Overview

Representatives from DAIM will be delivering an introduction to image analysis workshop in the Learning Zone @ MMC 2025 from 12:40 - 14:00 on July 1st 2025. We’ll commence with a brief introduction to the topic of image analysis and why it’s necessary to ensure reproducible results are derived from microscopy data. We’ll then run through a number of demonstrations to show how you can get started performing simple tasks like counting objects using three popular platforms for image analysis: FIJI, napari and Jupyter notebooks.

What Will I Learn?

You design your experiment, prepare your samples, acquire your images on a microscope and then transfer all your data to some storage device - now what? How do you go about converting all those images into a graph that succinctly communicates the result of your experiment? In this session, you will learn why manual inspection of your images (even with the use of “analysis” software) is generally a bad idea - aside from being tedious and time-consuming (and often impractical for very large data sets), it introduces (unconscious) bias into your analysis. You will learn what image analysis is, what it can (and, more importantly, what it cannot) do and how you can go about taking advantage of it (spoiler alert: it’s easier to get started than you think).

The demonstrations will illustrate a simple workflow, consisting of a number of simple steps, designed to accomplish the goal of counting objects in a microscopy image. The steps involved will vary slightly depending on the platform used, but will resemble the following:

1. Opening images
2. Using filters to suppress noise
3. Segmenting images using grey level thresholding
4. Counting objects
5. Basic morphological quantification

Slides & Other Materials

All slides are freely available on Google Drive and all code is available from this GitHub repository.

Schedule

12:40 - 12:50	Learning Zone Seminar Room	Open Source Software for Image Analysis	Dave Barry, Francis Crick Institute
12:50 - 13:15	Learning Zone Seminar Room	Counting objects using FIJI	Sara Salgueiro Torres, Francis Crick Institute
13:15 - 13:40	Learning Zone Seminar Room	Counting objects using a Jupyter Notebook	Stefania Marcotti, King's College London
13:40 - 14:00	Learning Zone Seminar Room	Counting objects using napari	Martin Jones, Francis Crick Institute