vanvalenlab/deepcell-spots issues and pull requests

#90 - Bump version to 0.4.2

Pull Request - State: closed - Opened by elaubsch 8 months ago
Labels: chore

#89 - Update CI action versions.

Pull Request - State: closed - Opened by rossbar 10 months ago

#88 - Prepare for 0.4.1 release

Pull Request - State: closed - Opened by rossbar 10 months ago
Labels: chore

#87 - Updating code, removing deprecated patterns, general future compat

Pull Request - State: closed - Opened by rossbar 10 months ago

#86 - Fix building/deployment of Python package and docker image

Pull Request - State: closed - Opened by rossbar 10 months ago
Labels: chore

#85 - Update model name for SpotDetection-8

Pull Request - State: closed - Opened by elaubsch 10 months ago
Labels: fix

#84 - Update spot detection model to SpotDetection-8

Pull Request - State: closed - Opened by elaubsch 10 months ago
Labels: enhancement

#83 - Remove deprecated parameter from training script

Pull Request - State: closed - Opened by elaubsch 10 months ago
Labels: fix

#82 - Improve print statements for Polaris application

Pull Request - State: closed - Opened by elaubsch 12 months ago

#81 - Move masking function outside of Polaris application

Pull Request - State: closed - Opened by elaubsch 12 months ago
Labels: enhancement

#80 - Is it possible to extract spots in 3D images?

Issue - State: closed - Opened by neugun about 1 year ago - 1 comment

#79 - CI: Add workflow for testing container.

Pull Request - State: closed - Opened by rossbar about 1 year ago - 2 comments
Labels: chore

#78 - Update requirements

Pull Request - State: closed - Opened by rossbar about 1 year ago - 1 comment

#77 - Update DEEPCELL_VERSION in README

Pull Request - State: closed - Opened by elaubsch about 1 year ago
Labels: documentation, chore

#76 - Update example data download in nbs

Pull Request - State: closed - Opened by elaubsch about 1 year ago
Labels: chore

#75 - Add authentication to SpotDetection

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

#74 - Fix bug for multi-batch predictions with pixel-wise decoding

Pull Request - State: closed - Opened by elaubsch about 1 year ago
Labels: fix

#73 - Pixel-wise decoding for Polaris

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

#72 - Update example notebooks

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#71 - Add tests for results visualization functions

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#70 - Add function for barcode assignment to cells for optical pooled screens

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

#69 - Update decoding probability threshold

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#68 - Add skip round functionality to spot prediction in Polaris

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

#67 - Add get_cell_counts to results utils

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

#66 - Remove one data validation check from Polaris

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: fix

#65 - Add gene scatter plot to results utils

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

#64 - Add arguments to expression_correlation

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

#63 - Add results_utils functions

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

#62 - Bug fix for output_to_df for mixed rescue

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: fix

#61 - Replace thres_prob with pred_prob_thresh

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#60 - Create utils module in deepcell_spots

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#59 - Update application docstrings

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: fix, chore

#58 - Standardize application classes

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#57 - Add masking of bright background objects

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

#56 - Add mixed barcode rescue to SpotDecoding

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

#55 - Fix bug in Polaris Bernoulli predictions

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: fix

#54 - Add Bernoulli to decoding distributions

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

#53 - Validate codebook in SpotDecoding

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

#53 - Validate codebook in SpotDecoding

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

#52 - Rescue spots during spot decoding

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

#51 - Fix bug in multi-batch E-step for spot decoding

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: fix

#50 - Update README and example notebooks

Pull Request - State: closed - Opened by elaubsch over 1 year ago
Labels: chore

#49 - Add mixture of Gaussians to decoding distributions

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

#48 - Update copyright to 2023

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

#47 - Bump default action versions.

Pull Request - State: closed - Opened by rossbar over 1 year ago - 1 comment
Labels: chore

#46 - Tighten CI configuration

Pull Request - State: closed - Opened by rossbar almost 2 years ago - 1 comment

#45 - Update docstring for decoding functions

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: chore

#44 - Maintenance to clip and threshold application arguments

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: chore

#43 - Update pinned deepcell version to 0.12.4 in Dockerfile

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: chore

#42 - Allow blank images in training data set

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: fix

#41 - Add command to install deepcell spots in docker container

Pull Request - State: closed - Opened by msschwartz21 almost 2 years ago
Labels: fix

#40 - Update pytest and rm pytest-pep8 dependency.

Pull Request - State: closed - Opened by rossbar almost 2 years ago - 1 comment
Labels: fix

#39 - Clips probabilities before decoding

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: fix

#38 - Bump scikit-learn to 1.0

Issue - State: open - Opened by rossbar almost 2 years ago

#37 - Maintenance of DotNetLosses scripts

Pull Request - State: closed - Opened by elaubsch almost 2 years ago
Labels: chore

#36 - Add decoding functionality to Polaris

Pull Request - State: closed - Opened by xuefei-wang almost 2 years ago - 3 comments
Labels: enhancement

#35 - Add back deleted function and bug fix

Pull Request - State: closed - Opened by elaubsch about 2 years ago

#34 - Update Python version in README

Pull Request - State: closed - Opened by elaubsch about 2 years ago
Labels: chore

#33 - Bump PyPI version to 0.3.2

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: chore

#32 - Add unit tests for model and loss scripts

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: chore

#31 - Add Read the Docs documentation

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

#30 - Update model version

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: chore

#29 - Bug fix for model output format

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: fix

#28 - Update image alignment functions and tests

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: fix

#27 - Update supported Python versions

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: fix

#26 - Update supported Python versions

Pull Request - State: closed - Opened by elaubsch over 2 years ago

#25 - Upgrade to TensorFlow 2.8

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: enhancement, dependencies

#24 - Refactor EM functions to use DataFrames

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

#23 - Update PyPI version

Pull Request - State: closed - Opened by elaubsch over 2 years ago
Labels: chore

#22 - Change model output to dictionary

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

#21 - Remove postcode import from setup.py

Pull Request - State: closed - Opened by elaubsch over 2 years ago

#20 - Remove PoSTcode import

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: chore

#19 - Remove PoSTcode import

Pull Request - State: closed - Opened by elaubsch almost 3 years ago

#18 - Update example notebook for singleplex app

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

#17 - Add Mesmer segmentation to Polaris app

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

#16 - return features of spots and include intensity thresholds

Issue - State: closed - Opened by klcolon almost 3 years ago

#15 - Singleplex Polaris app

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: chore

#13 - Rename SpotDetection application to Polaris

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

#12 - Update README badges and other minor touchups for first release.

Pull Request - State: closed - Opened by willgraf almost 3 years ago
Labels: chore

#11 - Remove unused code and files

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: chore

#10 - `rn_classification_head` uses unimported code.

Issue - State: closed - Opened by willgraf almost 3 years ago
Labels: bug

#9 - Update Dockerfile, fix imports, and lint docstrings.

Pull Request - State: closed - Opened by willgraf almost 3 years ago
Labels: documentation, dependencies, fix

#8 - Repo management

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

#7 - Repo management

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: chore

#6 - Model dev

Pull Request - State: closed - Opened by elaubsch almost 3 years ago
Labels: enhancement

#5 - Remove `opencv-python` from `requirements.txt`

Pull Request - State: closed - Opened by willgraf about 3 years ago - 1 comment
Labels: fix

#4 - Remove or upgrade `opencv-python`

Issue - State: closed - Opened by willgraf about 3 years ago
Labels: dependencies

#3 - Model dev

Pull Request - State: closed - Opened by elaubsch over 3 years ago
Labels: enhancement

#2 - Update Dockerfile

Pull Request - State: closed - Opened by elaubsch over 3 years ago
Labels: enhancement

#1 - Update to TensorFlow 2.4.1 and deepcell 0.9.0

Issue - State: closed - Opened by willgraf over 3 years ago

GitHub / vanvalenlab/deepcell-spots issues and pull requests