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Basics of Bioimage Analysis in Python

Center for Integrative Infectious Disease Research (CIID), Heidelberg

01.07.2024 - 02.07.2024 and 08.07.2024 - 09.07.2024

We are pleased to announce a Basics of Bioimage Analysis in Python course organized by Infectious Diseases Imaging Platform (IDIP) in collaboration with the EMBL Data Science Center, Bioimage analysis services (, scheduled for July 1st + 2nd and 8th + 9th 2024 at the Center for Integrative Infectious Disease Research, Heidelberg University. In this 4-day practical course, you will be introduced to digital image essentials and will learn how to use python for image analysis, taking advantage of the large and growing number of specialized python libraries. You will learn how to achieve image visualization with the python-based tool napari, which allows powerful and flexible n-dimensional image data visualisation, including overlay of segmentation and annotation layers. As python is currently the most popular language for scientific computing and data science, learning more about how to handle image analysis in python will enable you to access a rapidly-advancing and diverse pool of knowledge. This course is tailored for PhD students and postdocs keen on learning how to bring their image analysis skills to the next level. 
Basic prior python knowledge is recommended.
Further information about this course will be provided here shortly.
Key Course Highlights: 
  • Jupyter notebook and napari for image visualization
  • Digital image basics and handling of multi-dimensional data
  • Basic concepts of image analysis including thresholding, filtering, projections
  • Segmentation and measurement extraction of images and labels
Preliminary Course Details:  
Duration: 4 days, from 10:00-17:00. This includes a lunch break (1 hr) and two coffee breaks (20 minutes), resulting in approximately 5 hr of teaching time. As there are 6 modules per day that makes ~45 minutes per module.
Participation: The course is limited to 20 participants able to attend in person. Participants should bring their own laptop.
Registration: individuals interested in attending should send an email to including the basic contact information (name, position, group, institute). Participation spots are distributed on a first come, first served basis.
Costs: The course is free of charge. 
Contact: For any inquiries or additional information, please feel free to reach out to 
We look forward to seeing you at the workshop!

Preliminary Programme

Monday (July 01.)
​Basics of python programming.

Tuesday (July 02.)
​Image inspection basics

Monday (July 08.)
Image analysis basics I

Tuesday (July 09.)
Image analysis basics II


The workshop is limited to 20 participants.

To register, the applicants need to send a short email to

Participation spots are distributed on a first come, first served basis. 

The workshop is free of charge.
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