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)