brainglobe/cellfinder-core issues and pull requests

#232 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago

#231 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 months ago

#230 - Update to Python 3.11

Issue - State: open - Opened by adamltyson about 1 year ago
Labels: enhancement

#229 - Update cell classification network

Issue - State: open - Opened by adamltyson about 1 year ago
Labels: enhancement

#228 - Update to py311 and remove cibuildwheel

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

#227 - Save models into e.g. `.brainglobe/cellfinder/models`

Issue - State: open - Opened by adamltyson about 1 year ago
Labels: enhancement

#226 - Prepare for retirement

Pull Request - State: closed - Opened by willGraham01 about 1 year ago

#225 - Raise a more informative error message with 2.5D data

Issue - State: open - Opened by adamltyson about 1 year ago
Labels: enhancement

#224 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#223 - Investigate parameter combinations causing cellfinder to stall

Issue - State: open - Opened by adamltyson about 1 year ago
Labels: bug

#222 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#221 - Try different keras backends

Issue - State: closed - Opened by adamltyson about 1 year ago - 1 comment
Labels: enhancement

#220 - Update to work with keras 3.0

Issue - State: closed - Opened by adamltyson about 1 year ago - 1 comment
Labels: enhancement

#219 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago

#218 - Cellfinder merge

Pull Request - State: closed - Opened by willGraham01 over 1 year ago - 10 comments

#217 - Set pre-commit autoupdate frequency to monthly

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

#216 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#215 - Remove `test/data/brain` directory

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

#214 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#213 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#212 - Update links

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

#211 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#210 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#209 - How are `prep_classification` and `prep_training` different?

Issue - State: open - Opened by sfmig over 1 year ago - 1 comment
Labels: question

#208 - Benchmarks in CI [Feature]

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

#207 - Add benchmarks for training [Feature]

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

#206 - Add benchmarks for the main function [Feature]

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

#205 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#204 - CI Check against `tensorflow` include guard

Pull Request - State: closed - Opened by willGraham01 over 1 year ago - 2 comments

#203 - [Feature] Add test to validate include guards

Issue - State: closed - Opened by willGraham01 over 1 year ago
Labels: enhancement

#202 - Fix cellfinder tests in CI

Issue - State: open - Opened by alessandrofelder over 1 year ago

#201 - Run cellfinder-napari tests in CI

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

#200 - possible fix for mac error

Pull Request - State: closed - Opened by alessandrofelder over 1 year ago - 2 comments

#199 - [BUG] MacOS pytest doesn't work out of the box

Issue - State: closed - Opened by alessandrofelder over 1 year ago - 3 comments
Labels: bug

#198 - ensure cellfinder-core can run on single cpu

Pull Request - State: closed - Opened by alessandrofelder over 1 year ago - 4 comments

#197 - Cellfinder core should run on just one cpu

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

#196 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#195 - MANIFEST only necessary files for package install

Pull Request - State: closed - Opened by willGraham01 over 1 year ago - 1 comment

#194 - [BUG] `mypy` needs stub file for cellfinder-core

Issue - State: open - Opened by willGraham01 over 1 year ago
Labels: bug

#193 - exclude tests and benchmarks from distributed package

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

#192 - Update CHANGELOG with 0.5.0 changes

Pull Request - State: closed - Opened by willGraham01 over 1 year ago

#191 - Update README in light of possible noarch build

Pull Request - State: closed - Opened by willGraham01 over 1 year ago

#190 - Consider moving away from TensorFlow

Issue - State: open - Opened by adamltyson over 1 year ago - 2 comments
Labels: enhancement

#189 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#188 - Avoid hard-coding of `~/.cellfinder`

Issue - State: open - Opened by alessandrofelder over 1 year ago

#187 - Tensorflow requires manual install if going via `conda`

Pull Request - State: closed - Opened by willGraham01 over 1 year ago - 5 comments

#186 - Forbid import when `tensorflow` is not installed

Pull Request - State: closed - Opened by willGraham01 over 1 year ago

#185 - Tensorflow as optional dependency?

Pull Request - State: closed - Opened by willGraham01 over 1 year ago

#184 - asv benchmarks for imports and tools modules

Pull Request - State: closed - Opened by sfmig over 1 year ago - 2 comments

#183 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#182 - Update dependency (imlib -> brainglobe-utils)

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

#181 - Add typing to classification

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

#180 - Fix mypy type checking

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

#179 - [BUG] `conda install cellfinder-core==0.4.0` does not allow `pip` to read version correctly.

Issue - State: closed - Opened by willGraham01 over 1 year ago - 3 comments
Labels: bug

#178 - Un-pin tensorflow

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

#177 - Fix dynamic versioning

Pull Request - State: closed - Opened by willGraham01 over 1 year ago - 1 comment

#176 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#175 - Update links

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

#174 - Delete cell detection developer guide

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

#173 - Link to developer docs on the new website from the readme

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

#172 - Move cell_detection.md into developer docs

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

#171 - jp2 input format[Feature]

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

#170 - cell candidate speed issues

Issue - State: closed - Opened by adamltyson over 1 year ago - 17 comments
Labels: bug

#169 - Move test data to gin and fetch via `pooch`

Issue - State: open - Opened by alessandrofelder over 1 year ago

#168 - Add appropriate typing or refactor `get_cell_detector`

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

#167 - Structure splitting: Smoke test and refactor for numba

Pull Request - State: closed - Opened by alessandrofelder over 1 year ago - 5 comments

#166 - Test for cell splitting code

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

#165 - Use nopython mode for all jitting

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

#164 - Fix typo in error message

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

#163 - Deprecation warnings are raised in numba 0.59

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

#162 - Add numpy to typing deps

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

#161 - Force typing in detect sub-module

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

#160 - De-duplicate test dependency lists

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

#159 - More translation to `numba` needed in cell splitting code?

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

#158 - `split_cells` expects `Sequence[Point]` but receives `ndarray`, causes error

Issue - State: closed - Opened by adamltyson over 1 year ago - 6 comments
Labels: bug

#157 - Move any high-level docs from this repo to the central BG dev docs.

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

#156 - Update README.md

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

#155 - Remove cibuildwheel and build pure-Python wheel

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

#154 - Don't cast planes to uint64 in structure detection

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

#153 - Clip planes in-place

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

#152 - Use bool dtype for good tiles mask

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

#151 - Add high level overview of cell detection stages

Pull Request - State: closed - Opened by dstansby over 1 year ago - 5 comments

#150 - Reduce memory usage

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

#149 - Add tests for structure splitting code

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

#148 - Add docs to structure splitting code

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

#147 - Add typing to structure splitting code

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

#146 - Only check unique neighbour IDs

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

#145 - Numba error running on large datasets

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

#144 - Remove cibuildwheel

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

#143 - Start a changelog for next version

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

#142 - Use "plane" instead of "layer" in detection

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

#141 - Add testing on macOS arm

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

#140 - Investigate replacing custom connected-component labelling with 3rd party library

Issue - State: open - Opened by dstansby over 1 year ago - 3 comments
Labels: enhancement

#139 - Limit number of 2D filtering outputs stored in memory

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

#138 - Add docs to structure detection

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

#137 - Clean structure detection

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

#136 - Standardise on one of "plane" or "layer"

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

#135 - Add some docs on how bright points are marked

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

#134 - [Feature] Warn or error if ball_z or ball_xy_size is less than voxel sizes

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

#133 - Type ball filter

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

GitHub / brainglobe/cellfinder-core issues and pull requests