plexora project create
Register a project from an image, files, or a run folder.
Register a project without opening the viewer. Give one image and name
the other files with options, or give several paths (or a run folder)
and let Plexora work out what each one is. Anything you leave out can
be added later with plexora project set, and Plexora asks for what a
tool needs when it needs it.
Usage
plexora project create [-h] [--name NAME] [--segmentation SEGMENTATION] [--data DATA]
[--table TABLE] [--subset COLUMN=VALUE] [--cell-id CELL_ID] [--x X]
[--y Y] [--z Z] [--sample SAMPLE] [--celltype CELLTYPE]
[--markers COLUMN [COLUMN ...]] [--metadata COLUMN [COLUMN ...]]
[--layer LAYER] [--log1p] [--single-image] [--row-number-ids]
[--channel-names NAME [NAME ...]]
[--image-type {brightfield,fluorescence}] [--copy] [--node NAME]
[--dataset DATASET] [--from SPEC.json] [--exist-ok] [--json]
PATH [PATH ...]Arguments
PATHrequiredrepeatableOptions
--name NAMEWhat to call the project. Defaults to the image's filename.
--segmentation SEGMENTATIONA segmentation mask to attach.
--data DATAA feature table: CSV, Parquet, AnnData (.h5ad) or SpatialData (.zarr).
--table TABLEWhich table inside a .zarr store holds the cells. Optional -- Plexora asks when something needs it.
--subset COLUMN=VALUEWhich image, for a table that spans several.
--cell-id CELL_IDThe column holding the cell identifier.
--x XThe column holding the X coordinate.
--y YThe column holding the Y coordinate.
--z ZThe column holding the Z coordinate (each cell's plane), for a table over a z-stack.
--sample SAMPLEThe column holding the image or sample id.
--celltype CELLTYPEThe column holding a phenotype or cell type.
--markers COLUMN [COLUMN ...]Columns holding marker intensities. Naming one of the two lists is enough -- the columns left over become the other.
--metadata COLUMN [COLUMN ...]Columns describing the cells rather than measuring them. Naming one of the two lists is enough -- the columns left over become the other.
--layer LAYERWhich matrix to read intensities from, for AnnData.
--log1pLog-transform the intensities as they are read.
--single-imageThis table covers exactly one image.
--row-number-idsNumber the rows instead of reading an id column.
--channel-names NAME [NAME ...]One per image channel, in order.
--image-type {brightfield,fluorescence}one of: brightfield, fluorescenceOverride how the image is read.
--copyCopy the files into the project directory.
--node NAMEThe data node the files are on, for any path that does not say for itself. In a spec file, {"path": ..., "node": null} keeps one file on this machine.
--dataset DATASETA dataset to put it in, by name. Made if it does not exist.
--from SPEC.jsonA JSON file of the same options. Command-line arguments win over what is in it.
--exist-okReuse a project already registered for this image.
--jsonExamples
An image is enough
plexora project create slide.ome.tifName every file
plexora project create slide.ome.tif --segmentation slide_mask.tif --data cells.csv --x X_centroid --y Y_centroid --cell-id CellIDLet Plexora work out what each file is
plexora project create slide.ome.tif slide_mask.tif cells.csvInto a dataset
plexora project create slide.ome.tif --dataset "Pancreas"A table covering several images
plexora project create slide1.ome.tif --data all_cells.csv --subset imageid=slide1Python equivalent
plexora.create_project takes the same options by the same names
(dashes become underscores). plexora.import_sample is the
several-paths form.
import plexora
plexora.create_project(
"slide.ome.tif",
segmentation="slide_mask.tif",
data="cells.csv",
x="X_centroid",
y="Y_centroid",
cell_id="CellID",
)