Software Projects
Here are some of the computational tools and software projects I've developed or contribute to:
TomoDRGN
Deep learning framework for analyzing structural heterogeneity in cryo-ET sub-tomograms. Originally developed by Barrett Powell, I am currently maintaining the codebase and developing new iterations of the model.
PyTorch
Cryo-ET
Protein Dynamics
TomoTools
A suite of small scripts for streamlining the WarpTools cryo-ET preprocessing workflow. Currently hosted on Git Enterprise and accessible only to @mit.edu users (public version coming soon!)
Python
Cryo-ET
Data Visualization
CryoJAM
Generative AI framework that can bypass the process of fitting protein structures into cryo-EM maps, with an emphasis on medium-resolution density maps.
PyTorch
Cryo-EM/ET
Generative AI
TR-XES Data Processing
Tools for the processing and visualizaition of time-resolved X-ray emission spectroscopy data at SLAC National Accelerator Laboratory's LCLS Beamline.
XFEL
Data Visualization
X-ray Spectroscopy
PolypNET
Lightweight UNET++ architecture for identifying and segmenting cancerous polyps
from colonoscopy images with high accuracy.
PyTorch
Deep Learning
Computer Vision
Collaborations & Contributions
If you're interested in collaborating on a project or have any questions about available software, please feel free to reach out and I'll do my best to get back to you!
Open Source Philosophy
All my software projects are open-source and available on GitHub. I believe in
transparency, reproducibility, and community-driven development. Each tool should include
comprehensive documentation and clear installation instructions. If you have any questions or
suggestions, please feel free to contact me!
Contact
Please feel free to reach out to my email (jcarrion@mit.edu) if you have any questions or would like to chat!
Links to my social media accounts: X/Twitter | LinkedIn | GitHub | Google Scholar