Try out multiview-stitcher with WellAcquistion

[tibuch]

It would be awesome if we can use multiview-stitcher to update our tile positions before stitching.

See this issue to get started.

[tibuch]

Conclusion: It works! :tada:

Based on the demo code from the linked issue above:

tile_translations = []
a04 = plate_acquistion.get_well_acquisitions(["A04"])[0]
tile_scales = []
tile_paths = []
for t in a04.get_tiles():
    if t.get_position()[1] == 0 and t.get_position()[2] == 0:
        tile_translations.append(
            {
                'y': t.get_zyx_position()[1],
                'x': t.get_zyx_position()[2]
            } 
        )
        tile_scales.append(
            {
                'y': 1,
                'x': 1,
            }
        )
        tile_paths.append(t._paths[0])

msims = []
for tile_translation, tile_scale, tile_path in zip(tile_translations, tile_scales, tile_paths):
    print(tile_translation, tile_scale)

    sim = si_utils.get_sim_from_array(
        da.from_zarr(imread(tile_path, aszarr=True))[np.newaxis],
        dims=['c', 'y', 'x'],
        scale=tile_scale,
        translation=tile_translation,
        transform_key='stage_metadata',
        c_coords=["DAPI"],
    )

    msim = msi_utils.get_msim_from_sim(sim, scale_factors=[])
    msims.append(msim)

with ProgressBar():
    params = registration.register(
        msims,
        reg_channel_index=0,
        transform_key='stage_metadata',
        new_transform_key='translation_registered',
        registration_binning={'y': 1, 'x': 1},
        pre_registration_pruning_method=None,
        plot_summary=False,
    )

new_tiles = []
i = 0
for t in a04.get_tiles():
    if t.get_position()[1] == 0 and t.get_position()[2] == 0:
        ntile = copy(t)
        ntile.position = TilePosition(
            time=ntile.position.time,
            channel=ntile.position.channel,
            z=ntile.position.z,
            y=ntile.position.y + params[i][0][0, -1],
            x=ntile.position.x + params[i][0][1, -1]
        )
        new_tiles.append(
            ntile
        )
        i += 1

stitcher = DaskTileStitcher(
    tiles=new_tiles,
    chunk_shape=(2000, 2000), 
    output_shape = (1, 1, 3, 21500, 215000),
)
img = stitcher.get_stitched_image(
    fuse_func=stitching_utils.fuse_mean
)

In my toy example I see that the top-left tile is not aligned nicely to the rest. It might be related to different z-positioning. Currently I just chose z-pos == 0 and did not compute a max projection.