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.
You can register your interest in attending the workshop here. Please be advised that places are limited and a selection process will be used in the event that the workshop is over-subscribed.
The deadline for registering your interest is May 9th.
- Dave Barry, Francis Crick Institute
- Alicja Skórkowska, Francis Crick Institute
- 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 of the slides for this workshop are available here.
| Friday, June 6th 2025 | |||
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| 12:00 - 14:30 | Session 1 | Image Pre-Processing, Segmentation & Analysis Dave Barry |
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| 14:30 - 14:50 | Coffee Break | ||
| 14:50 - 17:00 | Session 2 | Assembling Pipelines and Interpreting Results Dave Barry |
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| Friday, June 20th 2025 | |||
| 12:00 - 13:30 | Session 3 | Introduction to Python and installations Alicja Skórkowska |
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| 13:30 - 13:50 | Coffee Break | ||
| 13:50 - 16:00 | Session 4 | Using Jupyter Notebooks for Reproducible Analysis Alicja Skórkowska |
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| 16:00 - 17:00 | Session 5 | Q&A and Discussion | |
The workshop will take place in Training Room 1 at the Francis Crick Institute.
| 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 |
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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.
