CHANGELOG.md

Changelog

v0.11.3 (2026-03-27)

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Fixed bugs:

• fix: always decode BYTEARRAY fields as list[int], removing base64 encoding path #295 (tlambert03)

Merged pull requests:

• ci(pre-commit.ci): autoupdate #291 (pre-commit-ci[bot])
• ci(pre-commit.ci): autoupdate #287 (pre-commit-ci[bot])

v0.11.2 (2026-01-07)

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Fixed bugs:

• fix: fix regression in experiment loop parsing #289 (tlambert03)

v0.11.1 (2026-01-05)

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Documentation:

• docs: update docs and rename to_ome_zarr to write_ome_zarr #286 (tlambert03)

v0.11.0 (2026-01-05)

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Implemented enhancements:

• feat: include all unstructured meta in to_ome_zarr #285 (tlambert03)
• feat: Add export to ome-zarr #284 (tlambert03)
• feat: parse JOBS information #280 (tlambert03)

Fixed bugs:

• fix: use absolute path resolution for file handling in ND2Reader #269 (tlambert03)

Merged pull requests:

• ci(dependabot): bump actions/download-artifact from 6 to 7 #283 (dependabot[bot])
• ci(dependabot): bump actions/upload-artifact from 5 to 6 #282 (dependabot[bot])
• ci(dependabot): bump actions/cache from 4 to 5 #281 (dependabot[bot])
• chore: update samples #279 (tlambert03)
• ci(pre-commit.ci): autoupdate #277 (pre-commit-ci[bot])
• ci(dependabot): bump actions/checkout from 5 to 6 #276 (dependabot[bot])
• ci(pre-commit.ci): autoupdate #273 (pre-commit-ci[bot])
• ci(dependabot): bump actions/upload-artifact from 4 to 5 #272 (dependabot[bot])
• ci(dependabot): bump actions/download-artifact from 5 to 6 #271 (dependabot[bot])
• ci(dependabot): bump astral-sh/setup-uv from 6 to 7 #270 (dependabot[bot])

v0.10.4 (2025-10-14)

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Implemented enhancements:

• feat: Export XYPosLoop position names in OME metadata. #265 (anntzer)

Fixed bugs:

• fix: Use periodDiff.avg instead of periodMs for xarray timing metadata. #264 (anntzer)

Merged pull requests:

• chore: update repo to uv style #266 (tlambert03)
• ci(dependabot): bump CodSpeedHQ/action from 3 to 4 #262 (dependabot[bot])
• ci(dependabot): bump actions/setup-python from 5 to 6 #261 (dependabot[bot])
• ci(dependabot): bump actions/checkout from 4 to 5 #260 (dependabot[bot])
• ci(pre-commit.ci): autoupdate #257 (pre-commit-ci[bot])

v0.10.3 (2025-04-16)

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Fixed bugs:

• fix: update cached chunk key structure and add cache invariance test #256 (tlambert03)

Documentation:

• docs: update API documentation #252 (tlambert03)

Merged pull requests:

• ci(pre-commit.ci): autoupdate #254 (pre-commit-ci[bot])
• build: drop python 3.8 #253 (tlambert03)
• ci(pre-commit.ci): autoupdate #251 (pre-commit-ci[bot])
• build: test py3.13 #241 (tlambert03)

v0.10.2 (2025-02-28)

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Fixed bugs:

• fix: fix size overflow #248 (tlambert03)
• fix: fix for dask 2024.8 #240 (tlambert03)
• fix: tqdm -> tqdm.auto, for notebook users #233 (georgeoshardo)

Tests & CI:

• test: drop aicsimageio test #227 (tlambert03)

Merged pull requests:

• ci(dependabot): bump codecov/codecov-action from 4 to 5 #245 (dependabot[bot])
• ci(pre-commit.ci): autoupdate #243 (pre-commit-ci[bot])
• ci(pre-commit.ci): autoupdate #236 (pre-commit-ci[bot])
• ci(dependabot): bump CodSpeedHQ/action from 2 to 3 #235 (dependabot[bot])
• ci(pre-commit.ci): autoupdate #234 (pre-commit-ci[bot])
• ci(pre-commit.ci): autoupdate #229 (pre-commit-ci[bot])

v0.10.1 (2024-04-22)

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Merged pull requests:

• fix: Fix datetime extraction #226 (tlambert03)
• ci(pre-commit.ci): autoupdate #220 (pre-commit-ci[bot])

v0.10.0 (2024-03-17)

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Implemented enhancements:

• feat: better color object #218 (tlambert03)
• feat: add to_ome_tif method #217 (fdrgsp)
• feat: add write_tiff export to OME-TIFF, include full metadata as StructuredAnnotation #216 (tlambert03)

Merged pull requests:

• ci(dependabot): bump softprops/action-gh-release from 1 to 2 #214 (dependabot[bot])
• chore: use ruff format, add typos #213 (tlambert03)

v0.9.0 (2024-02-22)

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Fixed bugs:

• fix: hacky fix for files with subloops #193 (tlambert03)

Tests & CI:

• tests: lxml on >=39 #200 (tlambert03)

Merged pull requests:

• chore: remove old deprecations #209 (tlambert03)
• build: drop python 3.7 #208 (tlambert03)
• ci(dependabot): bump codecov/codecov-action from 3 to 4 #205 (dependabot[bot])
• ci(dependabot): bump actions/cache from 3 to 4 #204 (dependabot[bot])
• ci(dependabot): bump actions/setup-python from 4 to 5 #198 (dependabot[bot])
• ci(dependabot): bump CodSpeedHQ/action from 1 to 2 #196 (dependabot[bot])
• refactor: simplify strides #194 (tlambert03)

v0.8.1 (2023-11-15)

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Fixed bugs:

• fix: access more frames via direct read_frame() method #192 (tlambert03)

Merged pull requests:

• docs: fix emoji links in docs build #191 (tlambert03)
• test: fix aicsimageio test #188 (tlambert03)
• chore: minor ROI updates #186 (tlambert03)

v0.8.0 (2023-10-10)

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Implemented enhancements:

• feat: add read_frame and loop_indices to public api #181 (tlambert03)

Fixed bugs:

• fix: fix extraction of xy points in extruded shapes #183 (tlambert03)

v0.7.4 (2023-09-29)

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Implemented enhancements:

• refactor: make binarylayer a dataclass #178 (tlambert03)

v0.7.3 (2023-09-28)

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Fixed bugs:

• fix: fix key error in binary data #176 (tlambert03)

Merged pull requests:

• ci(dependabot): bump actions/checkout from 3 to 4 #171 (dependabot[bot])
• build: support python 3.12 #168 (tlambert03)

v0.7.2 (2023-08-31)

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Implemented enhancements:

• fix: fix Z series values in events() output, and add individual axis indices #167 (tlambert03)

v0.7.1 (2023-07-15)

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Implemented enhancements:

• feat: accept file handles as well as paths #161 (tlambert03)
• feat: decode compressed lite variant, and read string type tags #159 (tlambert03)

Fixed bugs:

• fix: fix binary reshaping #164 (tlambert03)

Tests & CI:

• test: bump coverage #163 (tlambert03)

Documentation:

• docs: update readme #162 (tlambert03)

Merged pull requests:

• refactor: use common base class for legacy and modern reader, move logic from nd2file #160 (tlambert03)

v0.7.0 (2023-07-05)

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Implemented enhancements:

• feat: add ome_metadata output to ome-types #153 (tlambert03)
• feat: add row filtering to nd2.index, as well as binary/roi data #151 (tlambert03)

Fixed bugs:

• fix: fix extra kwargs to roi info #158 (tlambert03)
• fix: fix frame_metadata and various metadata typing #155 (tlambert03)
• fix: improve roi parsing for some files #150 (tlambert03)

Tests & CI:

• ci: add codspeed benchmarks #152 (tlambert03)

Documentation:

• docs: adding docs #149 (tlambert03)

v0.6.1 (2023-06-24)

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Implemented enhancements:

• feat: support files with custom experiment loops #148 (tlambert03)
• feat: add python -m nd2.index cli #147 (tlambert03)
• feat: big update to events parsing. add .events method, deprecate recorded_date #144 (tlambert03)

Merged pull requests:

• build: remove wurlitzer from build #142 (tlambert03)

v0.6.0 (2023-06-15)

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Implemented enhancements:

• feat: Remove sdk, use all python #135 (tlambert03)

Fixed bugs:

• fix: Make 'periodDiff' optional in TimeLoopParams construction #131 (SeanDuHare)

Tests & CI:

• feat: add more typed dicts to parsing #139 (tlambert03)
• ci: enable Strict mypy typing #138 (tlambert03)
• test: update rescue test #137 (tlambert03)

Merged pull requests:

• refactor: cleaning up reader #141 (tlambert03)
• chore: adding nd2_describe script #136 (tlambert03)
• ci(dependabot): bump pypa/cibuildwheel from 2.12.1 to 2.12.3 #130 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.12.0 to 2.12.1 #128 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.11.3 to 2.12.0 #125 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.11.2 to 2.11.3 #120 (dependabot[bot])

v0.5.3 (2022-12-08)

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Merged pull requests:

• fix: catch exception on file open and release handle #117 (tlambert03)

v0.5.2 (2022-12-08)

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Fixed bugs:

• fix: close handles on object deletion #116 (tlambert03)

Merged pull requests:

• style: use ruff linter and update pre-commit #115 (tlambert03)

v0.5.1 (2022-11-01)

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Implemented enhancements:

• feat: Add ND2File.binary_data property - extract binary layers from file #108 (tlambert03)

Merged pull requests:

• ci(dependabot): bump pypa/cibuildwheel from 2.11.1 to 2.11.2 #109 (dependabot[bot])

v0.5.0 (2022-10-29)

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Implemented enhancements:

• feat: Extract recorded data #107 (tlambert03)
• feat: support python 3.11 #106 (tlambert03)

Merged pull requests:

• ci(dependabot): bump pypa/cibuildwheel from 2.10.2 to 2.11.1 #104 (dependabot[bot])

v0.4.6 (2022-10-08)

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Implemented enhancements:

• feat: add roi parsing #102 (tlambert03)

v0.4.5 (2022-10-06)

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Implemented enhancements:

• feat: offer full unstructured data #101 (tlambert03)

Fixed bugs:

• fix: fix rounding error in numpy pre-release #96 (tlambert03)

Merged pull requests:

• ci(dependabot): bump pypa/cibuildwheel from 2.10.1 to 2.10.2 #98 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.9.0 to 2.10.1 #97 (dependabot[bot])

v0.4.4 (2022-09-12)

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Fixed bugs:

• fix: fix image width with sdk reader #94 (tlambert03)

v0.4.3 (2022-09-11)

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Implemented enhancements:

• Add unstructured_metadata method, fix missing position names in experiment. #93 (tlambert03)

v0.4.2 (2022-09-10)

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Fixed bugs:

• fix: better fix for images with non-normal strides #92 (tlambert03)

v0.4.1 (2022-09-09)

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Fixed bugs:

• fix: Fix images where widthPx x Bytes is not the same as expected width Bytes #90 (tlambert03)

v0.4.0 (2022-08-19)

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Implemented enhancements:

• feat: Add native macosx-arm64 (M1) support #87 (tlambert03)

Merged pull requests:

• ci(dependabot): bump pypa/cibuildwheel from 2.8.1 to 2.9.0 #84 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.8.0 to 2.8.1 #81 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.7.0 to 2.8.0 #80 (dependabot[bot])

v0.3.0 (2022-06-25)

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Implemented enhancements:

• feat: add read_using_sdk parameter, default to True for compressed files #74 (tlambert03)

Documentation:

• docs: update readme #66 (tlambert03)

Merged pull requests:

• ci(dependabot): bump pypa/cibuildwheel from 2.6.1 to 2.7.0 #69 (dependabot[bot])
• ci(dependabot): bump pypa/cibuildwheel from 2.6.0 to 2.6.1 #68 (dependabot[bot])
• ci(dependabot): bump actions/setup-python from 3 to 4 #67 (dependabot[bot])

v0.2.5 (2022-06-06)

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Fixed bugs:

• fix: remove print statement #65 (tlambert03)
• fix: fix pre-test by using PyArray_SetBaseObject directly #64 (tlambert03)

Tests & CI:

• ci: use flake8-pyprojecttoml #63 (tlambert03)
• ci: create dependabot.yml #59 (tlambert03)

Merged pull requests:

• ci: update prefix on dependabot commit message #61 (tlambert03)
• ci(dependabot): Bump codecov/codecov-action from 2 to 3 #60 (dependabot[bot])
• ci: General repo update, move to pyproject.toml #58 (tlambert03)
• build: remove extra numpy from install_requires #57 (tlambert03)

v0.2.4 (2022-05-26)

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Fixed bugs:

• fix numpy 1.22.4 bug #55 (tlambert03)
• Fix frame offsets when validate_frames != True, add validate_frames param to imread #54 (tlambert03)

v0.2.3 (2022-05-18)

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Fixed bugs:

• Refactor fixup #51 (shenker)

v0.2.2 (2022-03-13)

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Implemented enhancements:

• Add utility to try to rescue frames from a corrupted nd2 file #44 (tlambert03)

Fixed bugs:

• Fix numpy pinning in wheels #46 (tlambert03)

v0.2.1 (2022-03-02)

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Merged pull requests:

• update SDK license #43 (tlambert03)

v0.2.0 (2022-02-20)

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Merged pull requests:

• add gh release action #42 (tlambert03)
• make 2 utils public #41 (tlambert03)
• Use resource-backed-dask-array, copy dask chunks by default #40 (tlambert03)
• [pre-commit.ci] pre-commit autoupdate #37 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #36 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #35 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #34 (pre-commit-ci[bot])
• [pre-commit.ci] pre-commit autoupdate #33 (pre-commit-ci[bot])

v0.1.6 (2021-11-12)

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v0.1.5-1 (2021-11-12)

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v0.1.5 (2021-11-12)

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Merged pull requests:

• Small update to ND2File.sizes, expose frame_metadata method #32 (tlambert03)
• Add check-manifest during deploy #31 (tlambert03)
• move sdk files into arch subfolders #29 (tlambert03)
• make test dataset easier to get #28 (tlambert03)
• Add pickle test #27 (tlambert03)
• Better dask wrapper that obeys NEP18 #26 (tlambert03)
• Add support for python 3.10 #23 (tlambert03)
• add Dask-proxy #22 (tlambert03)
• Include SDK, move to src layout #21 (tlambert03)
• Add __getstate__ and __setstate__ methods to allow pickling. Addresses #19 #20 (VolkerH)
• [pre-commit.ci] pre-commit autoupdate #13 (pre-commit-ci[bot])
• fix coverage #12 (tlambert03)

v0.1.4 (2021-10-10)

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Merged pull requests:

• allow position arg to asarray #11 (tlambert03)

v0.1.3 (2021-10-10)

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Merged pull requests:

• Fix-legacy, put more in base readers #10 (tlambert03)

v0.1.2 (2021-10-09)

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Merged pull requests:

• add copy param to to_dask to avoid segfaults from closed file #9 (tlambert03)

v0.1.1 (2021-10-07)

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Merged pull requests:

• optional squeeze param for xarray #8 (tlambert03)
• add test that readme executes #7 (tlambert03)

v0.1.0 (2021-10-07)

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Merged pull requests:

• readme updates #6 (tlambert03)
• general cleanup, full legacy support #5 (tlambert03)
• add support for legacy SDK #2 (tlambert03)

* This Changelog was automatically generated by github_changelog_generator