API reference

Start with the workflow you want to run. These pages contain the supported pipeline entry points; implementation modules remain available in the complete reference below.

New to the Python interface? Follow the Python API quickstart first.

Applications and workflow

Every tile links to the API page used by that application’s in-product help. The bands below are the categories the home screen groups its applications into, in the same order and with the same members.

spaCR modules

Core

Core sequence from microscopy images through segmentation, measurements, annotations, classification, barcode mapping and regression.

Data

Import images and tables into spaCR projects and execute reproducible multi-plate workflows.

Tools

Point these at a project: edit masks by hand, stitch tiles, read an embedding, draw a gate, build a plot, check quality.

Assays

Quantitative readouts for biological assays.

Modules reached from another screen

These do not have a tile on the home screen. Each one answers a question about a run its host produced rather than starting a run of its own, so it opens as a page beside that host’s settings, already pointed at the same project.

They are not second-class: each is shipped, translated and documented like any other module, and the ones that are pipelines still run headlessly under spacr-run. Every module below can also be reached from the command palette, which is the only route that covers all of them.

Opened from a host’s masthead

• Annotate opens Annotator Agreement

• Classify opens Activation, Classifier Evaluation, Explain CV Model, Feature Explorer, Training Runs

• Database Browser opens Lineage, Tabulate

• Graph Builder opens Plate Viewer, Small Multiples

• Image UMAP opens Image Scatter, PCA

• Import opens Format Converter, External Masks, Import Images

• Make Masks opens Mask the whole folder, Curate, Model Compare, Model Zoo, Napari Bridge, Cellpose Workbench

• Map Barcodes opens Barcode QC

• Mask opens OPS, Timelapse

• Measure opens AnnData Export, Illumination, Motility Assay

• QC opens Control Charts, Layer Viewer, Outliers

• Regression opens Hit List, Investigate Hit, Methods & Results, Prediction Profiler, Diagnostics, Volcano Explorer

Opened from the Help menu

These inspect or administer work that already exists, rather than belonging behind any one module.

• Batch Runner

• Data Manager

• Database Browser

• Distributed Jobs

• Feature Dictionary

• Pipeline Graph

• Project Browser

• Plate Queue

• Report

• Run History

Stability

The pages above contain spaCR’s stable workflow entry points. Advanced and experimental functions state that status in their documentation. GUI widgets, workers, names beginning with an underscore and modules described as internal are implementation details rather than a compatibility promise.

Complete module reference

The complete reference is generated from the source so contributors can inspect every documented module. It is an alphabetical list of Python modules rather than of the applications above, so a reader who knows a module by the name it carries in the product should start from a tile: Mask is spacr.core and Recruitment is a function inside spacr.submodules, and neither is findable here by that name. Application code should prefer the curated workflow entry points above.

Every documented module, alphabetically

• spacr