Project Title: Mapping the Development of Repetitive Behaviors in Mice
BASIS Advisor: Dr. Hight
Internship Location: Graybiel Laboratory at MIT
Onsite Mentor: Dr. Emily Hueske
What does instigating and quantifying the development of repetitive behaviors in autism spectrum disorder (ASD) model mice reveal? The SHANK3 gene, which is found in the 22q13 chromosome, is one of the autism gene candidates. A mutation in this gene has been found in 1-2% of individuals with ASD. To this end, SHANK3 mice are used in studies focused on the development of repetitive behaviors, an aspect of autism. For my internship, I will work with Dr. Emily Hueske at Graybiel Laboratories to research the development of repetitive behaviors in SHANK3 model mice through the use of softwares: DeepLabCut and B-SOiD. DeepLabCut provides a marker-less (as opposed to the old method of attaching physical markers to animals) pose mapping software. B-SOiD can provide specific clustering of pose movement data from DeepLabCut. These softwares will provide information on model mice that have been affected by Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), which will allow for manipulation of the striatum, part of the brain involved in motor function. The goal of this project is to develop a better understanding of the development of repetitive behaviors in autism model mice.
My Posts
Week 10
May 31, 2022
Since this was the final week of my internship, my mentor had me write some workflow instructions for how we used DeepLabCut and B-SOiD along with some tips about file paths to make things more efficient/easier. Overall, since my internship took place during the pilot phase of my mentor’s research, I mainly assisted her with […]
Week 9
May 31, 2022
This week I went back with my mentor and looked at the WT vs SHANK model in BSOiD since it yielded useful results and more consistently identifiable features across mice videos. We had originally intended for this model to be more of a pilot for larger video sets so we only used 3 videos to […]
Week 8
May 31, 2022
This week I mainly worked with my mentor to try and identify the problem in B-SOiD wherein the model seems to focus on small shifts on marker position and mislabels as features across mouse videos. One problem that we thought of was the amount of videos used to make the model. Basically, the B-SOiD models […]
Week 7
May 27, 2022
This week I utilized the top down model I created in DeepLabCut last week to create a model in B-SOiD. It was somewhat notable that the UMAP plot consisted of little cluster overlap, but it was essentially a straight line. This was more apparent when analyzing video snippets, as the model seemed to be picking […]
Week 6
May 06, 2022
This week I worked on making a model from the top down perspective from older videos that my mentor sent me. The purpose of this is mainly for comparison to bottom up video data and for this type of work to be publishable both camera angles would be necessary. However, I ran into some noticeable […]
Week 5
May 04, 2022
This week I worked on making the model that my mentor and I intend to use for the bottom up camera perspective. I trained DeepLabCut on a total of 6 videos: 2 cane mice, 2 Shank mice, and 2 amphetamine mice. The reason for including these different types in addition to the shank mice is […]
Week 4
Apr 04, 2022
Hello! This fourth week I managed to figure out some solutions to the problems I mentioned last week. Regarding adding new videos to an already created project, the problem lies with the way they are added. When using the GUI feature to add new videos, a symlink is added to the project folder instead of […]
Week 3
Mar 28, 2022
For my third week, I did some labeling and created a model for a few habituation videos. These habituation videos are taken while the mice acclimate to the chamber in which they are recorded. I will later analyze videos from a later period after they have been in the chamber multiple times. I did encounter […]
Week 2
Mar 22, 2022
Hello! This second week I continued to work with DeepLabCut and B-SOID. The main change was that my advisor purchased 60fps cameras and I ran the two aforementioned programs on new videos of mice. This time there was a noticeable difference as I found labeling pose markers to be easier as the mouse body parts […]
Week 1
Mar 13, 2022
This first week I started my virtual internship with Graybiel Laboratory as part of my senior project. My work mainly consisted of working with my on-site mentor, Emily Hueske, to try and run a sample set of data through DeepLabCut and B-SOID. This sample video consisted of about 7 minutes wherein a mouse is filmed […]
Introduction Blog
Mar 07, 2022
Hello! My name is Jason Lee and I am currently a senior at Basis Independent McLean. For my senior project, I want to better understand how animal movement and behavior mapping programs can be used to understand repetitive behaviors due to mutations in mice. I have a particular interest in this topic because of my […]