alexcwsmith
I am an Assistant Professor in the Department of Neuroscience at the Medical University of South Carolina. My lab studies the neurobiology of drug addiction.
Charleston, SC
Pinned Repositories
3D-GAN-superresolution
3D super-resolution using Generative Adversarial Networks
alexcwsmith
B-SOID
Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is an unsupervised learning algorithm written in MATLAB and Python that serves to discover behaviors that are not pre-defined by users.
imageProcessing
Image Processing Scripts
imarisConverter
Convert .ims to .tif
PiRATeMC
A highly flexible, scalable, video recording system for behavioral neuroscience.
scNLP
Mining of PubMed and Natural Language Processing literature on results from single-cell sequencing data
scTriangulate
scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
singleCellTools
Tools for analysis of single-cell sequencing data, by Alex Smith in the lab of Paul Kenny @ Mount Sinai.
VAME
Variational Animal Motion Embedding
alexcwsmith's Repositories
alexcwsmith/imarisConverter
Convert .ims to .tif
alexcwsmith/PiRATeMC
A highly flexible, scalable, video recording system for behavioral neuroscience.
alexcwsmith/scNLP
Mining of PubMed and Natural Language Processing literature on results from single-cell sequencing data
alexcwsmith/scTriangulate
scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
alexcwsmith/singleCellTools
Tools for analysis of single-cell sequencing data, by Alex Smith in the lab of Paul Kenny @ Mount Sinai.
alexcwsmith/VAME
Variational Animal Motion Embedding
alexcwsmith/3D-GAN-superresolution
3D super-resolution using Generative Adversarial Networks
alexcwsmith/alexcwsmith
alexcwsmith/B-SOID
Behavioral segmentation of open field in DeepLabCut, or B-SOID ("B-side"), is an unsupervised learning algorithm written in MATLAB and Python that serves to discover behaviors that are not pre-defined by users.
alexcwsmith/imageProcessing
Image Processing Scripts
alexcwsmith/Backup2Drive
Python code for backing up files to a Drive account
alexcwsmith/CellCounting
This repository contains python scripts for counting cells in up to two channels, as well as cell overlap across channels.
alexcwsmith/ClearMap
ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
alexcwsmith/ClearMap2
ClearMap 2.0 with WobblyStitcher, TubeMap and CellMap
alexcwsmith/DeepFloorplan
alexcwsmith/DeepLabCut
Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals
alexcwsmith/DeepLabCut-live-GUI
GUI to run DeepLabCut on live video feed
alexcwsmith/DeepTraCE
Deep-learning based pipeline for analysis of whole-brain light sheet microscopy images
alexcwsmith/DLCutils
Various scripts to support deeplabcut...
alexcwsmith/GANfocal
A generative neural network for enhancement of 3D confocal or light-sheet fluorescence microscopy.
alexcwsmith/image_lddmm_tensorflow
Image mapping using the LDDMM algorithm, implemented in tensorflow
alexcwsmith/MotionMapper
Sample implementation of the MotionMapper behavioral analysis algorithms
alexcwsmith/neurosynth
Neurosynth core tools
alexcwsmith/pynapple
PYthon Neural Analysis Package :pineapple:
alexcwsmith/pystripe
An image processing package for removing streaks from SPIM images
alexcwsmith/pytorch-3dunet
3D U-Net model for volumetric semantic segmentation written in pytorch
alexcwsmith/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
alexcwsmith/simba
SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers
alexcwsmith/SmithJonkmanNatComm2021
Code for Smith & Jonkman, Nature Communications 2021
alexcwsmith/TRAILMAP