Welcome to spaCR¶

spaCR — Spatial phenotype analysis of CRISPR screens.

Note

You are reading the stable documentation for spaCR 1.5.0.7. The public site follows released main; nightly builds validate upcoming changes without replacing the stable site.

A Python toolkit for quantifying and visualising phenotypic changes in high-throughput microscopy screens. Ships with a modern PySide6 GUI (spacr), a headless pipeline (spacr.core), and a plate-to-classification workflow that runs on top of PyTorch, Cellpose, scikit-image, and scipy.

It is built for cell biologists running pooled or arrayed CRISPR screens who need per-cell measurements from plate images. The GUI route needs no programming; the same processing steps are available through the Python API for scripted and reproducible workflows.

The GUI groups its applications into four categories: Core for the segment-measure-classify pipeline, Data for getting images and tables in and running them at scale, Tools for the instruments you point at a project — hand mask correction, stitching, embeddings, gates, plots and quality control — and Assays for the parasite-specific readouts. The bands under “Applications and workflow” below are those categories, in that order, with the tiles each one holds.

Not every screen is a tile, which is why no count of them is printed here. Work that only makes sense inside another step opens from that step’s masthead instead — Timelapse from Mask, Illumination and the Motility Assay from Measure, Classifier Evaluation and Explain CV Model from Classify, Annotator Agreement from Annotate, and the Cellpose Workbench, Model Compare, Model Zoo and Curate from Make Masks, among them — so a screen with no tile below is one step further in rather than gone. Home lists whatever the running build offers.

🚀 Get started

Install spaCR from PyPI and launch the Qt GUI in two commands.

https://github.com/EinarOlafsson/spacr#install-spacr

🎓 Interactive tutorials

The lesson library — 75 narrated, step-by-step lessons covering the whole pipeline.

tutorials/

📖 API reference

Supported workflow entry points and the complete module reference.

API reference

🎬 Video tutorials

Narrated walkthroughs of each pipeline module.

tutorials/

🐛 Report an issue

File a bug, request a feature, or ask a question.

https://github.com/EinarOlafsson/spacr/issues/new

Applications and workflow¶

Every tile links to the API page used by that application’s in-product help.

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.

Installation¶

The GUI lives behind the qt extra, so the desktop install must ask for it — plain pip install spacr gives you the pipelines but no PySide6, and spacr will tell you so rather than launch.

python -m pip install "spacr[qt]"
spacr                    # launch the Qt GUI

Headless (cluster, server, CI) — no Qt, no display:

python -m pip install spacr
spacr-run --list         # list the headless pipeline modules

Learn spaCR¶

The interactive tutorial library contains 75 narrated, step-by-step lessons covering every module, with 50 voices across eight languages. It is also reachable from the GUI: Help → Tutorial (web).

Welcome to spaCR¶

Applications and workflow¶

spaCR modules¶

Core¶

Data¶

Tools¶

Assays¶

Installation¶

Learn spaCR¶

Contents¶