Help create a nudibranch brain connectome

Just as a genome is all of the genes that an organism has, a brain connectome is all of the synaptic connections that a brain has. We are determining the connectome of the brain from a nudibranch mollusc, called Berghia stephanieae. We are collaborating with Jeff Lichtman's lab at Harvard University. Together, we have taken part of the brain, called the rhinophore ganglion, and cut it into slices that are only 30 nanometers thick. Thousands of these ultrathin sections were imaged at 4nm resolution using an electron microscope. The images were then stitched together and aligned so that neurons can be traced from one section to the next. See this example from a mammalian brain (https://www.microns-explorer.org/cortical-mm3). This process is called segmentation. The images have been automatically segmented using a process that involved machine learning.

Now comes the part where we need your help.  The automatic segmentation has errors in it. We need you to help proofread and correct this segmentation. This is similar work that has been done in mouse visual cortex (https://www.nature.com/articles/s41586-025-08790-w) and the fruit fly brain (https://www.nature.com/articles/s41586-024-07558-y). 

The work is tedious; you will be clicking through in images and looking at detailed ultrastructure. You need to devote blocks of time to the task.

In your essay, please indicate why you are interested in this opportunity. Also share an example of when you devoted time to careful detailed work.

Name of research group, project, or lab
Katz Lab - Berghia Connectome Project
Why participate in this opportunity?

This project will provide an opportunity to work with cutting-edge, high-resolution electron microscopy dataset. The connectomics approach has been gaining importance in neuroscience research. This work experience will you an opportunity to gain a deeper understanding of how connectomes are generated and give them an edge when applying for future research opportunities in neuroscience. You will be part of the dynamic and fun Katz lab, which includes a postdoc, a PhD student, an MS student, and several undergraduates. You will be supervised by a graduate student, Alex Cook, who has been working directly with the Lichtman Lab.  Your work will help us determine if molluscan brains have similar circuit motifs to our own brains even if they look different.

Logistics Information:
Subject Category
Neuroscience
Student ranks applicable
Freshman
Sophomore
Junior
Student qualifications

This project is best for people who have patience. It involves staring at a computer screen and marking specific points in thousands of similar looking images in the dataset with either a mouse or a touch pad. Students will also be required to read software manuals to enable troubleshooting. An interest to learn new software and patience to do repetitive tasks is required. 

Time commitment
5-7 h/wk
8-10 h/wk
Position Types and Compensation
Research - Independent Study or Research Assistant credit
Research - Paid, Work-Study Required
Number of openings
2
Techniques learned

Students will learn about the Neuroglancer software platform, but they will also learn about all of the other research in the lab and the work of our collaborators.

Project start
Fall Semester 2025
Contact Information:
Mentor
pkatz@umass.edu
Faculty
Name of project director or principal investigator
Paul Katz
Email address of project director or principal investigator
pkatz@umass.edu
2 sp. | 11 appl.
Hours
5-7 h/wk (+1)
5-7 h/wk8-10 h/wk
Project categories
Neuroscience