Python

Everything Import Sample… and New dataset… do in the app is also a Python call. Use it to register a cohort in a loop, answer a project's open questions from a script, or open the viewer from a notebook. Registering a project writes to the same project list the app reads, so there is no server to start first.

import plexora

Every function on this page is then plexora.<name>. Each has a full reference page under Python API.

Common tasksCopy Anchor Link

Each section below is a separate task; use the ones you need.

Import a sampleCopy Anchor Link

Two calls register a sample. Use whichever matches what you know about your files:

import plexora

name = plexora.import_sample("slide.ome.tif", "slide_mask.tif", "cells.csv", wait=True)
print(name)
print(plexora.project_manifest(name)["summary"])

Fill in what is still openCopy Anchor Link

A project registered with only an image is complete, but a tool may later need a table or a column it does not have yet. configure_project answers with the same keywords and returns the project's manifest, so you can see what is still open.

import plexora

name = plexora.create_project("slide.ome.tif")
manifest = plexora.configure_project(name, data="cells.csv", cell_id="CellID")
print(manifest["manifest"]["table"]["status"])
print(manifest["manifest"]["role:cell_id"])

A keyword outside the vocabulary (plexora.PROJECT_SPEC_KEYS) is refused by name, not ignored.

Group samples into a datasetCopy Anchor Link

import plexora

cohort = plexora.create_dataset("Melanoma Cohort", projects=[
    {"image": "slide.ome.tif", "segmentation": "slide_mask.tif",
     "data": "cells.csv", "cell_id": "CellID"},
    {"image": "slide2.ome.tif"},
])
print(cohort.name, cohort.projects)

Open the viewerCopy Anchor Link

plexora.view(name) returns a viewer. In a notebook, make it the last line of a cell and it appears inline; it can also open what is already in memory. See Notebook.

plexora.view("tonsil_01", tool="gating")

TipsCopy Anchor Link

• The Dataset object is a snapshot. Its methods (add, remove, rename, describe, delete) return a fresh one, so write cohort = cohort.add("slide2"). Removing a project from a dataset, or deleting the dataset, never deletes the project.
• plexora.dataset("Melanoma Cohort") finds a dataset again by name; plexora.list_datasets() lists them all.
• plexora.add_layers(name, "slide2.ome.tif", wait=True) adds files to a project that already exists.
• The same spec dict works in three places: create_project(**spec), an entry in create_dataset(projects=[...]), and a JSON file for plexora project create --from spec.json.

RelatedCopy Anchor Link