Whole-Brain Connectomics Datasets
Stream whole-brain data now! Experience the intricate beauty of the mouse brain and help us map out its myriad connections!
For accessing the whole brain striatum SBEM dataset, you must download and install Knossos from knossostool.org. When you run Knossos, a Load Dataset window should appear. If it does not, then select the option from the dropdown menu at the top. In the Load Dataset window, you will want to click on the '...' button, which will bring up a "Select a KNOSSOS dataset" window, where you can select a text file. Download and select this text file. Now, you should be able to load the dataset remotely by clicking the 'Use' button. You may optionally check the 'load segmentation overlay' option if you wish to manually segment the dataset.
If you use this data in any of your publications, please cite the following:
Mikula, S. & Denk, W. (2015) High-Resolution Whole-Brain Staining for Electron Microscopic Circuit Reconstruction. Nature Methods. 12(6):541-6.
Voxel Painting for Ground Truth Generation
In order to train computers to automatically segment connectomics datasets for neural circuit reconstruction, it is necessary to first label dataset voxels and assign them to classes. Shown below is one example where voxels are labeled according to the classes, 'Cell Membrane', 'Vesicle Cloud', 'PSD', 'Mitochondria', and 'Myelin Sheath'.
---> Click here for a complete voxel painting tutorial using Knossos