What Is the Bioimage Analysis Bootcamp?

The Bioimage Analysis Bootcamp, established and organized by the Cimini Lab at the Broad Institute, is an intensive, week-long training designed to help biologists and researchers strengthen their image analysis skills. The course focuses on decision-making principles in bioimage analysis — such as how to choose the right tools, assess data quality, and determine when an analysis is “good enough.”

Participants gain a broad introduction to the rapidly evolving landscape of open-source image analysis software for light microscopy. Through lectures, demonstrations, and guided hands-on exercises, attendees learn directly from experts with deep connections to the global bioimage analysis community and develop practical strategies for applying these lessons within their own research environments.

What Do Past Participants Say?

“It was surprisingly understandable without prior knowledge in coding, microscopy or image processing. We got quickly to do some basic and less basic image processing analysis. ”
— Anonymous attendee

"After this bootcamp, I am immensely better equipped to consider different tools and identify one or two approaches that might be best suited for any particular image analysis problem I need to tackle.  It's clear how what I learned will greatly benefit the efficiency and impact of my image analysis workflows."
— Anonymous attendee

“I personally learned so many things—some of which I honestly thought were beyond my learning curve.”
— Postdoctoral attendee

What Do Participants Learn?

Participants gain practical, hands-on experience with several widely used, free, and open-source tools for bioimage analysis. The training includes:

• Manual annotation and data labeling

• Classical image segmentation approaches

• Retraining deep learning models

• Selecting appropriate tools for different biological questions

Attendees receive personalized guidance from expert image analysts who share best practices, demonstrate real-world applications, and help participants integrate these approaches into their own research groups or institutions.

Who Should Attend This Bootcamp?

The Bioimage Analysis Bootcamp is designed for biologists and researchers experienced in light microscopy who want to gain confidence in image analysis decision-making. It also benefits scientists, data analysts, and technical professionals interested in expanding their knowledge of open-source image analysis tools and applying them to biological data.

Participants come from a range of scientific and technical backgrounds and share a common goal of integrating quantitative image analysis into their research.
Note: All attendees are strongly encouraged to complete the Microtutor Course in Fluorescence Microscopy before the bootcamp.

What Makes This Bootcamp Stand Out?

The Bioimage Analysis Bootcamp brings together a diverse community of researchers eager to grow their skills and confidence in bioimage analysis. Participants highlight the supportive teaching environment, the depth of the material, and the hands-on opportunity to apply what they’ve learned to their own data.

“I unironically had no qualms or issues/notes with the course; it was really interesting and kept my focus the whole week.”
— Anonymous attendee

"Prior to taking the course, I dreaded image analysis simply because I was not sure what tool/program are appropriate to use as there is an overwhelming amount of information online. After this 1-week bootcamp, I feel confident in my ability to select the right tool for my purpose, and feel excited to begin analyzing my own results. This course has definitely made a positive impact in my research career."

— Anonymous attendee

"Before attending, I had limited experience with bioimage analysis. Though I was able to extract quantitative information from confocal microscopy images, I largely relied on one or two existing pipelines within my previous lab and was familiar with only one software package. When presented with a new image types or analysis challenge, I then did not exactly know which tools to use. Thanks to Beth and the course organizers, I now have a much clearer understanding of the principles and workflow behind bioimage analysis. The course exposed me to a diverse set of analytical software tools, open-source platforms and plugin systems, command-line and computational workflows, and even machine learning-based approaches for optimizing image analysis performance. As a result, I now have a clearer idea of the next steps to approach my current imaging datasets. Equally valuable were the resources introduced throughout the course, including documentation, community forums, and learning platforms. These resources give me confidence that I can continue learning independently and troubleshoot problems as they arise."

— Anonymous attendee

We’re excited to bring this same energy, expertise, and collaborative spirit to the 2026 Bioimage Analysis Bootcamp.

When and Where Is Our Bootcamp?

Our past Bioimage Analysis Bootcamp took place June 1-5, 2026, from 9:00 AM to 5:00 PM each day.
The course is held in person at the Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts.**

*This training is in-person only, allowing participants to fully engage in hands-on exercises, interactive sessions, and live discussions with expert instructors.

Our next bootcamp will likely be held in late 2026 or early 2027; please let us know if you would like us to contact you when application opens (approximately early fall 2026).

For additional questions about registration, logistics, or course content, contact us at imagingadmin@broadinstitute.org