spacr.qt.organisms

Sourced organism introductions and image-analysis module proposals.

The assay keys are existing pipeline identifiers. A proposal served by a general module opens that module through workflows; any other proposal has no route, so the organism pages cannot run an unimplemented analysis. Artwork provenance, licences and checksums ship in organism_sources.json.

Attributes

ORGANISMS

Organism guides keyed by toxoplasma, plasmodium, candida,

Functions

workflow(organism_key, icon)

Return the existing module route of one organism tile, if any.

Module Contents

spacr.qt.organisms.workflow(organism_key: str, icon: str)

Return the existing module route of one organism tile, if any.

Parameters:

• organism_key – an organism page key from ORGANISMS.

• icon – the tile’s icon key, unique within its organism.

Returns:

(app key, preset, note) or None for a Coming soon tile.

spacr.qt.organisms.ORGANISMS

Organism guides keyed by toxoplasma, plasmodium, candida, trypanosoma, leishmania, giardia, virus and mammalian.

Each record supplies a display name, description, biology source URL, bundled diagram filename and diagram note; source_label names the biology source when it is not the CDC. The last five pages are alpha features. sections contains heading, prose and linked assay-key triples; links contains display-label and URL pairs. modules contains route-key, title, description and icon-key tuples. A None route denotes an organism-specific assay with no pipeline of its own. workflows maps such a tile’s icon key to the existing module that measures its readout, a settings preset applied on opening, and a note on how to use it; a None tile absent from workflows is Coming soon. starplast launches an external app from the Toxoplasma page; it is not a spaCR analysis registry key or segmentation backend. Display prose is translated at use; route keys, URLs and asset names stay fixed.