Ground truth data

At present (November 2020) the list includes PV, SST, Axo-axonic cells, VGAT and VIP cells and Pyramidal cells, and we will continue to expand with more cells. The goal is to perform the classification from ground truth cell metrics. If you have opto-tagged data that you are interested in sharing/including, please reach out to us. See the ground truth tutorial to learn more about using the included ground truth data. The table below lists the cell-types, their counts and the contributors:

PV184Josh Siegle with the Allen Institute; Sam McKenzie & Yuta Senzai, Buzsaki lab
SST115Josh Siegle with the Allen Institute
Pyramidal cells44Roman Huszar, Buzsaki lab
Axo-axonic35Dan English & Sam McKenzie, Buzsaki lab
VGAT15Yuta Senzai, Buzsaki lab
VIP14Josh Siegle with the Allen Institute

Classifying your cells in CellExplorer

You can also implement your own ground truth cells into the pipeline or do the classification in CellExplorer. Once classified you can share your metrics list with collaborators or provide them for publications.

Please see the opto-tagging tutorial for how to do the ground truth classification on your own data.