> For the complete documentation index, see [llms.txt](https://rotsl.gitbook.io/rotsl/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://rotsl.gitbook.io/rotsl/projects/automator.md).

# Automator

## Embedded System

Automator is a robotic imaging system at The Sainsbury Laboratory, Norwich. It photographs QR-labelled Petri dishes automatically at set intervals over the course of an experiment. You set up a schedule in a web browser, place your plates in the workspace, and the system handles the imaging without you needing to be present.

Downstream analysis of *Magnaporthe oryzae* growth on Petri dishes is achieved by the R package grayleafspotr or Python package metrics-petri.

[![grayleafspotr](https://img.shields.io/badge/Open-grayleafspotr-276dc3?style=for-the-badge\&logo=r)](/rotsl/projects/bio-imaging.md#grayleafspotr)

[![metrics-petri](https://img.shields.io/badge/Open-metrics--petri-3776ab?style=for-the-badge\&logo=python)](/rotsl/projects/bio-imaging.md#metrics-petri)

The robot arm carries a camera. At each scheduled interval, it moves over a plate, uses a small suction cup to lift the lid slightly, takes a photograph with a high-resolution camera, replaces the lid, and moves to the next plate. This repeats on a schedule you define, for as long as you need.

I designed the workflow so everything is controlled through a web browser. There is no software to install on your computer.

## Imaging workflow

```mermaid
flowchart LR
    Schedule[Browser schedule] --> Plates[QR-labelled Petri dishes]
    Plates --> Robot[Robot arm]
    Robot --> Lid[Suction cup lifts lid]
    Lid --> Camera[High-resolution photograph]
    Camera --> Repeat[Repeat at set intervals]
    Repeat --> Analysis[Downstream growth analysis]
    Analysis --> R[grayleafspotr]
    Analysis --> Python[metrics-petri]
```

## Links

[![GitHub repository](https://img.shields.io/badge/GitHub-Repository-24292f?style=for-the-badge\&logo=github)](https://github.com/rotsl/Automator)

[![Documentation](https://img.shields.io/badge/Open-Documentation-2f80ed?style=for-the-badge)](https://rotsl.github.io/Automator/)

[![PyPI package](https://img.shields.io/pypi/v/automator-tsl?style=for-the-badge\&label=PyPI\&logo=pypi)](https://pypi.org/project/automator-tsl/)

[![PyPI downloads](https://static.pepy.tech/personalized-badge/automator-tsl?period=total\&units=INTERNATIONAL_SYSTEM\&left_color=BLUE\&right_color=RED\&left_text=downloads)](https://pepy.tech/projects/automator-tsl)

## PyPI package

This package is the installable distribution of the Automator controller and its reference assets. For the full source repository, contributor guidelines, and changelog, use the repository link above.