multiview-stitcher

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Simple example notebook with 4 tiles.

3

Hi Marvin @m-albert , that's a fantastic tool you are developing here! May I ask for a little documentation improvement? I deal a lot with programming beginners, who seek to...

haesleinhuepf

The idea/need for this feature came out in discussions with @folterj.

m-albert

When copying transform keys in the following way, an error is thrown during fusion. Found by @folterj (thanks!). ```python for msim in msims: transform = msi_utils.get_transform_from_msim(msim, 'before_registration') msi_utils.set_affine_transform(msim, transform, 'translation_registered')...

m-albert

plot_positions: fix inadvertent modification

2

plot_positions: fix inadvertent modification, added testing

folterj

Add optimization that simplifies fusion dask graphs in case of zarr input

1

This PR adds an optimization for fusing input tiles which are dask arrays created from zarr arrays. In this case, and if the option `circumvent_dask_for_zarr_backed_input` is enabled, the fusion function...

m-albert

... and remove upper setuptools requirements again in tox.ini and pyproject.toml. After https://github.com/soft-matter/pims/pull/463 is released.

m-albert

It'd be useful to be able to visualize tiles and channels in different / specified colors when using `vis_utils.view_neuroglancer`. Also mentioned in issue https://github.com/multiview-stitcher/multiview-stitcher/issues/54. Info on rendering / shading: https://github.com/google/neuroglancer/blob/master/src/sliceview/image_layer_rendering.md

m-albert

Bump tornado from 6.4.1 to 6.4.2 in /docs

1

Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4.1 to 6.4.2. Changelog Sourced from tornado's changelog. Release notes .. toctree:: :maxdepth: 2 releases/v6.4.2 releases/v6.4.1 releases/v6.4.0 releases/v6.3.3 releases/v6.3.2 releases/v6.3.1 releases/v6.3.0 releases/v6.2.0 releases/v6.1.0 releases/v6.0.4 releases/v6.0.3 releases/v6.0.2 releases/v6.0.1...

dependabot[bot]

MemoryError for large dataset at the register step

16

Dear, I encountering a memory issue while I am trying to register a large dataset (2 channels 2x10x402 ) XYZ stack of tiles 2048x2048px). I followed the jupyter notebook example...

bpavie

See https://github.com/multiview-stitcher/multiview-stitcher/pull/36#issuecomment-2417192182.

m-albert