What can I find here?

This pipeline is dedicated to coregister 3D neuronal morphology traced in Neurolucida into the Allen atlas, making use of 2d-sections from which it was traced.

The pipeline consists of several steps:

- neuron and image preprocessing;

- projection of neuron-points into pixel coordinates in the associated experimental slice;

- QuickNII (https://ebrains.eu/service/quicknii-and-visualign/) mapping between the atlas and the experimental slice;

-  Elastix (https://simpleelastix.github.io/) coregistration of images and, consequently, neuron-points;

- linear mapping of the reconstructed neuron into the original shape;

- evaluation of the reconstructed neuron by comparison with the same neuron coregistered with a corresponding point technique, and with the ground truth extracted by the neuroanatomist.

The code, intermediate and final results are stored in this collection.

For whom is this interesting?

Neuroscientists and neuroanatomists working with neuronal morphologies and who would like to register their data to an atlas. In particular the Allen mouse atlas is very interesting because large numbers of neurons are already available in that space from two large initiatives: Mouselight (https://www.janelia.org/project-team/mouselight) and Braintell (https://doi.org/10.35077/g.25).