CellMap

This script is the main pipeline to analyze immediate early gene expression data from iDISCO+ cleared tissue [Renier2016].

See the CellMap tutorial for a tutorial and usage.

../_images/cell_abstract_2016.jpg
../_images/CellMap_pipeline.png

Figure 6 iDISCO+ and ClearMap: A Pipeline for Cell Detection, Registration, and Mapping in Intact Samples Using Light Sheet Microscopy.

References

Renier2016

Mapping of brain activity by automated volume analysis of immediate early genes. Renier* N, Adams* EL, Kirst* C, Wu* Z, et al. Cell. 2016 165(7):1789-802