Awesome
connectomic-paper-datasets
Collection of connectomic papers and datasets. Public available annotated EM datasets with papers and download paths are in connectomic-datasets.xlsx. Please tell me if any dataset is missing.
Recommended code: a deep learning framework powered by PyTorch for automatic and semi-automatic semantic and instance segmentation in connectomics, which is called PyTorch Connectomics (PyTC). [paper]
Dataset Papers
MICrONS | Cell 2022
- Multiscale and multimodal reconstruction of cortical structure and function [Paper] [Dataset] [Neuroglancer]
- Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex [Paper]
H01 | preprint
- A connectomic study of a petascale fragment of human cerebral cortex [Paper] [Dataset] [Neuroglancer]
Open Organelle | Nature 2021
FAFB | Cell 2018
- A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster [Paper] [Dataset] [Neuroglancer]
FlyWire | Nature methods 2022
C. elegans. Connectomes across development | Nature 2021
- Connectomes across development reveal principles of brain maturation [Paper]
Hemi Brain | elife 2020
- A connectome and analysis of the adult Drosophila central brain [Paper][neuroglancer]
Fly VNC | Cell 2021
- Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy [dataset(Larva)]
Algorithm Papers -- Segmentation
SyConn2 | Nature Methods 2022 & Nature Communication 2019
- Learning cellular morphology with neural networks [paper]
- SyConn2: dense synaptic connectivity inference for volume electron microscopy [paper] [dataset]
FFN | Nature Methods 2018
- High-precision automated reconstruction of neurons with flood-filling networks [paper]
LSD | Nature Methods 2022
- Local shape descriptors for neuron segmentation [paper]
Algorithm Papers -- Error Correction
Split Error Correction Through Biologically-Constrained Graphs | CVPR 2019
- Biologically-Constrained Graphs for Global Connectomics Reconstruction [paper]
Multimodal Split Error Correction | AAAI 2024
- Learning Multimodal Volumetric Features for Large-Scale Neuron Tracing [code&dataset]
Algorithm Papers -- Subcompartment Classification
Segmentation-Guided Contrastive Learning | Nature Methods 2023
- Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning [paper]
Cluster-Instance Contrastive Learning | MICCAI 2022
- Self-Supervised Learning of Morphological Representation for 3D EM Segments with Cluster-Instance Correlations [paper][code&dataset]
Skeleton-Aware Morphological Representation | 3DV 2024
- Self-Supervised Learning of Skeleton-Aware Morphological Representation for 3D Neuron Segments
visualization
If you want to use neuroglancer to visualize your own EM image and segmentation, please refer to my notes in neuroglancer_EM&seg
Our dataset
FAFB-CellSeg dataset for subcompartment classification: FAFB-CellSeg
FlyTracing dataset for split error correction: FlyTracing