Segment Anything in Python for Microscopy Data

Date: February 28th 2024
Time: 1pm - 5pm
Location: HMS, Longwood (In-person)
Cost: Free

About

The Image Analysis Collaboratory and Nikon Imaging Center are 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 to ~20 people. The format will be a combination of tutorials and hands-on exercises.

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

Requirements

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

Scope

  • Introduction to SAM
  • Installation of SAM and relevant packages
  • Segment everything and visualization
  • Segment with points prompt
  • Segment with box prompt
  • Testing specialized SAM models such as micro-SAM

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