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brainglobe / brainglobe-stitch

A napari plugin for stitching large tiled 3D imaging datasets
BSD 3-Clause "New" or "Revised" License
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Add functionality to save stitched image as h5 or zarr #14

Closed IgorTatarnikov closed 3 weeks ago

IgorTatarnikov commented 2 months ago

Description

What is this PR

Why is this PR needed? There is no way to save the fused image in the preview as one 3D image.

What does this PR do? Adds functionality to save the fused image as either a BigDataViewer compatible h5 file or as an OME-Zarr.

How has this PR been tested?

Tests have been added to cover the new functionality.

NOTE: To test the functionality locally you must install Fiji and also add BigStitcher to the update sites. This can be done using the GUI see here or via the command line after installing Fiji.

./ImageJ-linux64 --update add-update-sites "BigStitcherUpdate" "https://sites.imagej.net/BigStitcher/"
./ImageJ-linux64 --update update

Replace ImageJ-linux64 with the path to the local ImageJ executable.

Three different datasets are available for testing:

  1. Tiny (~28 MB): this is mostly used for automated testing and doesn't work for visual inspection. It can be downloaded here.
  2. Small (~1.8 GB): this dataset is more useful for visual inspection. It can be downloaded here.
  3. A full size dataset is available (~130 GB): this dataset works best for testing overall performance, especially when reading or writing data. It's available by request.

Is this a breaking change?

No.

Does this PR require an update to the documentation?

No.

Checklist:

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 91.84549% with 19 lines in your changes missing coverage. Please review.

Project coverage is 95.20%. Comparing base (58db8aa) to head (5e55376). Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
brainglobe_stitch/stitching_widget.py 79.51% 17 Missing :warning:
brainglobe_stitch/image_mosaic.py 98.66% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #14 +/- ## ========================================== - Coverage 96.89% 95.20% -1.69% ========================================== Files 6 6 Lines 419 626 +207 ========================================== + Hits 406 596 +190 - Misses 13 30 +17 ```

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