spacr.qt.screens.organism_screen

Workflow inputs and outputs

Toxoplasma

Open the organism guide from Home, inspect the compartment diagram, then select Plaque Assay, Recruitment, Invasion Assay or Replication Assay. The four Coming soon tiles describe proposals and cannot run. The guide itself does not analyse a project or produce a measurement table.

Open: Home → Toxoplasma.

Inputs and outputs below include conditional alternatives. The guidance and handoff notes say which route applies.

Inputs

  • Bundled organism reference — Installed organism descriptions and SwissBioPics cell diagrams; no project input is required.

Outputs

  • Organism guide and assay selection — GUI-only compartment highlights and navigation to available assays; no measurements or files are produced.

API reference.

Module tutorial.

Explore organism guides and open the available image-analysis modules.

From Home, choose an organism to read its introduction, explore the cell diagram and browse its assay tiles. These guide pages require no input files and produce no analysis files. Drag the divider to give the information or module pane more space; each pane scrolls independently. Hover over a diagram component to read its description, select several components to keep them highlighted, and use Clear components to reset the selection.

Toxoplasma

Open Home > Toxoplasma and choose Plaque Assay, Recruitment, Host–Pathogen, Invasion Assay or Replication Assay. The selected module provides its input selectors, settings, preview and Run controls. Use its Test data control when an example is available. Plaque Assay starts with images; the other assays use the corresponding measurement tables and object relationships. Follow each module’s input help before running, then open the results in its selected output folder. Starplast opens a separate application for exploring the Toxoplasma knowledge map; its first launch offers installation. Gliding motility opens the Motility Assay with infection QC off. Egress, Bradyzoite conversion and Host cell damage say Coming soon and are disabled.

Plasmodium

Open Home > Plasmodium to browse blood-stage, liver-stage, motility and compound-response topics. Explore the apicomplexan diagram and follow the PlasmoDB or UniProt links for organism-specific information. Three tiles open existing modules: Parasitaemia opens Host–Pathogen Analysis, Sporozoite motility opens the Motility Assay with infection QC off, and Drug response imaging opens Dose–Response. Each tile’s tooltip says which inputs to prepare. The other five tiles say Coming soon and are disabled. This page itself writes no results; the opened module writes to its selected output folder.

Candida

Open Home > Candida to browse morphology, filamentation, biofilm and host-cell interaction topics. Explore the budding-yeast diagram and follow the Candida Genome Database or UniProt links for gene and protein information. Four tiles open existing modules: Adhesion and Epithelial invasion open the Invasion Assay, Phagocytosis opens Host–Pathogen Analysis, and Antifungal response opens Dose–Response. Filamentation, Germ tube formation, Biofilm and Morphology say Coming soon and are disabled. This page requires no data; the opened module writes to its selected output folder.

Trypanosoma, Leishmania, Giardia, Virus infection and Mammalian cells

These five pages appear on Home only with Preferences > Show alpha features on. Each follows the same layout: an introduction, a SwissBioPics cell whose selectable compartments are the UniProt subcellular locations annotated for that taxon, four topic sections, and eight tiles. Live tiles open an existing module with a preset (Motility Assay, Invasion Assay, Host–Pathogen Analysis, Dose–Response, Plaque Assay, Recruitment, Mask or Measure), and the others say Coming soon. Giardia uses the generic eukaryotic cell, the virus page the host cell with a virion, and the mammalian page the animal cell. The pages need no input files; the opened module writes to its selected output folder.

Classes

OrganismScreen

Show one organism and its existing or proposed image-analysis modules.

Functions

open_workflow(window, route[, fallback])

Open route's module in window and apply the route's preset.

Module Contents

class spacr.qt.screens.organism_screen.OrganismScreen(app_key: str, host=None, parent=None)[source]

Bases: PySide6.QtWidgets.QWidget

Show one organism and its existing or proposed image-analysis modules.

Parameters:

  • app_key – an organism page key from ORGANISMS.

  • host – optional main window receiving module navigation requests.

  • parent – owning Qt widget.

Build the independently scrollable introduction and Home tile grid.

eventFilter(watched, event) → bool[source]

Reflow after viewport resize, including vertical scrollbar changes.

Parameters:

  • watched – Qt object that received the event.

  • event – Qt event to inspect before delegating to the base filter.

Returns:

the base event filter’s result.

open_workflow(icon: str)[source]

Open the existing module behind a tile and apply its preset.

Parameters:

icon – the tile’s icon key in this organism’s workflows.

Returns:

the module screen the preset went to, or None.

spacr.qt.screens.organism_screen.open_workflow(window, route, fallback=None)[source]

Open route’s module in window and apply the route’s preset.

Shared by the organism tiles and the spaCR menu, so both reach the same screen with the same settings. Keys the module lacks are skipped.

Parameters:

  • window – the main window, or None when no window hosts the page.

  • route – (app key, preset, note) from the organism workflows.

  • fallback – called with the app key when window cannot open it.

Returns:

the module screen the preset went to, or None.