jmrk84
Neurosience, Connectomics, Machine Learning; PI at MPI for Biological Intelligence near Munich
MPI for Biological IntelligenceMunich
Pinned Repositories
ELEKTRONN
A highly configurable toolkit for training 3D/2D CNNs and general Neural Networks (superceded by https://github.com/ELEKTRONN/elektronn3)
elektronn3
A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data
Alignment_Projects
Aligner for large serial section image data
CAT
Connectome Analysis Toolbox
FijiBento
Render transformed image tiles
HVC_paper
Supplementary code and URLs to data
parallel-elastic-alignment
A script collection and workflow description to parallelize elastic alignment with TrakEM2 on a cluster
knossos
KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
knossos_utils
Python library for interacting with KNOSSOS data sets and annotation files
SyConn
Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.
jmrk84's Repositories
jmrk84/HVC_paper
Supplementary code and URLs to data
jmrk84/parallel-elastic-alignment
A script collection and workflow description to parallelize elastic alignment with TrakEM2 on a cluster
jmrk84/Alignment_Projects
Aligner for large serial section image data
jmrk84/CAT
Connectome Analysis Toolbox
jmrk84/FijiBento
Render transformed image tiles