Workshop Description (Intermediate Course)

The analysis of imaging datasets is both exciting and challenging. New and increasingly powerful techniques try to maximize the information derived from multi-dimensional imaging datasets. Yet, every dataset can be a unique analysis challenge, and packages may not always work out-of-the-box. In this workshop, we will explore some popular computational tools to extract quantitative information from imaging data. Our focus will be to first grasp the principles underlying image analysis, and see how they can be logically applied to different kinds of imaging datasets. We will cover image generation, filtering, object identification, measurement of object properties, and the basics of object tracking. Through a series of stepwise hands-on exercises for each concept, we will build up to the goal of designing a full image analysis pipeline. Some programming experience in Python is highly recommended (but optional). Participants are also welcome to bring their own images and videos for discussion.

Workshop Topics

Day 1:

  • Core concepts and motivation.
  • What is a digital image?
  • Pixel-level operations.

Day 2:

  • Pixel-level operations (cont.)
  • Variance balancing (thresholding)
  • Image segmentation

Day 3

  • Image segmentation (cont.)
  • Feature extraction
  • Intro to Modern Computer Vision

Technical Requirements

A MacOS, Windows or Linux computer with Anaconda– Installed (Python 3.8 version). With this installation you will automatically receive Python interpreter as well as Spyder IDE. Please try to ensure, prior to the workshop, that Anaconda & Spyder have been successfully installed.


Dr. Haripriya Vaidehi Narayanan is a postdoctoral fellow in Prof. Alexander Hoffmann‘s lab in the Department of Microbiology, Immunology, and Molecular Genetics. She is interested in cross-scale collective and emergent dynamics in immune responses. Her current research is on how signaling and regulatory networks within B-cells shape the evolution of antibody responses, using a combination of methods in microscopy, genomics, and multi-scale modeling. Hari received her PhD in 2019 from Prof. Manu Prakash’s lab in Bioengineering at Stanford University, where she worked on insect flight biomechanics, tools for mosquito-borne disease surveillance, and transcriptome analysis in marine invertebrates. She received her B.Tech in Mechanical Engineering and M.Tech in CAD/Automation from the Indian Institute of Technology Bombay, where she worked on designing hardware systems for nanosatellites. Her hobbies include scientific art, amateur astronomy, hiking, biking, comics, and sci-fi/fantasy. Email:



I was afraid this course would be too advanced for me to follow but the way it was taught was very well paced and easy to follow for someone with basic microscopy and python knowledge. –

The instructor takes time to listen to questions and provides clear answer

The instructor is an excellent communicator, listener, clearly answers questions, and a great teacher.

Workshop Details

Prerequisites: Intro to Python (W9) is recommended
Length: 3 days, 3 hrs per day
Level: Intermediate
Location: Boyer 529
Seats Available: 28

Winter 2024 Dates

Jan 23, 24 and 25
1:30 PM – 4:30 PM