Standalone tools

Standalone tools distributed with neuro

Manually segment brain regions or tracks

To manually segment brain regions or tracks in standard space that can then be visualised along with other samples (e.g. in BrainRender) see Manually segment in standard space.

Heatmap generation

To generate a heatmap of detected cell positions, see Heatmap generation

Overlay on raw data and segmentation from amap added separately

Export cell positions to brainrender

To convert cell positions to a format that can be used in brainrender, see Exporting detected cell positions to brainrender.

Input cell somas detected by cellfinder, aligned to the Allen Reference Atlas, and visualised in brainrender along with retrosplenial cortex. Data courtesy of Sepiedeh Keshavarzi and Chryssanthi Tsitoura.