - State: open - Opened by ngreenwald almost 5 years ago

#79 - Fig 8 and AWS update

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 6 comments

#78 - Changelist for PR #4

Issue - State: open - Opened by ngreenwald almost 5 years ago

#77 - ModuleNotFoundError: No module named 'caliban_toolbox.utils.io_utils'

Issue - State: closed - Opened by epao111 almost 5 years ago - 1 comment

#76 - Figure8-related scripts need name change after Apr 16

Issue - State: open - Opened by geneva-miller almost 5 years ago

#75 - optional flags not getting passed to CSV

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: bug

#74 - Improve test coverage

Issue - State: open - Opened by ngreenwald almost 5 years ago

#73 - Code improvements

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 2 comments

#72 - Changelist for PR #3

Issue - State: closed - Opened by ngreenwald almost 5 years ago

#71 - Update README!

Issue - State: open - Opened by willgraf almost 5 years ago
Labels: enhancement, not urgent

#70 - Toolbox refactor

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 2 comments

#69 - Changelist for PR #2

Issue - State: closed - Opened by ngreenwald almost 5 years ago

#68 - add support for multiple label dimensions

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#67 - How to deal with distinct save_versions from caliban?

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 4 comments
Labels: help wanted

#66 - Master todo-list for integrating NPZ branch into master

Issue - State: closed - Opened by ngreenwald almost 5 years ago

#65 - make single log file and i/o functions for cropping and slicing

Issue - State: closed - Opened by ngreenwald almost 5 years ago

#64 - make crop size visualization interactive

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 1 comment
Labels: enhancement

#63 - refactor relabeling functions to work with in-memory arrays

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#62 - Generate overlapping z-stack slices

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 1 comment
Labels: enhancement

#61 - least confusing nomenclature

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 2 comments
Labels: help wanted

#60 - add separate crop dimension for x/y crops and t/z crops

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#60 - add separate crop dimension for x/y crops and t/z crops

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#59 - abstract out npz saving functionality from reshape functions

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#58 - refactor z-stack/t-stack splitting to work with in-memory arrays

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: enhancement

#57 - data ingest ontology

Issue - State: open - Opened by ngreenwald almost 5 years ago - 2 comments

#56 - consolidate image preprocessing into single notebook

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

#55 - switched to python3.6 docker

Pull Request - State: closed - Opened by ngreenwald almost 5 years ago - 3 comments

#54 - add optional contrast adjustment step to caliban upload pipeline

Issue - State: closed - Opened by geneva-miller almost 5 years ago
Labels: enhancement

#53 - reconstruct_image_stack fails with single column of crops

Issue - State: closed - Opened by ngreenwald almost 5 years ago
Labels: bug

#52 - reconstruct_image_stack overlap produces aliasing

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 1 comment

#51 - crop_image_stack doesn't distinguish between X and y data

Issue - State: closed - Opened by ngreenwald almost 5 years ago - 1 comment

#50 - Remove deploy stage from travis.yaml

Pull Request - State: closed - Opened by willgraf almost 5 years ago

#49 - refactor deepcell-toolbox references to caliban-toolbox.

Pull Request - State: closed - Opened by willgraf almost 5 years ago

#48 - What is this repository for?

Issue - State: closed - Opened by willgraf almost 5 years ago - 6 comments
Labels: question

#47 - preview color overlay/set defaults

Issue - State: open - Opened by ngreenwald about 5 years ago - 1 comment
Labels: enhancement

#46 - Unused code cleanup

Pull Request - State: closed - Opened by ngreenwald about 5 years ago - 4 comments

#45 - Remove tensorflow from dependencies

Issue - State: closed - Opened by willgraf about 5 years ago - 2 comments

#44 - Bump tensorflow from 1.11.0 to 1.15.2

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#43 - refactor pipeline away from npz folder structure

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

#42 - clean up / refactor preprocessing functions

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

#41 - visualize crops during creation

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

#40 - clean up test suite

Issue - State: closed - Opened by ngreenwald about 5 years ago - 6 comments

#39 - add test functions for basic i/o

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

#38 - add caliban-friendly chopper and stitcher

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

#37 - Bump tensorflow from 1.11.0 to 1.15.0

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#36 - Bump tensorflow from 1.11.0 to 1.12.2

Pull Request - State: closed - Opened by dependabot[bot] over 5 years ago - 1 comment
Labels: dependencies

#35 - Reuse data from figure8 npz creation for training data creation

Issue - State: closed - Opened by ngreenwald over 5 years ago

#34 - Add option for color overlays

Issue - State: closed - Opened by ngreenwald over 5 years ago

#33 - add cap function to image adjustment

Issue - State: closed - Opened by ngreenwald over 5 years ago - 1 comment

#32 - multichannel image overlay extension + refactor

Issue - State: closed - Opened by ngreenwald over 5 years ago

#31 - contrast slider adjustment timeout/lag

Issue - State: open - Opened by ngreenwald over 5 years ago

#30 - refactoring plan for multichannel data/caliban

Issue - State: closed - Opened by ngreenwald over 5 years ago

#29 - defined variables not used

Issue - State: closed - Opened by ngreenwald over 5 years ago

#28 - chopper is rescaling data

Issue - State: closed - Opened by ngreenwald over 5 years ago

#27 - add support to chop for uncorrected training data labels

Issue - State: closed - Opened by ngreenwald over 5 years ago - 3 comments

#26 - support for multi-channel data

Issue - State: closed - Opened by ngreenwald over 5 years ago

#25 - aws bucket region is hardcoded into aws_upload

Issue - State: open - Opened by geneva-miller over 5 years ago - 1 comment
Labels: bug

GitHub / vanvalenlab/caliban-toolbox issues and pull requests