Fluorescence image analysis workshop
Introduction to BioImage Analysis for Microscopy - GloBIAS & CNR Naples 2025
7-11 July 2025
Consiglio Nazionale delle Ricerche (CNR)
Istituto degli endotipi, in oncologia, metabolismo e immunologia (IEOMI)
“G. SALVATORE”
Naples (Italy)
Local organizers:
Domenico Russo, Simone Di Paola, Seetharaman Parashuraman (CNR, Naples)
This training is developed and delivered by Rocco D’Antuono (The Francis Crick Institute, London, UK), Ana Stojiljkovic (University of Bern, Switzerland), Sebastian Gonzalez Tirado (Heidelberg University, Germany), Daniel Waiger (Hebrew University of Jerusalem, Rehovot, Israel).
Learning outcomes:
at the end of the course, trainees will be able to describe the basic concepts of fluorescence image formation and bioimage analysis, quantify shape and fluorescence intensity of cells and organelles, measure colocalization, measure spatial relationships between classed of objects, track objects in 3D, render image data sets in 3D for animations, run basic 3D segmentation, create basic plots to show results, prepare figures for scientific publications.
The course will include talks, practical sessions, and project work on trainees own data or test data sets from public image databases.
Programme:
Day 1
Monday 7th July 2025
Introduction & Basics of Image Analysis
| Time | Topic |
|---|---|
| 08:30-09:00 | Introduction to the course - Domenico Russo, Simone Di Paola, Seetharaman Parashuraman |
| 09:00-09:30 | Participants self introduction - All Trainers and Trainees |
| 09:30-10:30 | Image formation in fluorescence microscopy - Rocco D’Antuono |
| 10:30-11:00 | Coffee break |
| 11:00-12:00 | Introduction to bioimage analysis - Rocco D’Antuono |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | Introduction to FIJI - Daniel Waiger |
| 14:00-15:00 | Showcase of FIJI plugins for bioimage analysis - All trainers |
| 15:00-15:30 | Coffee break |
| 15:30-16:30 | ilastik for interactive segmentation - Daniel Waiger |
| 16:30-17:30 | Project working groups with own data or test data - Ana Stojilkovic and Rocco D’Antuono |
Day 2
Tuesday 8th July 2025
Advanced Image Processing
| Time | Topic |
|---|---|
| 09:00-09:30 | Progress check on project work and trainees’ expectations |
| 09:30-10:00 | Introduction to ImageJ macro language - Ana Stojiljkovic |
| 10:00-10:30 | Automatisation of bioimage analysis with ImageJ macro powered by large language models- Daniel Waiger |
| 10:30-11:00 | Coffee break |
| 11:00-12:00 | ImageJ macro practical session - Ana Stojiljkovic and Daniel Waiger |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | TrackMate for cell and organelle tracking - Sebastian Gonzalez Tirado |
| 14:00-15:00 | Tracking hands-on session - Sebastian Gonzalez Tirado and Rocco D’Antuono |
| 15:00-15:30 | Coffee break |
| 15:30-17:00 | Project working groups with own data or test data - Daniel Waiger and Sebastian Gonzalez Tirado |
| 17:00-17:30 | Progress report on project work - How to do better? - All the trainers |
Day 3
Wednesday 9th July 2025
Batch analysis of large data sets
| Time | Topic |
|---|---|
| 09:00-09:30 | Progress check on project work and trainees’ expectations |
| 09:30-10:30 | CellProfiler pipelines for the analysis of HCS data - Ana Stojiljkovic |
| 10:30-11:00 | Coffee break |
| 11:00-12:00 | CellProfiler practical session - Ana Stojiljkovic and Rocco D’Antuono |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | CellProfiler Analyst to visualise and plot image analysis results - Rocco D’Antuono and Ana Stojiljkovic |
| 14:00-15:00 | Build your own CellProfiler pipeline - hands-on session - Ana Stojiljkovic and Rocco D’Antuono |
| 15:00-15:30 | Coffee break |
| 15:30-17:00 | Project working groups with own data or test data - Rocco D’Antuono and Ana Stojilkovic |
| 17:00-18:00 | Progress report on project work - How to do better? - All the trainers |
Day 4
Thursday 10th July 2025
3D Segmentation and figure preparation
| Time | Topic |
|---|---|
| 09:00-09:30 | Progress check on project work and trainees expectations |
| 09:30-10:30 | napari for 3D rendering and segmentation - Rocco D’Antuono and Sebastian Gonzalez Tirado |
| 10:30-11:00 | Coffee break |
| 11:00-12:00 | napari for 3D segmentation - practical session - Sebastian Gonzalez Tirado and Rocco D’Antuono |
| 12:00-13:00 | Lunch |
| 13:00-14:00 | Figure preparation with FIJI and Inkscape - Rocco D’Antuono |
| 14:00-15:00 | Project working groups with own data or test data - Sebastian Gonzalez Tirado and Ana Stojilkovic |
| 15:00-15:30 | Coffee break |
| 15:30-16:00 | Project working - Conclusions - All the Trainers |
| 16:00-17:00 | Trainees presentation on own project work |
| 17:00-17:30 | Wrap up on the use of open-source for bioimage analysis- All the trainers |
Day 5
Friday 11th July 2025
Introduction to ZEISS arivis Advanced Image Analysis
| Time | Topic |
|---|---|
| 09:00-10:30 | Part 1 |
| 10:30-11:00 | Coffee break |
| 11:00-12:00 | Part 2 |
| 12:00-13:00 | Lunch |
| 13:00-15:00 | Part 3 |
| 15:00-15:30 | Coffee break |
| 15:30-17:00 | Part 4 |
Preparation for the course
Installation instructions
Day 1
Two software needed: FIJI and ilastik. Trainees need to
-
Download FIJI from www.fiji.sc, selecting your operative system, and extract the .zip folder. The softwar eis ready for use.
-
Download and install ilastik from https://www.ilastik.org/, selecting your operative system.
Day 2
The hands-on session will rely on the use of FIJI and ilastik (installed on Day 1).
Day 3
Two software needed: CellProfiler and CellProfiler Analyst. Trainees need to
-
Download and install CellProfiler from https://cellprofiler.org/, selecting your operative system.
-
Download and install CellProfiler Analyst https://cellprofileranalyst.org/.
Day 4
Two sofware needed: Inkscape for figure preparation and napari.
-
Download and install Inkscape from inkscape.org
-
Install napari
During the hands-on sessions we will extensively try and retry the software installation with conda environments, however to gain some practice and proceed smoothly to more interesting topics, please proceed with the following homework before the workshop
1. Install Anaconda Navigator
2. Install napari within conda prompt
Please make sure to have at least 10-15 GB free on the pc you will bring with you for participating in the workshop. Please let us know well in advance if you cannot bring a pc with you, we might be able to get a loan, however this is not guaranteed and you might risk to have no pc to follow along.
1. Install Anaconda Navigator
This is a method that use the graphical user interface to download and install Anaconda Navigator. Please visit https://docs.anaconda.com/ and click on the green button “Download Anaconda”. You will be asked to provide an email address and will receive the link to the download page, where you will choose the version for your OS.
Before installing Anaconda Navigator, please identify a folder in your computer over which you have full permission of read and write file: we will create and update many times conda environments, this means that the software will install and remove files all the times.
2. Install napari within conda prompt
The successful installation of Anaconda Navigator will make available an app called “Anaconda prompt”. Thsi is the terminal that we will use to create and work with conda environments.
a) Update conda, by typing the following line and pressing Enter.
conda update -n base -c conda-forge conda
b) create a new environment with a meaningful name: substitute with your choice the string “mymeaningfulname”. E.g. “cbias-workshop-env”. Please do not simplify with “napari-env”, as half of the tutorial use that and you might risk to overwrite a previous environment which contain packages used in previous analyses.
conda create -n mymeaningfulname-env python=3.12
c) activate the new environment
conda activate mymeaningfulname-env
You should notice a change in the prompt where the name base at the beginning of the prompt has been changed to “mymeaningfulname-env”. This confirms that it is safe to install new packages, as you are not altering the base environment (safe choice is not touch “base”).
d) install napari
conda install -c conda-forge napari pyqt
e) check that napari opens At this point, if no error appears in the terminal as result of the operations above, you are ready to open napari executing
napari
Create a conda environment with a recipe
If a working environment cannot be created through the commands above, the following recipe can be used to create an environment with napari
a) Download the file cbias2024-napari-env.yml into a local folder
b) use the Anaconda prompt to navigate to the local folder and execute
conda env create -f cbias2024-napari-env.yml
This should create an environment with the same name of the .yml file unless otherwise specified.
c) check that napari opens
At this point, if no error appears in the terminal as result of the operations above, you are ready to open napari executing
napari