DeepD3 Datasets

In this repository, you will find: The DeepD3 benchmark dataset - a TIFF stack with an extent of 135.7 by 34.4 by 35.5 µm from the rat hippocampal CA1 region (94 x 94 x 500 nm voxel size) The dendrite tracings of the DeepD3 benchmark dataset by three human annotators U, V and W in SWC file format, traced with neutube The pixel-precise spine annotations of the DeepD3 benchmark dataset by three human annotators as *.mask files (compatible with pipra, but easy to open with any HDF5 reader) The human annotations and clusters for the DeepD3 benchmark dataset as CSV file A Jupyter notebook that shows how we assigned the human annotations to individual clusters that pertain to individual dendritic spines The DeepD3 training data as d3set file The DeepD3 validation data as d3set file (see paper for further information, basically HDF5 files)