General Information

This 2 day, in-person course will teach introductory image analysis using napari, a Python-based image viewer. We will start from first principles, so no prior image analysis or coding experience is necessary.

We will focus on the analysis of light microscopy data, including the fundamentals of how to design and optimise a light microscopy experiment. It is aimed at anyone who is / will be working with light microscopy data as part of their research projects - and is open to anyone at UCL.

As napari is a Python-based image viewer, we will be covering some introductory concepts in Python as part of this course. Note: no prior experience is necessary, but some introductory knowledge would be useful e.g. from following the online software carpentry course or an in-person course at UCL.

After attending the workshop you will be able to:

• Open and manipulate light microscopy images in napari
• Understand the structure of image data e.g. pixel values, dimensions, bit depth…
• Read image metadata with Python
• Install napari plugins
• Create image histograms, and adjust image display in napari
• Open and navigate multi-dimensional images (e.g. 3D, time series, RGB, multi-channel)
• Explain the pros and cons of common image file formats (e.g. tiff, zarr, png and jpeg)
• Segment cells / nuclei in napari manually, and with simple automated methods like filtering, thresholding and connected components.
• Make measurements from segmented features and export them for further analysis
• Describe the key steps in designing a light microscopy experiment and choosing acquisition settings

Note: we won't be providing lunch or refreshments for this course, so please either bring something with you or use the 1-hour lunch breaks to buy something nearby.

Where: B07 - Teal Room, UCL Torrington Place Training Centre, 1-19 Torrington Place, Fitzrovia, London WC1E 7HB. Get directions with OpenStreetMap or Google Maps.

When: June 10-11, 2026; 9:30am - 5:00 pm BST Add to your Google Calendar.

Signup: To signup for the course, please fill out the registration form. The deadline for registration is 5pm on 27th May, and selected participants will be informed by the 29th May.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. Before joining the course, please follow the instructions on the the lesson homepage. This will guide you through setting up the required software, and downloading the required data. If you would prefer to work through this with an instructor's help, please join the drop-in session at 09:30am on the first day of the course.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

• The room is wheelchair / scooter accessible.
• Accessible restrooms are available.

Please see the AccessAble guide for more information about the venue (1-19 Torrington Place). We are dedicated to providing a positive and accessible learning environment for all. We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information. However, we do want to help create an inclusive, accessible experience for all participants. We encourage you to share any information that would be helpful to make your experience accessible. To request an accommodation for this workshop, or to ask any questions, please send us an email.

Contact: Please email k.meechan@ucl.ac.uk or arc.education@ucl.ac.uk for more information.

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Code of Conduct

Everyone who participates in our courses is required to conform to the Code of Conduct.

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Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

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Surveys

Please be sure to complete this survey after the workshop:

Post-workshop Survey

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Schedule

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