Unmix

Spectral spillover in images are removed using the unmixing parameters computed with PICASSOnn. Images are saved as marker instead as channel/cycle.

<xarray.DataArray ‘m387ntga1’ (marker: 13, obj_step: 10, row: 10532, col: 8960)> dask.array<getitem, shape=(13, 10, 10532, 8960), dtype=uint16, chunksize=(1, 1, 10532, 1792), chunktype=numpy.ndarray> Coordinates: channel (marker) int64 dask.array<chunksize=(4,), meta=np.ndarray>

• col (col) int64 0 1 2 3 4 5 6 7 … 8953 8954 8955 8956 8957 8958 8959 cycle (marker) int64 dask.array<chunksize=(4,), meta=np.ndarray>
• marker (marker) <U7 ‘LMNB1_1’ ‘ELAVL2’ ‘GFAP’ … ‘PDGFRA’ ‘MBP’
• obj_step (obj_step) int64 8847 9082 9317 9552 … 10257 10492 10727 10962
• row (row) int64 0 1 2 3 4 5 6 … 10526 10527 10528 10529 10530 10531

Input

Zarr store of processed images YAML unmixing parameters

Output

Zarr store of final images

Logs

Script log Dask performance report