UCL Great Ormond Street Institute of Child Health


Great Ormond Street Institute of Child Health


Training & courses

Microscope training

Training is open to all UCL staff and students, including summer students and visiting staff. However, junior researchers (including Masters students, BSc students, summer students) must be supervised by a group member while using high end systems such as the confocals & live imaging systems.

Training on all systems can be requested through the facility booking system.

Please plan ahead. Training slots are often booked up 1-2 weeks in advance.

Microscope training should be done when you have samples ready to image, so the training can be tailored to your needs. Training is not available more than 2 weeks in advance of intended use. The facility manager may suggest an alternative system if more appropriate for the users samples. For example, very thin sections of a few microns & cell monolayers are often better imaged on a widefield microscope rather than a confocal.

Custom image analysis

I can offer customized scripts and image analysis workflows by collaboration. Please contact me if you would like to discuss this.

Published Macros available on the publications page, here...

Image processing Courses

An image analysis course is available for imaging facility users. This will run twice a year and is advertised internally.

Feedback from previous courses is overwhelmingly positive. Click this link to see all feedback.

    The course is spread over 3 days (10am-5pm) and offers an introduction to image analysis with the free software ImageJ / Fiji.

    It is a mixture of lectures, demos, hands on sessions and exercises.

    Day 1 Understanding digital images. Bit depth, brightness, colours & pixels. ImageJ / Fiji basics, getting to grips with the software. Image presentation (generating figures for publication). ROIs and simple measurements.

    Day 2 Image analysis. Pre-processing (Filters, background), thresholding for feature identification and counting. Alterntaive segmentation strategies. 2D 3D and timeseries. Identifying double / triple stained cells, (and why this isn't colocalisation).

    Day 3 ImageJ / Fiji macros. Recording and writing custom scripts to automate image analysis.

    The course is designed as a single course. You should attend all 3 days. However, if you have attended previous IA courses at ICH you are welcome to join for Day 3 for the macros session.

    Course Fees

    • Free for ICH imaging facility users. You must be an active registered user of the facility.
    • UCL staff and students can request a place on upcoming courses here. If space is available you will be contacted 4 weeks before the course and offered a free place.