Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
BrianWhitneyAI created a branch on AllenCellModeling/czi-to-ome-xslt
bugfix/parse-missing-wavelength - A repository of XSL transform sheets to map CZI metadata to OME.
BrianWhitneyAI pushed 1 commit to bugfix/cloud_metadata_update bioio-devs/bioio-ome-zarr
- lint 26fc81b
BrianWhitneyAI pushed 1 commit to bugfix/cloud_metadata_update bioio-devs/bioio-ome-zarr
- remove debug 84ee85e
BrianWhitneyAI created a comment on a pull request on bioio-devs/bioio-imageio
> I tried to run tests locally from instructions in contributing.md (`just build`). My goal was to compare the present `example.gif` to the aicsimageio `example.gif` since they appear to be in diff...
BrianWhitneyAI opened a pull request on bioio-devs/bioio-ome-zarr
bugfix/cloud_metadata_update
###Description A few of our zarr cloud tests are dependent on nucmorph production files, these files recently had updates to channel names and physical pixel size. As a result of this, our test...
BrianWhitneyAI created a branch on bioio-devs/bioio-ome-zarr
bugfix/cloud_metadata_update - A BioIO reader plugin for reading Zarr files in the OME format.
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-czi
hey @lukasjarzembowski thanks again for posting this. I think we missed the window that your test file was available. Would you mind posting a new link!
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-czi
Hey @leclercsimon74 thanks for submitting this! bioio-czi uses ome_types to parse metadata to ome_metadata. Comparing the laser metadata from your file ``` <ome:Laser ID="MTBLKM980LaserLine561" ...
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-czi
hey @ShanJiangEmugen Thanks again for your submission. I'm sorry the `.scenes` functionality isn't working for you. Do you have some test files that you could provide so I can look into this issue ...
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-czi
@manerotoni Thank you for submitting this! If I am understanding your issue correctly you want to try to access `.ome_metadata` for your czi, bioio-czi fails to interpret this metadata and raises a...
BrianWhitneyAI opened a pull request on bioio-devs/bioio-tiff-glob
bugfix/supported_files
The purpose of this PR is to distinguish glob files from tiff files in `_is_supported_image()` by calling the init directly. This Pr also adds some error handling to the init so that if the file fa...
BrianWhitneyAI created a branch on bioio-devs/bioio-tiff-glob
bugfix/supported_files - A BioIO reader plugin for reading Tiff Glob images.
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-tiff-glob
@TimMonko I think this is partially resolved. A recent check of the plugin feasibility has ``` {'bioio-tifffile': PluginSupport(supported=True, error=None), 'bioio-tiff-glob': PluginSupport(su...
BrianWhitneyAI created a comment on an issue on bioio-devs/bioio-lif
@toloudis Is there a reason the base reader does not have physical pixel size in _reset_self? If this is an issue that can easily show up on plugins and is not plugin-specific I feel like it should...
BrianWhitneyAI pushed 1 commit to bugfix/failing-tests bioio-devs/bioio-bioformats
- echo java 3eb1e3b
BrianWhitneyAI pushed 1 commit to bugfix/failing-tests bioio-devs/bioio-bioformats
- echo java 4eb34cb
BrianWhitneyAI opened a pull request on bioio-devs/bioio-bioformats
pin numpy
Pinning numpy to reflect pinning in bioio
BrianWhitneyAI created a branch on bioio-devs/bioio-bioformats
bugfix/failing-tests - A BioIO reader plugin for reading bioformats formatted images.
BrianWhitneyAI pushed 6 commits to main bioio-devs/bioio-bioformats
- Remove dask upper bound c10f577
- Use uv for installing deps 4d41fba
- Try uv system flag 39a57f4
- Merge branch 'main' into bug/remove-upper-dask-bound 5943476
- Merge branch 'main' into bug/remove-upper-dask-bound 7099bd3
- Merge pull request #15 from bioio-devs/bug/remove-upper-dask-bound bugfix/remove-dask-upper-bound c3f78ad
BrianWhitneyAI closed a pull request on bioio-devs/bioio-bioformats
bugfix/remove-dask-upper-bound
<!-- Thank you for submitting a pull request! ⚠️⚠️ Please do the following before submitting: ⚠️⚠️ - Read the CONTRIBUTING.md guide and make sure you've followed all the steps given. ...
BrianWhitneyAI pushed 3 commits to bug/remove-upper-dask-bound bioio-devs/bioio-bioformats
- ci(dependabot): bump codecov/codecov-action from 3 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/co... 32ac953
- Merge pull request #16 from bioio-devs/dependabot/github_actions/codecov/codecov-action-5 ci(dependabot): bump codec... 6e995e2
- Merge branch 'main' into bug/remove-upper-dask-bound 7099bd3
BrianWhitneyAI created a review comment on a pull request on bioio-devs/bioio-imageio
@evamaxfield @toloudis any thoughts here? np.stack expects same-size arrays, not sure why the first one is missing a dim.
BrianWhitneyAI created a review comment on a pull request on bioio-devs/bioio-imageio
for example.gif we have an issue with the reader here. ``` elif image_length > 1: # Read and stack all frames frames = [] for frame...
BrianWhitneyAI created a review comment on a pull request on bioio-devs/bioio-imageio
why'd we lose a scene here?
BrianWhitneyAI pushed 3 commits to bugfix/missing-comma-was-creating-a-fake-file-format bioio-devs/bioio-imageio
- ci(dependabot): bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/co... a65adbc
- Merge pull request #13 from bioio-devs/dependabot/github_actions/codecov/codecov-action-5 ci(dependabot): bump codec... 5b6f27e
- Merge branch 'main' into bugfix/missing-comma-was-creating-a-fake-file-format 0266ca0