czbiohub/iohub issues and pull requests

#133 - Convert a list of input datasets

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

#132 - WIP: universal reader output base classes

Pull Request - State: open - Opened by JoOkuma over 1 year ago - 5 comments
Labels: enhancement

#131 - Refactored typing Tuple/List/Dict to tuple/list/dict

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

#130 - License of the documentation

Issue - State: closed - Opened by ziw-liu over 1 year ago - 2 comments
Labels: documentation, meta

#129 - Docs index fix path

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

#128 - Fix multiversion links

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

#127 - Fix theme dependency

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, documentation

#126 - Use built-in generics to annotate sequence types

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: maintenance

#125 - Fix `setuptools-scm` installation error

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

#124 - bump ndtiff version to >1.12.1

Issue - State: open - Opened by ieivanov almost 2 years ago - 3 comments
Labels: μManager, maintenance, upstream

#123 - Unable to pip install dev mode after our tag releases

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 1 comment
Labels: bug, meta, maintenance

#122 - Set transformation metadata for existing NGFF datasets

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: enhancement, NGFF

#121 - NDTiffReader cannot be pickled

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

#120 - added helper property to easily access clear control scale

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

#119 - add ngff node pyramid initialization

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago - 1 comment
Labels: enhancement, NGFF

#118 - Convert scale metadata

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 10 comments
Labels: enhancement, NGFF, μManager

#117 - Contrast limit should follow the datatype of the dataset

Issue - State: open - Opened by edyoshikun almost 2 years ago - 1 comment
Labels: bug, NGFF

#116 - Fix Windows CLI tests

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, CI

#115 - Add code coverage check on PRs

Issue - State: open - Opened by ziw-liu almost 2 years ago
Labels: meta, CI

#114 - Add Clear Control dataset support

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago - 3 comments
Labels: enhancement

#113 - Fix documentation link in package metadata

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

#112 - Pydata theme for documentation

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: documentation, CI

#111 - Test failing on Windows

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 2 comments
Labels: bug, CI

#110 - Fix python version requirement

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

#109 - adding a coordinate transformation example.

Pull Request - State: closed - Opened by edyoshikun almost 2 years ago
Labels: documentation, enhancement

#108 - Added pre-commit

Pull Request - State: closed - Opened by JoOkuma almost 2 years ago - 13 comments

#107 - Preparing for dev pre-release on PyPI

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: documentation, maintenance, CI

#106 - modify the coordinateMetadata for old stacks

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 1 comment
Labels: enhancement, NGFF

#105 - Trouble opening ndtiff dataset

Issue - State: closed - Opened by talonchandler almost 2 years ago - 3 comments
Labels: bug, μManager

#104 - Add short description to `setup.cfg`

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

#103 - Can `convert` pass the most important information from micromanager image plane metadata?

Issue - State: open - Opened by talonchandler almost 2 years ago - 7 comments
Labels: enhancement, μManager

#102 - Use fixed separator `/` to join row_name and col_name

Pull Request - State: closed - Opened by talonchandler almost 2 years ago
Labels: bug, NGFF

#101 - Adding automatic channel name to Hex color mapping

Pull Request - State: closed - Opened by edyoshikun almost 2 years ago - 3 comments
Labels: enhancement, good first issue

#100 - Suppress CLI warning for NGFF v0.1 datasets

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: bug, NGFF

#99 - add TIFF writer

Issue - State: open - Opened by rachel-banks almost 2 years ago - 8 comments
Labels: enhancement

#98 - Deprecation warning from `iohub info <ome-zarr v0.1 dataset>`

Issue - State: closed - Opened by talonchandler almost 2 years ago
Labels: bug, NGFF

#97 - Initialize Zarr arrays in TIFF readers as zero-filled

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: bug, μManager

#96 - Skip empty image instead of failing in conversion

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, μManager

#95 - Avoid the `tifffile` version with breaking changes

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, maintenance, CI

#94 - New `tifffile` version breaks the OME-TIFF reader

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: bug, maintenance, CI

#93 - Add converter for OpenCell data

Issue - State: open - Opened by ieivanov almost 2 years ago - 2 comments
Labels: enhancement, μManager

#92 - Improve CLI and API reading entry points

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 6 comments
Labels: bug, enhancement

#91 - Allow different tile data types for NGFF

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: bug, NGFF

#90 - NGFF version is not found by `imread`

Issue - State: closed - Opened by talonchandler almost 2 years ago - 1 comment
Labels: bug

#89 - Default `ngff.TiledPositions.make_tiles()` sets dtype=np.float64

Issue - State: closed - Opened by edyoshikun almost 2 years ago
Labels: bug, NGFF

#88 - `None` in dataset makes converter fail

Issue - State: closed - Opened by talonchandler almost 2 years ago - 4 comments
Labels: bug, μManager

#87 - NGFF method to create zero-filled lazy images

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: bug, enhancement, NGFF

#86 - Makes examples output directory temporary

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

#85 - Refactor `_set_mm_meta` in `BaseReader` and its children

Issue - State: open - Opened by JoOkuma almost 2 years ago - 4 comments
Labels: enhancement, μManager

#84 - Writing large data for positions

Issue - State: closed - Opened by Christianfoley almost 2 years ago - 1 comment
Labels: documentation, enhancement, NGFF

#83 - Automatically generate display metadata for fluorescence channels

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 8 comments
Labels: enhancement, good first issue, NGFF

#82 - `get_zarr` returns incorrect data from 3D + 2D MM datasets

Issue - State: closed - Opened by talonchandler almost 2 years ago - 2 comments
Labels: bug, μManager

#81 - Update docs.yml

Pull Request - State: closed - Opened by AhmetCanSolak almost 2 years ago
Labels: bug, documentation

#80 - Update docs.yml

Pull Request - State: closed - Opened by AhmetCanSolak almost 2 years ago
Labels: bug, documentation

#79 - Specify minimum zarr-python version

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: bug, maintenance

#78 - Specify zarr-python version

Issue - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, maintenance

#77 - Viewing multiple positions per well

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 4 comments
Labels: NGFF, upstream

#76 - Micro-Manager TIFF formats Converter

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 12 comments
Labels: enhancement, NGFF, μManager

#75 - Unable to apply CoordinateTransformations with napari-ome-zarr

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 5 comments
Labels: NGFF, upstream

#74 - add support for writing RGB data

Issue - State: closed - Opened by mattersoflight almost 2 years ago - 7 comments
Labels: enhancement, NGFF

#73 - Convenient tiled array I/O with NGFF

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 7 comments
Labels: enhancement

#72 - Update package metadata

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: meta, maintenance

#71 - Image reading entry point

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 8 comments
Labels: enhancement

#70 - Get NGFF channel index from name

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: enhancement, NGFF

#69 - Run and check examples on CI

Issue - State: open - Opened by JoOkuma almost 2 years ago - 1 comment
Labels: enhancement, good first issue, CI

#68 - Package metadata

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 3 comments
Labels: meta, maintenance

#67 - Count valid TIFF pages when gathering index map

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: bug

#66 - Performance comparison between tifffile and iohub's custom OME-TIFF implementation

Issue - State: open - Opened by ziw-liu almost 2 years ago - 24 comments
Labels: μManager, performance

#65 - Wrong page indexing for an incomplete dataset

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 2 comments
Labels: bug

#64 - Chunking option for writing dataset

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 4 comments
Labels: bug, documentation, NGFF

#63 - Infer Zarr dimension separator from NGFF version

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago
Labels: bug, NGFF

#62 - Attempting to read old dataset with legacy ZarrReader

Issue - State: closed - Opened by edyoshikun almost 2 years ago - 1 comment
Labels: bug, NGFF

#61 - Add shorthand to get raw data in NGFF positions

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 9 comments
Labels: enhancement, NGFF

#60 - Should `ngff.ImageArray` have a different name?

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 9 comments
Labels: question, NGFF

#59 - Make it easier to write and read `tiled` dataset.

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 4 comments
Labels: enhancement, NGFF

#58 - Methods for modifying channels in NGFF positions

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: enhancement, NGFF

#57 - Benchmarking

Issue - State: open - Opened by AhmetCanSolak almost 2 years ago - 4 comments
Labels: enhancement, performance, CI

#56 - Method to delete or rename channel in NGFF datasets

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 9 comments
Labels: enhancement, NGFF

#55 - Dev pre-release on PyPI

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 12 comments
Labels: enhancement, meta

#54 - Fix example in README

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 1 comment
Labels: bug, documentation

#53 - Improve TIFF I/O stack

Issue - State: open - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: help wanted, μManager, performance

#52 - `README` example does not run; opens in read-only by default

Issue - State: closed - Opened by talonchandler almost 2 years ago - 3 comments
Labels: bug, documentation

#51 - Add zarr to install_requires

Pull Request - State: closed - Opened by talonchandler almost 2 years ago
Labels: bug, maintenance

#50 - Depend on `zarr`

Pull Request - State: closed - Opened by talonchandler almost 2 years ago - 1 comment

#49 - clarify pip install instructions

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

#47 - Open source iohub

Issue - State: closed - Opened by ziw-liu almost 2 years ago - 4 comments
Labels: enhancement, meta

#46 - Rename `WaveorderReader` to `ImageReader`

Pull Request - State: closed - Opened by ziw-liu almost 2 years ago - 5 comments
Labels: enhancement

#45 - Improve API for the NGFF module

Issue - State: closed - Opened by ziw-liu almost 2 years ago
Labels: enhancement, NGFF

#42 - CLI needs tests

Issue - State: closed - Opened by AhmetCanSolak about 2 years ago - 1 comment
Labels: CI

#41 - iohub needs a `convert` CLI command

Issue - State: closed - Opened by talonchandler about 2 years ago - 4 comments

#40 - Universal entry points

Issue - State: open - Opened by AhmetCanSolak about 2 years ago - 19 comments
Labels: enhancement, help wanted

#33 - identify optimal chunk size for computational imaging, DL, and visualization workflows

Issue - State: open - Opened by mattersoflight about 2 years ago - 8 comments
Labels: NGFF, performance

#28 - Docs

Pull Request - State: closed - Opened by AhmetCanSolak about 2 years ago - 15 comments
Labels: documentation

#26 - tensorstore support

Issue - State: open - Opened by JoOkuma about 2 years ago - 15 comments
Labels: enhancement, NGFF, performance

#22 - support multi-pos datasets that are not complete multi-well plate acquisitions

Issue - State: closed - Opened by mattersoflight about 2 years ago - 6 comments
Labels: enhancement, NGFF

#21 - CLI for summarizing and converting between data formats

Issue - State: closed - Opened by mattersoflight about 2 years ago - 1 comment
Labels: enhancement

#20 - writing to single OME-zarr store from multiple processes

Issue - State: closed - Opened by mattersoflight about 2 years ago - 2 comments
Labels: enhancement, NGFF, performance

#17 - Supported Python versions

Issue - State: closed - Opened by ziw-liu about 2 years ago - 7 comments
Labels: meta

#15 - Support multiple-MDA (OME-Tiff) datasets

Issue - State: open - Opened by talonchandler about 2 years ago - 1 comment
Labels: enhancement, μManager

#13 - added current implementation of HCSZarrModifier

Pull Request - State: closed - Opened by Christianfoley about 2 years ago - 2 comments
Labels: enhancement, NGFF

GitHub / czbiohub/iohub issues and pull requests