Ground truth data

At present (September 2020) the list includes PV, SST, Axo-axonic cells, VGAT and VIP cells and will continuesly be expanded with a further cells. The plan is to ultimately do classification from ground truth cell metrics so if you have opto-tagged data that you are interested in sharing/including, please reach out to us. Please see the ground truth tutorial to learn more about using the included ground truth data. The table below shows the current cell-types, their counts and the contributers:

PV184Josh Siegle with the Allen Institute; Sam McKenzie & Yuta Senzai, Buzsaki lab
SST115Josh Siegle with the Allen Institute
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.