mantispy.ds.blobs

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mantispy.ds.blobs#

mantispy.ds.blobs(*, n_wells=4, n_sites=2, n_cells=12, shape=(64, 64), plate='BLOBS01', seed=0)[source]#

A small synthetic Cell Painting plate, laid out like one mantispy.io.read_plate() returns.

Round cells with a concentric nucleus are stained in the five Cell Painting channels and measured. The result is complete without a download: Images, Labels for the three compartments, well Shapes, and cells and wells Tables whose features carry CellProfiler names.

Every element sits in three coordinate systems, {plate}_{well}_s{site}, {plate}_{well} and {plate}, laying the fields of a well out as a mosaic and the wells as a plate map.

Parameters:

  • n_wells (int (default: 4)) – Wells to simulate, filled across the rows of a 96-well plate from A01.

  • n_sites (int (default: 2)) – Fields of view per well, laid out in a square mosaic.

  • n_cells (int (default: 12)) – Cells per field, or as many as fit without overlapping.

  • shape (tuple[int, int] (default: (64, 64))) – Pixel height and width of one field.

  • plate (str (default: 'BLOBS01')) – Plate barcode, which every element name is prefixed with.

  • seed (int (default: 0)) – Seed of the random generator. Two calls with one seed give the same plate.

Return type:

SpatialData

Returns:

The plate.

Examples

>>> import mantispy as mt
>>> sdata = mt.ds.blobs()
>>> sdata.tables["cells"].var["channel"].value_counts()
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