BioQCPy

Overview

This notebook provides a set of simple quality control analyses for microscopy images, allowing users to flag issues such as saturation, crosstalk or inappropriate bit depth.

QC checks implemented:

• Histogram oddities
• Background flatness
• Bit depth assessment
• Dynamic range calculation
• Saturation percentage

⚠️ WORK IN PROGRESS The code is based on a prototype script.

Try It!

You can run the notebook now on Binder by clicking here.

Acknowledgements & Contact

This notebook was developed as part of the py-bioimage-qc project at the Crick Advanced Light Microscopy (CALM) department in the Francis Crick Institute.
Its goal is to provide an accessible, practical toolkit for basic quality control of bioimaging data.

Authors:

• Dave Barry (david.barry@crick.ac.uk)
• Sara Salgueiro Torres (sara.salgueirotorres@crick.ac.uk)
• Alicja Skórkowska (alicja.skorkowska@crick.ac.uk)

Feedback & Contributions:
We welcome your suggestions, feedback, and pull requests!
For questions or to report issues, please open an issue here or contact the authors directly.

---

CALM, Francis Crick Institute
1 Midland Rd, London NW1 1AT
2025