CAMDU 2 Day Image Analysis Workshop 3-4 July 2025
Course Leader
Laura Cooper, camdu@warwick.ac.uk and l.cooper.5@warwick.ac.uk
Schedule
3rd July |
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Time |
Location |
Activity |
| 10:00 | CTU T0.09 | Fiji says Hello! |
| 10:30 | CTU T0.09 | Introduction to Image Analysis |
| 11:30 | CTU T0.09 | Introduction to Programming in Fiji |
| 12:00 | Break | |
| 13:00 | CTU T0.08 | Hands on with Fiji: See worksheets for topics |
| 16:00 | Finish | |
4th July |
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| 10:00 | CTU T0.08 | Technical set up for Python and Napari |
| 11:00 | CTU T0.08 | Image Analysis with Python and Napari |
| 12:00 | Break | |
| 13:00 | CTU T0.08 | Hands on: CAMDU Challenge or Bring Your Own Data |
| 15:45 | CTU T0.08 | Closing comments and feedback |
| 16:00 | Finish | |
Course Information
Before the course
3rd July
If you have any issues please email me so I can help!
4th July
There is a mixture of Python experience among the attendees. The aim of this part of the course is not to teach python, but to give you an idea of how it can be used for image analysis.
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Everyone: Download and unzip this folder (make sure you know where you've saved it)
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Beginner Python users: I recommend installing AnacondaLink opens in a new window. After installing please follow the step by step instructions in AnacondaSetup.pdf.
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Experienced Python users: Set up a virtual or conda environment with Python 3.9. Within the environment please install napariLink opens in a new window (I use ​python -m pip install napari[all], check the instructions for your operating system if you have issues). I will be using jupyter notebooks on the day, so if you'd like to follow along with me, please install jupyter notebookLink opens in a new window. However, if you'd rather use your favourite IDE that should be fine too. After activating the environment, please check you can run the SetupCheck.py script (or SetupCheck.ipynb if using jupyter notebook) from the attached .zip folder.
You should get a Napari window that opens and looks like the picture SetupCheck.png. If you do not, please email me so I can help! There is an hour on the day to fix issues, but it will be easier if we can sort out some of them before. You can also come and find me during the Drop InLink opens in a new window on Tuesday. If we aren't able to get you set up can still attend the training, but will not be able to follow along with the coding. You are welcome to use your own images during the training session if they are in .tif format.
CAMDU Challenge
Download the data set provided. The data set contains six microscopy images (.tif files), each with three channels: in the first, you have a a GFP-tagged protein of interest, which forms foci; on the second a cytoplasmic marker; and on the third a brightfield image of the cells.
Write a well annotated script (or scripts) that counts the foci inside each cell. This will involve:
- Identifying cell boundaries
- Detecting the relevant foci in the GFP channel
- Counting the foci to specific cells
Use the most in focus plane for identifying the cell boundaries. Use a maximum projection for detecting the foci. You do no need to use the brightfield channel.