In this workshop, we will bridge the gap between advanced microscopy data generation and the computational skills required for its analysis. By leveraging open-source tools like FIJI and Jupyter, participants will learn to automate image analysis, enhancing the precision, efficiency, and reproducibility of their research. This two-day event, led by experienced core facility staff from the Francis Crick Institute, offers a practical approach to mastering quantitative analysis and workflow automation, essential for advancing research across multiple domains.
Registration for this workshop has now closed.
- Sara Salgueiro Torres, Francis Crick Institute
- Stefania Marcotti, Francis Crick Institute
- Martin Jones, Francis Crick Institute
- Cameron Shand, Francis Crick Institute
- Kimberly Meechan, UCL
- Dave Barry, Francis Crick Institute
- Please remember to bring your laptop (and charger).
- Ensure your laptop can connect to WiFi networks outside your host institute (eduroam would be ideal) - check with your local IT support team if you're not sure.
- Please install the required software before the workshop - follow the installation instructions on this page.
- Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
- You will be assigned to a specific group, with whom you will be sitting - your group number will be displayed in the training room.
- PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.
| Monday, October 27th 2025 | |||
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| 09:30 - 11:00 | Session 1 | Introduction & Installations |
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| 11:00 - 11:15 | Coffee Break | ||
| 11:15 - 13:00 | Session 2 | Image Pre-Processing, Segmentation & Analysis |
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| 13:00 - 14:00 | Lunch | ||
| 14:00 - 16:00 | Session 3 | Assembling Pipelines and Interpreting Results |
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| 16:00 - 16:15 | Coffee Break | ||
| 16:15 - 17:45 | Session 4 | Extending Analyses to Three Dimensions |
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| 17:45 | Dinner & Drinks | ||
| Tuesday, October 28th 2025 | |||
| 09:30 - 10:30 | Session 5 | Using Jupyter Notebooks for Reproducible Analysis - Part 1 |
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| 10:30 - 10:45 | Coffee Break | ||
| 10:45 - 12:30 | Session 6 | Using Jupyter Notebooks for Reproducible Analysis - Part 2 |
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| 12:30 - 13:30 | Lunch | ||
| 13:30 - 15:30 | Session 7 | Introduction to Batch Processing with Jupyter Notebooks |
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| 15:30 - 15:45 | Coffee Break | ||
| 15:45 - 16:45 | Session 8 | Introduction to napari, wrap-up, and Q&A |
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The workshop will take place in the Francis Crick Institute, London, UK:
<iframe src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d737.902638676005!2d-0.1278312633519172!3d51.53158304203475!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x48761b2356c7b3d9%3A0xb8647f199e3caae7!2sFrancis%20Crick%20Institute!5e0!3m2!1sen!2suk!4v1726748251051!5m2!1sen!2suk" width="100%" height="450" style="border:0;" allowfullscreen="" loading="lazy" referrerpolicy="no-referrer-when-downgrade"></iframe>Please note that the building entrance is on Midland Road. The workshop will take place in Training Room 1 on the first floor:
| Date | Venue | Content |
|---|---|---|
| 8 / 9th April 2024 | King's College London | Click here |
| 24 / 25th April 2024 | Royal College of Surgeons in Ireland | Click here |
| 21 / 22nd October 2024 | Francis Crick Institute | Click here |
| 8 / 9th April 2025 | University of Galway, Ireland | Click here |
| 6 & 20th June 2025 | Francis Crick Institute | Click here |
| 18 / 19th August 2025 | Francis Crick Institute | Click here |
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Do I need any prior knowledge of image analysis, FIJI or python to attend?
No, this workshop is aimed at complete beginners, but a basic understanding of image acquisition would be beneficial.
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Do I need to have any experience of coding?
While some basic knowledge would be helpful, it's not essential and even if you have no knowledge of python, Jupyter notebooks or FIJI scripts/macros, you should still apply.
