Segment Anything in Python for Microscopy Data


The Image Analysis Collaboratory is running a workshop: Segment Anything (SAM) in Python. SAM is a deep learning-based segmentation model introduced by researchers at Meta. Originally SAM was trained with natural images, however, since its publication multiple different domain-specific fine-tuned models have been published. In this workshop, we will focus on using SAM using Python for different segmentation tasks and learn about different parameters to fine-tune results. Participation will be limited.
The format will be a combination of tutorials and hands-on exercises.


Monday 11th November 2024, 1 PM to 5 PM
Wednesday 13th November 2024, 1 PM to 5 PM


Harvard Medical School.



Skill level:



This course will be taught in Python so previous coding experience in Python and a laptop is required.


  1. Introduction to SAM
  2. Installation of SAM and relevant packages
  3. Segment everything and visualization
  4. Segment with points prompt
  5. Segment with box prompt
  6. Testing specialized SAM models such as micro-SAM


Free of charge.


We will open for applications some time in advance—to be notified, please join our mailing list, if you didn’t already.

Deadline for application:



Mostly based on your short motivation. In case of oversubscription, the available spaces will be distributed evenly between labs and departments.


Our workshops are often oversubscribed by a factor of two or three, so please be considerate to your fellow applicants and let us know well in advance if you are accepted and cannot make it.

Looking forward to see you there
Ranit Karmakar, Antoine Ruzette, Federico Gasparoli, Maria Theiss, and Simon F. Nørrelykke.