Cohort Research Investigating Micro-Scale Optimized Networks (CRIMSON) offers Johns Hopkins University (JHU) students an opportunity to participate in a cutting-edge research experience to map the brain at nanoscale resolution, while building skills to make significant contributions to science in a fun, collaborative environment.

Program Timeline

Application Period Opens:
September 16, 2021
Priority Deadline:
October 10, 2021
Application Period Closes:
October 24, 2021
October 18 – November 3, 2021
Decision Notification:
November 3, 2021
Proofreading Training:
November 8–30, 2021
Academic Session:
December 1, 2021 – May 6, 2022
Core Summer Session:
May 23 – August 19, 2022


As neural-imaging techniques and image-processing capabilities have improved, so has our ability to analyze the brain. We are able to interrogate large volumes of the brain at scales ranging from millimeter to nanometer resolution using a variety of methods, including magnetic resonance imaging (MRI), positron emission tomography/computed tomography (PET/CT), array tomography, CLARITY, and serial section electron microscopy. This has resulted in a deluge of data available for analysis to answer questions that have puzzled humans for centuries.

Computational neuroscience has enabled these efforts to unfold and expand over the last few decades with large-scale projects (e.g., the Human Brain Project, the Human Connectome Project, BRAIN initiative efforts) underway that will revolutionize the way we do brain research. Currently, the community is working to image petabytes (tissue volume of 1 cubic millimeter) of electron microscopy data and reconstruct large brain maps. As a result, we will have the ability to investigate the underlying network structure of these neuronal circuits, working toward unlocking the capability of new, intelligent machine learning algorithms.

These datasets enable the identification of individual neurons, their synaptic connections, and other key features. This will provide information about brain structure and function as well as insight into pathologies. Manually proofreading these datasets, although the most accurate method, is such a monumental effort that it would take years to analyze even a small section of cortex. This approach is infeasible for the larger (petascale) sized volumes being explored in this effort. Therefore, we are currently using computer vision and machine learning to train computers “to see” and automate the process of reconstructing these brain maps, called connectomes.

It is critical to analyze the resulting network estimates to understand their accuracy, so that we can use the underlying information to understand more about intelligence. To support this work, we are looking for talented students to participate in high-impact, cutting-edge research to trace and proofread these putative networks and assess their quality.

We are excited to work with cutting-edge, synapse-resolution connectomics data. You can learn more about our dataset here:

Core Program Description

The CRIMSON program follows the CIRCUIT model but supports a particular project with additional compensation and responsibilities (especially several hundred hours of manual neuroanatomical proofreading). Our program will focus on research in data science, computational neuroscience, machine learning, and artificial intelligence applications.

This program is offered in collaboration with the Hopkins Office of Undergraduate Research (HOUR) at JHU and the Johns Hopkins Applied Physics Laboratory (APL). Program and leadership support will come from the Intelligent Systems Center (ISC) and APL BRAIN (Breakthrough Research in Artificial Intelligence and Neuroscience). The ISC is an APL cross-disciplinary research center spanning machine learning, robotic and autonomous systems, and applied neuroscience. APL BRAIN is a research lab focused on developing synthetic brains to adapt to real-world environments.

Who Should Apply

All students affiliated with JHU are invited to apply! Students do not need a background in neuroscience, computer science, or engineering. However, students should be able to demonstrate a commitment to science and inquiry in their application. Examples of majors include but are not limited to: chemical and biomolecular engineering, biomedical engineering, computer science, computer engineering, mechanical engineering, electrical engineering, neuroscience, biology, molecular and cellular biology, and applied mathematics & statistics. There is not a minimum GPA requirement to apply.

Trailblazers wanted: We especially encourage applications from trailblazing students. We define trailblazers as high-achieving students from underserved backgrounds (e.g., first-generation students, students from low-income backgrounds), women in STEM, other students who are underrepresented in STEM fields, and those who may not have previously had an opportunity for a research experience. Our program will provide training and mentoring to support students in the broader research community.


Students must be committed to the program and its time requirements.

Our program will provide training and mentoring to support students in the broader research community.

We welcome applications from all students affiliated with JHU through fall 2022.

Apply Here

In our past program session, most applicants were sophomores and juniors. Although we welcome all undergraduate and graduate students, but students must be affiliated with JHU through fall 2022.

Program Details

During Academic Session: Hybrid at JHU Homewood
During Summer Session: On-Site at APL

Schedule: CRIMSON consists of a training session, a part-time academic year session, and a full-time summer session, with the optional opportunity to continue for research credit in fall 2022 and spring 2023.

Students will initially participate in proofreading training through November 2021 (approximately 12 hours per week) as a paid activity as part of their final selection process. Students who successfully complete this training, based on their professionalism and performance, will be invited to be full members of the CRIMSON cohort. Those not ultimately selected may be considered for a spot in the CIRCUIT 2022 class.

CRIMSON cohorts will complete further proofreading assignments and technical training throughout the remainder of the fall semester (12 hours per week) and the spring semester (approximately 20 hours per week). Holidays include Thanksgiving week, winter break (December 21, 2021 – January 3, 2022), Memorial Day, Juneteenth, July 4, and five additional flex vacation days. Students are required to be full-time during intersession. Technical training will consist of online courses pertaining to data science in Python, machine learning, linear algebra, and more. Over the summer, students will continue proofreading and will work within a cohort of peers and mentors on a neuroscience- or machine-learning-themed research project at APL that will result in a poster showcasing original research. Students may optionally continue for academic credit during fall 2022 and spring 2023 with the concurrence of their mentors, which will likely result in coauthorship on a peer-reviewed paper.

Compensation: Compensation has not been finalized, but we expect total compensation of about $14,000, divided between the initial training period in November and continued work through August 2022. We will provide research credit during the school year following the core session for those students who qualify.

Transportation: Students are responsible for their transportation, but we will help with carpooling coordination, and your stipend will be sufficient to cover these expenses. Hop Vans may be available in the summer, and many of the academic-year activities will take place on Homewood campus.