tlambert03/nd2 issues and pull requests

#241 - build: test py3.13

Pull Request - State: open - Opened by tlambert03 21 days ago - 2 comments

#240 - fix: fix for dask 2024.8

Pull Request - State: closed - Opened by tlambert03 21 days ago - 2 comments

#239 - Warning about garbage collection, even with "with", with dask 2024.8

Issue - State: closed - Opened by cmalinmayor 28 days ago - 3 comments

#238 - Export position names to OME metadata

Issue - State: open - Opened by anntzer about 1 month ago

#237 - [test-bot] pip install --pre is failing

Issue - State: open - Opened by github-actions[bot] about 2 months ago
Labels: bug

#236 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 months ago - 2 comments

#235 - ci(dependabot): bump CodSpeedHQ/action from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#234 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 3 months ago - 2 comments

#233 - fix: tqdm -> tqdm.auto, for notebook users

Pull Request - State: closed - Opened by georgeoshardo 3 months ago - 2 comments

#232 - How to convert ROI coordinates from relative to pixels

Issue - State: open - Opened by Kees-van-der-Oord-Nikon 3 months ago - 3 comments

#231 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 4 months ago
Labels: bug

#230 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 4 months ago
Labels: bug

#229 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 5 months ago - 2 comments

#228 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 5 months ago
Labels: bug

#227 - test: drop aicsimageio test

Pull Request - State: closed - Opened by tlambert03 5 months ago - 2 comments
Labels: tests

#226 - fix: Fix datetime extraction

Pull Request - State: closed - Opened by tlambert03 5 months ago - 2 comments

#225 - Issue with saving nd2 to ome-tiff

Issue - State: closed - Opened by BornKrefeld 6 months ago - 1 comment

#224 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 6 months ago - 1 comment
Labels: bug

#223 - Error with saving nd2 file as ome-tiff file

Issue - State: closed - Opened by BornKrefeld 6 months ago - 2 comments

#222 - Save a single channel in nd2 to numpy

Issue - State: closed - Opened by BornKrefeld 6 months ago - 1 comment

#221 - Update _ome.py

Pull Request - State: closed - Opened by rysk-t 6 months ago - 5 comments

#220 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago - 2 comments

#219 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 6 months ago
Labels: bug

#218 - feat: better color object

Pull Request - State: closed - Opened by tlambert03 7 months ago - 2 comments
Labels: enhancement

#217 - feat: add to_ome_tif method

Pull Request - State: closed - Opened by fdrgsp 7 months ago - 5 comments
Labels: enhancement

#216 - feat: add `write_tiff` export to OME-TIFF, include full metadata as StructuredAnnotation

Pull Request - State: closed - Opened by tlambert03 7 months ago - 8 comments
Labels: enhancement

#215 - feat: export to OME-TIFF, include full metadata as StructuredAnnotation

Issue - State: closed - Opened by tlambert03 7 months ago

#214 - ci(dependabot): bump softprops/action-gh-release from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: dependencies

#213 - chore: use ruff format, add typos

Pull Request - State: closed - Opened by tlambert03 7 months ago - 2 comments

#212 - todo: improve handling of files with subloops

Issue - State: open - Opened by tlambert03 7 months ago

#211 - bioio-nd2 failing to load from large file

Issue - State: closed - Opened by toloudis 8 months ago - 1 comment

#210 - ci: try reusable workflow

Pull Request - State: closed - Opened by tlambert03 8 months ago - 1 comment

#209 - chore: remove old deprecations

Pull Request - State: closed - Opened by tlambert03 8 months ago - 2 comments

#208 - build: drop python 3.7

Pull Request - State: closed - Opened by tlambert03 8 months ago - 2 comments
Labels: dependencies

#207 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 8 months ago
Labels: bug

#206 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 2 comments
Labels: hide

#205 - ci(dependabot): bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#203 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] 9 months ago
Labels: bug

#201 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago - 2 comments
Labels: hide

#200 - tests: lxml on >=39

Pull Request - State: closed - Opened by tlambert03 9 months ago - 2 comments
Labels: tests

#197 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 2 comments
Labels: hide

#193 - fix: hacky fix for files with subloops

Pull Request - State: closed - Opened by tlambert03 11 months ago - 4 comments
Labels: bug

#190 - Missing axis

Issue - State: closed - Opened by aaristov 11 months ago - 10 comments

#184 - todo: turn color integers into tuples (or something meaningful)

Issue - State: closed - Opened by tlambert03 12 months ago

#165 - ci(pre-commit.ci): autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] about 1 year ago - 2 comments

#164 - fix: fix binary reshaping

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: bug

#163 - test: bump coverage

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 1 comment
Labels: tests

#162 - docs: update readme

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: documentation

#161 - feat: accept file handles as well as paths

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: enhancement

#160 - refactor: use common base class for legacy and modern reader, move logic from nd2file

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: refactor

#159 - feat: decode compressed lite variant, and read string type tags

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: enhancement

#158 - fix: fix extra kwargs to roi info

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 1 comment
Labels: bug

#157 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] about 1 year ago
Labels: bug

#156 - ci: test on py3.12

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 3 comments

#155 - fix: fix frame_metadata and various metadata typing

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: bug

#154 - ci(pre-commit.ci): autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 2 comments
Labels: hide

#153 - feat: add ome_metadata output to ome-types

Pull Request - State: closed - Opened by tlambert03 about 1 year ago - 2 comments
Labels: enhancement

#152 - ci: add codspeed benchmarks

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 2 comments
Labels: tests

#151 - feat: add row filtering to nd2.index, as well as binary/roi data

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: enhancement

#150 - fix: improve roi parsing for some files

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: bug

#149 - docs: adding docs

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: documentation

#148 - feat: support files with custom experiment loops

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: enhancement

#147 - feat: add `python -m nd2.index` cli

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: enhancement

#146 - ci: try dropbox

Pull Request - State: closed - Opened by tlambert03 over 1 year ago

#145 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: bug

#144 - feat: big update to events parsing. add .events method, deprecate recorded_date

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: enhancement

#143 - refactor: possibly move binary parse

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 2 comments

#142 - build: remove wurlitzer from build

Pull Request - State: closed - Opened by tlambert03 over 1 year ago

#141 - refactor: cleaning up reader

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: refactor

#140 - [Task] Add benchmarks

Issue - State: closed - Opened by tlambert03 over 1 year ago - 1 comment

#139 - feat: add more typed dicts to parsing

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: tests

#138 - ci: enable Strict mypy typing

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 1 comment
Labels: tests

#137 - test: update rescue test

Pull Request - State: closed - Opened by tlambert03 over 1 year ago
Labels: tests

#136 - chore: adding nd2_describe script

Pull Request - State: closed - Opened by tlambert03 over 1 year ago

#135 - feat: Remove sdk, use all python

Pull Request - State: closed - Opened by tlambert03 over 1 year ago - 3 comments
Labels: enhancement

#134 - ci(dependabot): bump pypa/cibuildwheel from 2.12.3 to 2.13.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#133 - ci(pre-commit.ci): autoupdate

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

#132 - ci(dependabot): bump pypa/cibuildwheel from 2.12.3 to 2.13.0

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

#131 - fix: Make 'periodDiff' optional in TimeLoopParams construction

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 6 comments
Labels: bug

#130 - ci(dependabot): bump pypa/cibuildwheel from 2.12.1 to 2.12.3

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

#129 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] over 1 year ago
Labels: bug

#128 - ci(dependabot): bump pypa/cibuildwheel from 2.12.0 to 2.12.1

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

#127 - ci(pre-commit.ci): autoupdate

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

#126 - Package not found on conda-forge channels

Issue - State: closed - Opened by metalmicrobe over 1 year ago - 4 comments

#125 - ci(dependabot): bump pypa/cibuildwheel from 2.11.3 to 2.12.0

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

#124 - ci(pre-commit.ci): autoupdate

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

#123 - ci(dependabot): bump pypa/cibuildwheel from 2.11.3 to 2.11.4

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#122 - feat: [wip] native implementation of SDK

Pull Request - State: closed - Opened by tlambert03 almost 2 years ago

#121 - Difference between NETimeLoop and TimeLoop?

Issue - State: open - Opened by gatoniel almost 2 years ago - 6 comments

#120 - ci(dependabot): bump pypa/cibuildwheel from 2.11.2 to 2.11.3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#119 - liblimfile.so: cannot open shared object file on CentOS

Issue - State: closed - Opened by joshua-gould almost 2 years ago - 3 comments

#118 - bug: Lim_FileGetAttributes failing in certain linux environments

Issue - State: closed - Opened by tlambert03 almost 2 years ago - 4 comments

#117 - fix: catch exception on file open and release handle

Pull Request - State: closed - Opened by tlambert03 almost 2 years ago - 6 comments

#116 - fix: close handles on object deletion

Pull Request - State: closed - Opened by tlambert03 almost 2 years ago
Labels: bug

#115 - style: use ruff linter and update pre-commit

Pull Request - State: closed - Opened by tlambert03 almost 2 years ago

#114 - File handle left open when an nd2 file fails to read

Issue - State: closed - Opened by manthey almost 2 years ago - 18 comments

#113 - ci: [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago

#112 - ci: [pre-commit.ci] autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago
Labels: hide

#111 - [test-bot] pip install --pre is failing

Issue - State: closed - Opened by github-actions[bot] almost 2 years ago
Labels: bug

#110 - please pull from main... the download script was recently updated:

Issue - State: closed - Opened by winston1716 almost 2 years ago - 5 comments

GitHub / tlambert03/nd2 issues and pull requests