NucMM dataset: 3d neuronal nuclei instance segmentation¶
The goal is to segment and identify automatically each cell nuclei in EM images. To solve such task pairs of EM images and their corresponding instance segmentation labels are provided. Below a pair example is depicted:
In this dataset
27 3D images of size
(64, 64, 64) voxels, for
(z,x,y) axes, are used for train while the test is
done over the whole Zebrafish volume. Here is a training sample and its ground truth:
You need to download NucMM dataset first from these link. Once you have donwloaded this data you need to create a directory tree as described in Data preparation. To adapt the
.h5 file format provided by MitoEM authors into
.tif files you can use the script h5_to_tif.py.
To create the YAML file you can use the template resunet_3d_instances.yaml which is prepared for this tutorial.