Shared research facilities

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:

 

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

By Matthieu Vermeren