Alternatives and similar repositories for connectomics

Users that are interested in connectomics are comparing it to the libraries listed below

• funkelab / lsd
  🌈
  ☆65Updated 3 weeks ago
• funkelab / daisy
  Block-wise task scheduling for large nD volumes.
  ☆32Updated 7 months ago
• seung-lab / cloud-volume
  Read and write Neuroglancer datasets programmatically.
  ☆161Updated last week
• funkelab / gunpowder
  A library to facilitate machine learning on multi-dimensional images.
  ☆86Updated this week
• AllenInstitute / MicronsBinder
  A collection of notebooks to provide examples of using Microns-explorer.org datasets
  ☆37Updated last year
• google-research / sofima
  Scalable Optical Flow-based Image Montaging and Alignment
  ☆81Updated this week
• kreshuklab / MorphoFeatures
  MorphoFeatures code and data
  ☆22Updated 2 years ago
• seung-lab / igneous
  Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
  ☆56Updated 2 weeks ago
• AllenCellModeling / cyto-dl
  ☆28Updated last month
• AllenCell / aics-ml-segmentation
  ☆32Updated 3 months ago
• funkey / waterz
  Simple watershed and agglomeration library for affinity graphs.
  ☆25Updated last month
• MMV-Lab / mmv_im2im
  Python package for deep learning based image to image transformation
  ☆53Updated 2 months ago
• vanvalenlab / deepcell-label
  Cloud-based data annotation tools for biological images
  ☆82Updated last year
• seung-lab / fastremap
  Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
  ☆63Updated last month
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆26Updated last year
• erturklab / delivr_cfos
  End-to-end light-sheet image analysis for mouse brains, with DL training data generated in VR
  ☆34Updated last month
• stardist / augmend
  simple package for augmentation of n-dimensional arrays
  ☆33Updated 2 years ago
• seung-lab / chunkflow
  Compose chunk operators to create a pipeline for local or distributed petabyte-scale computation
  ☆54Updated 4 months ago
• marissaweis / ssl_neuron
  Code to the paper "Self-Supervised Graph Representation Learning for Neuronal Morphologies"
  ☆13Updated last year
• manzt / napari-lazy-openslide
  Lazily load multiscale whole-slide images with openslide and dask
  ☆33Updated 2 years ago
• BiomedSciAI / fuse-med-ml
  A python framework accelerating ML based discovery in the medical field by encouraging code reuse. Batteries included :)
  ☆148Updated last month
• janelia-cellmap / dacapo
  A framework for easy application of established machine learning techniques on large, multi-dimensional images.
  ☆60Updated last month
• janelia-flyem / NeuTu
  Software package for neuron reconstruction and visualization
  ☆39Updated 5 months ago
• constantinpape / elf
  Utils and convenience functions for large-scale bio-image analysis.
  ☆58Updated 3 months ago
• zudi-lin / pytorch_connectomics
  PyTorch Connectomics: segmentation toolbox for EM connectomics
  ☆179Updated last week
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆88Updated last month
• HumanBrainProject / neuroglancer-scripts
  Conversion of neuroimaging data for display in Neuroglancer
  ☆29Updated last month
• e11bio / volara
  Block-wise operations for large nD volumes
  ☆42Updated this week
• bunnelab / virtues
  A foundation model framework for analyzing multiplexed tissue imaging data across molecular, cellular and tissue scales enabling clinical…
  ☆39Updated 8 months ago
• AllenInstitute / aics-ml-segmentation
  AICS ML Segmentation (One-Way) Mirror
  ☆27Updated 4 years ago