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bioio-tifffile and bioio-ome-tiff parse ome-tiff metadata differently

2

### Describe the Bug bioio-tifffile.Reader does not properly parse ome-tiff metadata, but bioio-ome-tiff does. There is not notice given to the user which reader is being used, and given bioio-tifffile...

TimMonko

### Feature Description BioImage should be able to wrap an already in memory numpy array. ### Use Case This previously existed in aicsimageio and some scientists have asked for it....

toloudis

writer compression parameter

1

### Feature Description It may benefit many users to be able to set compression parameters for both zarr and tiff writing. ### Use Case See https://github.com/AllenCellModeling/aicsimageio/issues/553 ### Solution Add compression...

toloudis

read physical time metadata

1

### Feature Description Put physical T units on same level as physical pixel dimensions. ### Use Case For time series data we need to be able to read the time...

toloudis

### Feature Description Allow more specificity in requested chunk_dims for get_image_dask_data (_read_delayed). ### Use Case Dask best practices for chunk sizing: https://docs.dask.org/en/latest/delayed-best-practices.html Currently bioio only allows you to choose a...

toloudis

Unable to open czi line-scan kymographs - missing raw frame(t) pixel data

1

First, thanks for working on this critical package. I understand and appreciate how complex opening proprietary binary file formats can be. I followed the package from aicsimageio to its new...

cudmore

Improve error message on UnsupportedFileFormatError

2

### Describe the Bug `UnsupportedFileFormatError` not useful ```python im = bioio.BioImage('some.nd2') ``` ```python File ~/miniforge3/envs/chunglab/lib/python3.11/site-packages/bioio/bio_image.py:171, in BioImage.determine_reader(image, fs_kwargs, **kwargs) 168 # If we haven't hit anything yet, we likely don't...

tlambert03

Surface more information during reader/plugin selection

5

[See the original issue here for more information](https://github.com/AllenCellModeling/aicsimageio/issues/420) from aicsimageio. In short, it would be useful in some use cases to provide more information about what `BioImage` (previously `AICSImage`) is...

SeanDuHare

### Describe the Bug The first and third tests which are commented out [here](https://github.com/bioio-devs/bioio/pull/9/commits/8552a3c910e2a299f86ebe62e6dd75318532158a#diff-4a26e04cac22023b008db8ba21a4361dbc31343d9e4e708aa09d9818d80cb0cc) (on `test_timeseries_writer `) fail when uncommented because the data array created has inconsistent shapes for the...

SeanDuHare

Consider a public plugin registry

2

### Feature Description Idea: If we encourage community development of plugins, it would be nice to have a registry of plugins. ### Use Case How will users find plugins for...

toloudis