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 napari, 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 and King's College London, offers a practical approach to mastering quantitative analysis and workflow automation, essential for advancing research across multiple domains.
Apply here.
- Dave Barry, Francis Crick Institute
- Martin Jones, Francis Crick Institute
- Stefania Marcotti, King's College London
- Sara Salgueiro Torres, Francis Crick Institute
- Please remember to bring your laptop (and charger).
- 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.
All the slides for the workshop are on Google and accesible here.
Please note that all catering, as well as attendance of the social on the evening of the 8th, is covered by your registration fee.
| Tuesday, April 8th 2025 | |||
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| 09:30 - 10:30 | Registration | ||
| 10:30 - 11:45 | Session 1 | Introduction - Automated Image Analysis is Essential for Reproducible Science Dave Barry |
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| 11:45 - 12:00 | Coffee Break | ||
| 12:00 - 13:30 | Session 2 | Image Pre-Processing, Segmentation & Analysis Sara Salgueiro Torres |
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| 13:30 - 14:30 | Lunch | ||
| 14:30 - 16:15 | Session 3 | Assembling Pipelines and Interpreting Results Dave Barry |
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| 16:15 - 16:30 | Coffee Break | ||
| 16:30 - 18:00 | Session 4 | Introduction to Batch Processing Dave Barry |
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| 18:00 - ? | Evening Social | TBC | |
| Wednesday, April 9th 2025 | |||
| 09:30 - 10:30 | Session 5 | Introduction to Python and installations Stefania Marcotti |
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| 10:30 - 10:45 | Coffee Break | ||
| 10:45 - 12:30 | Session 6 | Using Jupyter Notebooks for Reproducible Analysis Stefania Marcotti |
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| 12:30 - 13:30 | Lunch | ||
| 13:30 - 15:30 | Session 7 | Using napari as an image analysis tool and as a viewer Martin Jones |
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The workshop will take place in the University of Galway, Galway, Ireland:
<iframe src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d8022.615056807473!2d-9.071864966743952!3d53.28706786442751!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x485b96f169862607%3A0x8b41e03d8f400270!2sUniversity%20of%20Galway!5e0!3m2!1sen!2suk!4v1733484459965!5m2!1sen!2suk" width="100%" height="450" style="border:0;" allowfullscreen="" loading="lazy" referrerpolicy="no-referrer-when-downgrade"></iframe>- Dave Barry, Francis Crick Institute
- Martin Jones, Francis Crick Institute
- Stefania Marcotti, King's College London
| 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 |
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Do I need any prior knowledge of image analysis, FIJI or napari 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.
