LucaMarconato
commented
1 year ago @quentinblampey thanks, merging this now (sorry that it took so long). Now the alignment problem is fixed by https://github.com/scverse/spatialdata/pull/322/files.
Closed quentinblampey closed 1 year ago
LucaMarconato
commented
1 year ago @quentinblampey thanks, merging this now (sorry that it took so long). Now the alignment problem is fixed by https://github.com/scverse/spatialdata/pull/322/files.
Added to
vizgen_merscope:download.py: download and unzip a file from Zenodoto_zarr.py: make a zarr folder (using the merfish reader in spatialdata-io, see PR: https://github.com/scverse/spatialdata-io/pull/33)NB: for ease of sharing, this is a very small crop of a public vizgen image, and some channels were removed to make it lighter. Since VPT (https://vizgen.github.io/vizgen-postprocessing/) was run on this crop, it gave the latest file format/structure into a dedicated subfolder that I called
vpt-run.