Overview

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.

The application deadline for this workshop has now passed.

Instructors

• Dave Barry, Francis Crick Institute
• Martin Jones, Francis Crick Institute
• Stefania Marcotti, King's College London
• Temilade Adegoke, University of Limerick
• Brenton Cavanagh, Royal College of Surgeons in Ireland
• Moein Azimi, Royal College of Surgeons in Ireland

Preparation

1. Please remember to bring your laptop (and charger).
2. Please install the required software before the workshop - follow the installation instructions on this page.
3. Download the workshop data by clicking on the link to the ZIP archive at the top of this page.
4. You have been assigned to a specific group, with whom you will be sitting - you can find your group number here.
5. PLEASE CONTACT US BEFORE THE WORKSHOP IF YOU ENCOUNTER ANY DIFFICULTIES WITH ANY OF THE ABOVE.

Program

Please note that all catering, as well as attendance of the social on the evening of the 24th, is covered by your registration fee.

Wednesday, April 24th
09:30 - 10:30	Registration
10:30 - 11:45	Session 1	Introduction - Automated Image Analysis is Essential for Reproducible Science
	Why manual analysis is a bad idea Embracing uncertainty What is metadata and why do you need it
11:45 - 12:00	Coffee Break
12:00 - 13:30	Session 2	Image Pre-Processing, Segmentation & Analysis
	Practical Applications: Basic segmentation using thresholding Use of filtering to suppress noise Obtaining numbers from images
13:30 - 14:30	Lunch
14:30 - 16:15	Session 3	Assembling Pipelines and Interpreting Results
	Practical Applications: Counting and quantifying morphology of objects Quantifying fluorescence intensities
16:15 - 16:30	Coffee Break
16:30 - 18:00	Session 4	Introduction to Batch Processing
	Practical Application: Record commands to form the basis of a script
18:00 - ?	Evening Social	Against the Grain, 11 Wexford St, Dublin, D02 HY84
Thursday, April 25th
09:30 - 10:30	Session 5	Introduction to Python and installations
	Creating Python environments Installing Jupyter notebooks and napari
10:30 - 10:45	Coffee Break
10:45 - 12:30	Session 6	Using Jupyter Notebooks for Reproducible Analysis
	Variables and arrays Practical Application: quantify morphology of objects in a 2D image with Jupyter
12:30 - 13:30	Lunch
13:30 - 15:30	Session 7	Using napari as an image analysis tool and as a viewer
	Overview of napari GUI Practical Application: batch processing with Jupyter Practical Application: using napari as a viewer from Jupyter

Venue

The workshop will take place in the Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin 2, D02 YN77:

<iframe src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d1191.1111825530415!2d-6.2625410119408595!3d53.33927557919478!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x48670e9e94070b7b%3A0xd480ab326993b5ef!2sRoyal%20College%20of%20Surgeons%20in%20Ireland%20(RCSI)!5e0!3m2!1sen!2suk!4v1713202098336!5m2!1sen!2suk" width="100%" height="450" style="border:0;" allowfullscreen="" loading="lazy" referrerpolicy="no-referrer-when-downgrade"></iframe>

Note that the building entrance is on York Street. The workshop room will be sign-posted from the main entrance.

At 18:00 on Wednesday the 24th, we will walk a few hundred metres to Against the Grain, 11 Wexford St, Dublin, D02 HY84 for food and drinks - we have an area reseved on the 1st floor:

<iframe src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d2382.345731538679!2d-6.268058322993518!3d53.33706707541738!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x48670e9fd2a70a05%3A0x759ae9759599eae6!2sAgainst%20the%20Grain!5e0!3m2!1sen!2suk!4v1713208125766!5m2!1sen!2suk" width="100%" height="450" style="border:0;" allowfullscreen="" loading="lazy" referrerpolicy="no-referrer-when-downgrade"></iframe>

Organisers

• Dave Barry, Francis Crick Institute
• Martin Jones, Francis Crick Institute
• Stefania Marcotti, King's College London
• Heiko Duessman, Royal College of Surgeons in Ireland
• Kerry Thompson, University of Galway
• Emma McDermott, University of Galway

Slides

All of the presentation material for this workshop is available on Zenodo and can be referenced as follows:

Barry, D. J., Jones, M. and Marcotti, S. (2024) Introduction to Image Analysis. Zenodo. doi: https://dx.doi.org/10.5281/zenodo.11072759

Previous Workshops

Date	Venue	Content
8 / 9th April 2024	King's College London	Click here

FAQ

1. 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.

2. 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.