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.

No fee will be charged for participation, but attendance is restricted to staff from The Crick, King’s College London, University College London and Imperial College London.

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
• Vanessa Dao, Francis Crick Institute

Program

Monday, April 8th
10:00 - 11:00	Session 1	Introduction to Image Analysis
	Understanding the importance of image analysis in reproducible science Foundational concepts of image formation and quantification
11:00 - 11:15	Coffee Break
11:15 - 13:00	Session 2	Image Pre-Processing & Segmentation
	Practical Application: Image filtering and basic image segmentation.
13:00 - 14:00	Lunch
14:00 - 15:30	Session 3	Analysing Images
	Practical Application: Quantifying morphology of objects in a 2D image
15:30 - 15:50	Coffee Break
15:50 - 17:30	Session 4	Introduction to Batch Processing
	Practical Application: Record commands to form the basis of a script for automated processing and analysis
17:30	Pub
Tuesday, April 9th
09:30 - 10:30	Session 5	Introduction to Python and installations
	Creating Pyton environments Installing Jupyter notebooks and napari
10:30 - 10:50	Coffee Break
10:50 - 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 Lecture Theatre 4, Bush House (South East Wing), King’s College, London WC2B 4PJ:

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://doi.org/10.5281/zenodo.10952549

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.