Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ome/ome-zarr-py issues and pull requests

#296 - Check Well exists before trying to load data

Pull Request - State: closed - Opened by will-moore about 1 year ago - 2 comments

#295 - Set minimum fsspec version

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

#294 - writer.write_image requires fsspec>=0.8.0

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

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

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

#292 - Test suite failure for commit

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

#291 - Test suite failure for commit

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

#290 - Changes to scale.py and writer.py to support scaling methods.

Pull Request - State: open - Opened by sandip-shah about 1 year ago - 4 comments

#289 - Changelog 0.8.0

Pull Request - State: closed - Opened by will-moore about 1 year ago - 2 comments

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

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

#287 - Test suite failure for commit

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

#286 - Test suite failure for commit

Issue - State: closed - Opened by snoopycrimecop over 1 year ago - 2 comments

#285 - View in validator

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

#284 - Writing ome-zarr in a serial fashion, one 2D slice at a time

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

#281 - POC validation of NGFF with pydantic_ome_ngff

Pull Request - State: closed - Opened by will-moore over 1 year ago - 6 comments

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

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

#279 - allow main with empty args

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

#278 - Writing 384-Well Plates

Issue - State: closed - Opened by r0f1 over 1 year ago - 2 comments

#277 - Test suite failure for commit

Issue - State: closed - Opened by snoopycrimecop over 1 year ago - 2 comments

#276 - Test suite failure for commit

Issue - State: closed - Opened by snoopycrimecop over 1 year ago - 2 comments

#275 - Zarr dev build

Pull Request - State: open - Opened by joshmoore over 1 year ago

#274 - Expose storage_options in parse_url

Issue - State: open - Opened by sebsacuna over 1 year ago - 1 comment

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

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

#272 - codespell: config + workflow + pre-commit

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

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

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

#270 - Pre commit ci update config

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

#269 - Drop py37

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

#268 - Scaling issues

Issue - State: open - Opened by will-moore over 1 year ago - 1 comment

#267 - changelog entry for 0.7.0

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

#266 - Don't handle exception in Multiscales init()

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

#265 - Labels not loaded from cloud buckets

Issue - State: open - Opened by joshua-gould over 1 year ago

#264 - reader() is not idempotent

Issue - State: open - Opened by joshua-gould over 1 year ago - 1 comment

#263 - Sparse plate, with "missing" Wells shouldn't throw exceptions

Issue - State: closed - Opened by will-moore over 1 year ago - 3 comments

#262 - Scaler not scaling all dimensions

Issue - State: open - Opened by FIrgolitsch over 1 year ago - 1 comment

#261 - add omero metadata to writer

Pull Request - State: closed - Opened by giovp over 1 year ago - 30 comments

#260 - writer for omero metadata

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

#259 - Upgrade action

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

#258 - use declarative representation of the spec

Issue - State: open - Opened by d-v-b over 1 year ago - 14 comments

#257 - Optimize zarr multiscale writing based on #237

Pull Request - State: closed - Opened by camilolaiton over 1 year ago - 11 comments

#256 - Read tables using anndata._io.read_zarr for local data

Pull Request - State: closed - Opened by will-moore over 1 year ago - 3 comments

#255 - Two questions about converting larger than memory ND data into ome-zarr

Issue - State: open - Opened by dpshepherd over 1 year ago - 4 comments

#254 - Multiscale method in write_images ignored (e.g. nearest vs gaussian)

Issue - State: open - Opened by maweigert over 1 year ago - 1 comment

#253 - Use zarr default compressor by default

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

#252 - Reactivate zarr-dev build

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

#251 - Deactivate Zarr dev build

Pull Request - State: closed - Opened by joshmoore over 1 year ago - 3 comments

#250 - write_multiscale defaults to no compression

Issue - State: closed - Opened by jni over 1 year ago - 2 comments

#249 - Cannot write an image with axis names only

Issue - State: closed - Opened by andy-sweet over 1 year ago - 3 comments

#248 - FOV names and array names are hard-coded for the HCS dataset reader

Issue - State: closed - Opened by ziw-liu over 1 year ago - 7 comments

#246 - Fix sphinx package typo in README

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

#245 - Unable to Read/Write Multiscale data correctly

Issue - State: closed - Opened by frankblubaugh over 1 year ago - 2 comments

#244 - resize each block to custom shape

Pull Request - State: closed - Opened by will-moore over 1 year ago - 12 comments

#243 - Bug fix io

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

#241 - [WIP] Support plate loading for varying well sizes (ref #240)

Pull Request - State: open - Opened by jluethi over 1 year ago - 12 comments

#240 - Plate loading for wells with varying zyx dimensions

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

#239 - Provide a remote/s3 example in the docs

Issue - State: closed - Opened by joshmoore over 1 year ago - 2 comments

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

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

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

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

#235 - Don't hard-code dimension_separator when reading

Pull Request - State: closed - Opened by will-moore almost 2 years ago - 3 comments

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

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

#233 - scaler.local_mean() maintains dype

Pull Request - State: closed - Opened by will-moore almost 2 years ago - 4 comments

#232 - Memory usage can be improved by avoiding dtype conversions

Issue - State: open - Opened by LucaMarconato almost 2 years ago - 1 comment

#231 - ome_zarr download uses wrong dimension_separator

Issue - State: open - Opened by will-moore almost 2 years ago - 1 comment
Labels: bug

#230 - rgb_to_5d image code does not follow the spec

Issue - State: open - Opened by ktsitsi almost 2 years ago - 1 comment

#229 - Draft implementation of the new transform specs

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

#228 - node.show() to render an Image with set_active_channels

Issue - State: open - Opened by will-moore almost 2 years ago - 1 comment

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

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

#226 - question: transition from hdf5 to ome-zarr-py

Issue - State: closed - Opened by kasasxav about 2 years ago - 6 comments

#225 - Handling “acquisitions” in plate & well reading

Issue - State: open - Opened by jluethi about 2 years ago - 14 comments

#224 - Add changelog 0.6.0

Pull Request - State: closed - Opened by will-moore about 2 years ago - 3 comments

#223 - Dask docs update

Pull Request - State: closed - Opened by will-moore about 2 years ago - 1 comment

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

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

#221 - Storage options copy

Pull Request - State: closed - Opened by will-moore about 2 years ago - 2 comments

#220 - Use integer division for new_shape in resize_image

Pull Request - State: closed - Opened by will-moore about 2 years ago - 4 comments

#219 - Error when writing to disk a dask-backed xarray

Issue - State: closed - Opened by LucaMarconato about 2 years ago - 18 comments

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

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

#217 - scaler.local_mean changes the data type to float64

Issue - State: closed - Opened by constantinpape about 2 years ago - 2 comments
Labels: bug

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

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

#215 - Best practices for generating multiscale zarr data?

Issue - State: open - Opened by GenevieveBuckley about 2 years ago - 5 comments

#214 - Use multiscales name for node metadata['name']

Pull Request - State: closed - Opened by will-moore about 2 years ago - 2 comments

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

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

#212 - Disable auto_mkdir when path begins with `s3`

Pull Request - State: closed - Opened by colobas about 2 years ago - 4 comments

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

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

#210 - How to write image array with 6 or more dimensions to ome-azrr

Issue - State: open - Opened by sebi06 about 2 years ago - 5 comments

#209 - Read multi-resolution pyramids in Well class (closes #208)

Pull Request - State: closed - Opened by tcompa over 2 years ago - 7 comments

#208 - Read multi-resolution pyramids in Well class

Issue - State: closed - Opened by tcompa over 2 years ago

#207 - Plate labels fix

Pull Request - State: open - Opened by will-moore over 2 years ago - 25 comments

#206 - Write version attribute to image-label specification

Pull Request - State: closed - Opened by sbesson over 2 years ago - 1 comment

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

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

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

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

#203 - Read data from protected s3?

Issue - State: closed - Opened by BioinfoTongLI over 2 years ago - 2 comments

#202 - Fix the Zarr development GH workflow following branch renaming

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

#201 - Output is all zeros

Issue - State: closed - Opened by ahnsws over 2 years ago - 4 comments

#200 - Read multiple fields of view on a grid, for HCS dataset

Issue - State: open - Opened by tcompa over 2 years ago - 16 comments

#199 - Dask write image

Pull Request - State: closed - Opened by will-moore over 2 years ago - 2 comments

#198 - Dask poc

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

#197 - bugfix in chunks when providing storage_options as dict

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