How can I identify brain regions in my images?

By using QuickNII, you will be able to register this image series to the mouse reference atlas version of your choice and obtain adapted atlas maps and coordinates. Further, in-plane non-linear adjustments can be made with VisuAlign in order to obtain a more precise registration. The regions shown in the example below are color coded and correspond to Mouse CCFv3_2017 atlas¹ .

Histological data available on EBRAINS: DOI 10.25493/AYBB-BXV

How can I map the position of my reconstructed neuron?

After in-vivo electrophysiology experiments, the recorded neurons are filled with neurobiotin making them visible on histological images. These images are registered to the Mouse atlas CCFv3_2017¹. The extracted coordinates of the neuron soma and the coordinates of the neuronal arbor, could then be mapped in the 3D reference space.

Image from Bjerke et al. 2018. Front. Neuroinform. 12:82. doi:10.3389/fnana.2018.00082 

Electrophysiological data available on EBRAINS: DOI: 10.25493/ADRK-VJP

How can I count my labelled cells?

If you have 2D image series with labelled cells, you can use the QUINT workflow in order to determine the cell load per atlas region and even create a personalized analysis by defining your own grouping of regions from the reference atlas regions. You will start with registration using QuickNII and VisuAlign, then segment the cells  with ilastik and quantify with Nutil Quantifier. More details can be found here: QUINT workflow

Image from Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020) Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 14:37. doi: 10.3389/fninf.2020.00037

1. (Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., et al. (2014). A mesoscale connectome of the mouse brain. Nature 508, 207–214. doi: 10.1038/nature13186)