Napari-aicsimageio

napari-aicsimageio is a plugin for napari that utilizes AICSImageIO for image reading. In doing so, this plugin allows the reading of hundreds of different file formats. Most with channel, scale, axis, and metadata extraction.

This release includes some minor admin changes, some bugfixes, and some UX improvements.

The main bugfix is that, before this plugin hands the data to napari to render, we squeeze the proper dimensions out of it. And the UX improvement is to change the layer names for single scene images. For example, single scene images used to be added with `Image :: 0` but will now be added with `FILENAME` to add more clarity to the layers when working with multiple files at once.

Thanks psobolewskiPhD and tlambert03 for your work on these!

What's Changed
* build/use-setuptools-scm-for-versioning by tlambert03 in https://github.com/AllenCellModeling/napari-aicsimageio/pull/52
* Bugfix: Fix napari-plugin-check version by psobolewskiPhD in https://github.com/AllenCellModeling/napari-aicsimageio/pull/59
* Bugfix: Check the squeezed data for scale vals by psobolewskiPhD in https://github.com/AllenCellModeling/napari-aicsimageio/pull/60
* Use filename if single scene & no scene name by psobolewskiPhD in https://github.com/AllenCellModeling/napari-aicsimageio/pull/58


**Full Changelog**: https://github.com/AllenCellModeling/napari-aicsimageio/compare/v0.7.1...v0.7.2

This release includes a major change.

Previously after installing and using this plugin, users would be able to manually select between how to read a file (either in-memory or delayed). Due to upgrading to `npe2` however, we can no longer ship multiple readers with the same package anymore.

So instead we have made it so the file reading mode (in-memory or delayed) is determined via filesize and available memory.

> Reading Mode Threshold
> This image reading plugin will load the provided image directly into memory if it meets the following two conditions:
>
> The filesize is less than 4GB.
> The filesize is less than 30% of machine memory available.
> If either of these conditions isn't met, the image is loaded in chunks only as needed.

Currently, the user cannot select which reading mode to enforce. However coming soom^tm, napari users will be able to edit a configuration file and we plan to expose such settings there.

What's Changed
* admin/bump-min-aicsimageio-to-resolve-czi-physical-pixel-sizes by evamaxfield in https://github.com/AllenCellModeling/napari-aicsimageio/pull/44
* mention conda in installation instructions by haesleinhuepf in https://github.com/AllenCellModeling/napari-aicsimageio/pull/48
* feature/convert-to-npe2 by tlambert03 in https://github.com/AllenCellModeling/napari-aicsimageio/pull/49
* feature/cleanup-np2 by evamaxfield in https://github.com/AllenCellModeling/napari-aicsimageio/pull/50

New Contributors
* haesleinhuepf made their first contribution in https://github.com/AllenCellModeling/napari-aicsimageio/pull/48

**Full Changelog**: https://github.com/AllenCellModeling/napari-aicsimageio/compare/v0.6.1...v0.7.0

This release can be summed up by the [new addition in the README](https://github.com/AllenCellModeling/napari-aicsimageio#access-to-the-aicsimage-object-and-metadata):

> ![napari viewer with console open showing `viewer.layers[0].metadata`](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/console-access.png)
>
> You can access the `AICSImage` object used to load the image pixel data and
> image metadata using the built-in napari console:
>
> python
> img = viewer.layers[0].metadata["aicsimage"]
> img.dims.order TCZYX
> img.channel_names ["Bright", "Struct", "Nuc", "Memb"]
> img.get_image_dask_data("ZYX") dask.array.Array
>
>
> The napari layer metadata dictionary also stores a shorthand
> for the raw image metadata:
>
> python
> viewer.layers[0].metadata["raw_image_metadata"]
>
>
> The metadata is returned in whichever format is used by the underlying
> file format reader, i.e. for CZI the raw metadata is returned as
> an `xml.etree.ElementTree.Element`, for OME-TIFF the raw metadata is returned
> as an `OME` object from `ome-types`.
>
> Lastly, if the underlying file format reader has an OME metadata conversion function,
> you may additionally see a key in the napari layer metadata dictionary
> called `"ome_types"`. For example, because the AICSImageIO
> `CZIReader` and `BioformatsReader` both support converting raw image metadata
> to OME metadata, you will see an `"ome_types"` key that stores the metadata transformed
> into the OME metadata model.
>
> python
> viewer.layers[0].metadata["ome_types"] OME object from ome-types
>

What's Changed
* bugfix/windows-tests-fix by psobolewskiPhD in https://github.com/AllenCellModeling/napari-aicsimageio/pull/41
* bugfix/windows-build-main-yml-matrix by psobolewskiPhD in https://github.com/AllenCellModeling/napari-aicsimageio/pull/42
* feature/store-access-to-aicsimage-and-raw-meta-in-layer-meta by JacksonMaxfield in https://github.com/AllenCellModeling/napari-aicsimageio/pull/43
* Update minimum `aicsimageio` version to v4.6.0: https://github.com/AllenCellModeling/napari-aicsimageio/commit/40d8f8a779d35f4cd7f9056c1fe8dc7a29316ee9
* Update PyPI license to reflect the repo license: https://github.com/AllenCellModeling/napari-aicsimageio/commit/c18b6d06dd06ad0da67c30926be4ee2b34a0d22f

New Contributors
* psobolewskiPhD made their first contribution in https://github.com/AllenCellModeling/napari-aicsimageio/pull/41

**Full Changelog**: https://github.com/AllenCellModeling/napari-aicsimageio/compare/v0.5.0...v0.6.0

Thanks
* psobolewskiPhD
* pr4deepr
* tlambert03

All readers / file formats / deps are now installable (the main culprit was aicspylibczi not being installable on M1 macs), and as such we have added them all to the deps list. Additionally with this move, the package has become a GPL licensed package.

What's Changed
* admin/make-script-for-downloading-test-resource-use-cache by sir-sigurd in https://github.com/AllenCellModeling/napari-aicsimageio/pull/31
* bugfix/squeeze-extra-dims by JacksonMaxfield in https://github.com/AllenCellModeling/napari-aicsimageio/pull/32
* admin/update-min-aicsimageio-ver-and-move-to-gpl3 by JacksonMaxfield in https://github.com/AllenCellModeling/napari-aicsimageio/pull/36

Doc Updates
* grammar fix in readme by ianhi in https://github.com/AllenCellModeling/napari-aicsimageio/pull/38

New Contributors
* sir-sigurd made their first contribution in https://github.com/AllenCellModeling/napari-aicsimageio/pull/31
* ianhi made their first contribution in https://github.com/AllenCellModeling/napari-aicsimageio/pull/38

**Full Changelog**: https://github.com/AllenCellModeling/napari-aicsimageio/compare/v0.4.1...v0.5.0

This release adds support for multi-scene files! When `napari-aicsimageio` reads a multi-scene image it will pop open a widget with a list of all scenes in that file as well as some options for how to load those scenes.


This feature is marked as experimental so please give it a go and give us feedback! If reception is positive we are even considering making this the default loading pattern for `napari-aicsimageio` so that the user can set even more parameters before loading with options like 28 and 29.

Major thanks to psobolewskiPhD for the large majority of this work, to tlambert03, jwindhager, and Czaki for being readily available for questions, and to the napari community as a whole. This was a lot of work and feedback from a lot of people.

With napari-hub launch just around the corner and with the 4.0 release of AICSImageIO, I thought it would be good to release and fix the plugin in preparation.

This brings the plugin up-to-date with AICSImageIO==4.0.2 :tada:

With that, the plugin now directly reads and returns the reconstructed / restitched mosaic tile images for certain file formats. It has generally more bug fixes, and should be faster across the board (especially the `out-of-memory` variant).