Future events
If you have ever wanted to get more from your microscopes/camera than just pretty pictures, “Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware” workshop is for you.
Recording of the course will be made available to those who have registered.
TO REGISTER: email Matthieu.Vermeren@ed.ac.uk
Location: wherever you have access to a computer and a good internet.
Fee: £180 for academia, £360 for commercial. Please give me the name of your PI and the Centre/institute/University where you are working. UoE users need to provide People & Money details.
Pre-requisites: You will need to install the following software:
- Fiji (https://imagej.net/software/fiji/).
- Ilastik (https://www.ilastik.org/)
- CellProfiler and CellProfiler Analyst (https://cellprofiler.org/)
NOTE 1: You probably will need to ask an administrator for permission. Install well on time.
NOTE 2: We are using Fiji, which has extra functionalities over ImageJ. Make sure you install Fiji.
NOTE 3: Fiji needs installing at the root of your C:\ drive, nowhere else.
Course material in form of test files and detailed booklets will be provided.
Programme:
Tuesday 22 April 2025, 3-5pm: What is a (good) image?
- What is a (good) digital image, and why you should care that your data is suitable for analysis.
- What you can and cannot do with digital images: avoiding manipulation and fraud.
- FAIR principles: Why sharing your data with the wide world is good science
- Installation of Fiji, update, chosen extensions.
Friday 25 April 2025, 2-5pm: Introduction to Fiji
- Simple images
- Stacks, movies, projections, 3D viewing
- How to make a scientific figure in five minutes using Fiji
- Checking picture quality
- Mosaic stitching
- Measurements, plot profile, 3D plots
- Regions of Interest
Tuesday 29 April 2025, 2-5pm: Segmentation
- Segmentation: separate what you are interested in from the rest of your image
- Filters, mathematical operations
- Thresholding (simple, colour)
- Modifying binary figures: erosion, dilation, watersheds…
Friday 2 May 2025, 2-5pm: Artificial Intelligence for segmentation
- Using Artificial Intelligence for segmentation and analysis with standalone and Fiji-integrated software: Stardist, Ilastik, CellPose
Tuesday 6 May 2025, 2-5pm: Skeletons and 3D images
- Skeletonising complex objects and their analysis
- 3D image analysis with 3D suite and 3D tools
Friday 9 May 2025, 2-5pm: Tracking
- Manual tracking
- Trackmate, AI segmentation+Trackmate, and Label images+TrackMate
Tuesday 13 May 2025, 2-5pm: Macro writing for beginners
- Introduction to the Macro language and writing simple macros: automate tasks, get the computer analyse your images for you.
- Using Mistral AI’ Le Chat to write a macro: advantages and limitation.
Friday 16 May 2025, 2-5pm: CellProfiler and CellProfiler Analyst
- Introduction to CellProfiler and CellProfiler Analyst: making a custom pipeline from available tools
Tuesday 20 May 2025, 2-5pm: Colocalisation
- What colocalization means, what it does not.
- Colocalisation: the Coloc2, JACoP, and DIANA plugins, what they do tell you and what they don’t and can’t.
Friday 30 May 2025, 2-5pm: Catch up and Q&A
- Show us your data, we guide your analysis
Past events
Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware - February/March 2024
Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware - September/October 2023
Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware - January/February 2023
Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware - September 2022