Training programmes by CMVM Research Facilities
Training courses are regularly offered by expert technical facility managers and staff
Future events
“Introduction to image processing and analysis with Fiji/ImageJ and other analysis freeware” - February/March 2024
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: £150 for academia, £200 for commercial. Please give 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: 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.
NOTE3: 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:
Monday 19th of February, 3-5pm: What is an 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.
Friday 23rd of February, 2-5pm: Introduction to Fiji
- Installation, update, chosen extensions.
- Looking at simple images
- Stacks, movies, projections, 3D viewing
- Checking picture quality
- Mosaic stitching
- Measurements, plot profile, 3D plots
- Regions of Interest
- How to make a scientific figure in five minutes using Fiji
Monday 26th of February, 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 1st of March, 2-5pm: Artificial Intelligence for segmentation
- Using Artificial Intelligence for segmentation and analysis with standalone and Fiji-integrated software: Stardist, Ilastik, CellPose
Monday 4th of March, 2-5pm: Skeletons and 3D images
- Skeletonising complex objects and their analysis
- 3D image analysis with 3D suite and 3D tools
Friday 8th of March, 2-5pm: Tracking
- Manual tracking
- Trackmate, StarDist and Label images+TrackMate
Monday 11th of March, 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 ChatGPT to write a macro: advantages and limitation.
Friday 15th of March, 2-5pm : CellProfiler and CellProfiler Analyst
- Introduction to CellProfiler and CellProfiler Analyst: making a custom pipeline from available tools
Monday 18th of March, 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.
Monday 25th of March, 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 - 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