Pinned Repositories
autoseg
Automated deep learning segmentation for large-scale biological datasets.
catmaid_tools
Tools for accessing data from a catmaid server
cb2_project_analysis
Analysis source code for CB2 project
FANC_auto_recon
Code for processing and analyzing the automated reconstruction of the Lee lab's Female Adult Nerve Cord EM dataset
funlib.show.neuroglancer_v2
Scripts and helpers for the neuroglancer WebGL viewer.
GridTape_VNC_paper
Resources related to the GridTape/VNC EM dataset paper
GridTapeStage
GridTape TEM imaging stage
pymaid_addons
A collection of modules built on top of pymaid, a python package for interacting with CATMAID reconstructions.
raygun
An image enhancement and segmentation pipeline for generating connectomic reconstructions from X-ray holographic nanotomography, using CycleGANs, Local Shape Descriptors, and Mutex Watershed. Built with PyTorch, Daisy, and Gunpowder.
tobin17
Tobin WF, Wilson RI, Lee WC. eLife 2017
Lee Lab's Repositories
htem/FANC_auto_recon
Code for processing and analyzing the automated reconstruction of the Lee lab's Female Adult Nerve Cord EM dataset
htem/cb2_project_analysis
Analysis source code for CB2 project
htem/autoseg
Automated deep learning segmentation for large-scale biological datasets.
htem/raygun
An image enhancement and segmentation pipeline for generating connectomic reconstructions from X-ray holographic nanotomography, using CycleGANs, Local Shape Descriptors, and Mutex Watershed. Built with PyTorch, Daisy, and Gunpowder.
htem/GridTapeStage
GridTape TEM imaging stage
htem/funlib.show.neuroglancer_v2
Scripts and helpers for the neuroglancer WebGL viewer.
htem/GridTape_VNC_paper
Resources related to the GridTape/VNC EM dataset paper
htem/pymaid_addons
A collection of modules built on top of pymaid, a python package for interacting with CATMAID reconstructions.
htem/segway
Common scripts for segmentation
htem/PPC_inhibitoryMotifs
htem/2p_preprocess_ppc
align imaging and behavior data, motion correct, acq2p init
htem/aedes_public
htem/cb2-meshes
Surface renderings of neurons in the paper "Structured cerebellar connectivity supports resilient pattern separation"
htem/cb2_data_availability
Data availability for the CB2 dataset
htem/cb2_project_analysis_files
htem/gt_pickup_annotation
Annotate relative position of section to slot from staining/pickup images
htem/itfbarcode
htem/lsd
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htem/neuroglancer-mdseg
htem/neuroglancer_mdseg
WebGL-based viewer for volumetric data
htem/run_elastix
A pipeline for running elastix to register two 3D image volumes
htem/segway.graph
Extraction and analysis of connectomic graph
htem/segway.mdseg
htem/segway.synapse.area
htem/segway.utils
htem/tem-tomo
Code for processing and evaluating TEM tomography data
htem/waterz
Simple watershed and agglomeration library for affinity graphs.
htem/xpress
htem/xpress-challenge-files
File repo for the XPRESS challenge
htem/ztools
A toolbox for Zarr creation/manipulation scripts