Table of contents cellfinder documentation Installation Installation System requirements Cluster installation Installation with SLURM Using conda Setting up your GPU Downloading files User guide Getting started Data requirements Command line options Specifying pixel size Cell candidate detection Cell candidate classification Historical options Training the network Using supplied training data Visualisation Group-level analysis Summarising multiple cell counts Standalone tools Rescale xml file Cropping xml file Transforming cells to standard space Summarising cell counts Tutorial Tutorial Troubleshooting How to troubleshoot Error messages cellfinder is slow neuro Introduction Standalone tools Exporting detected cell positions to brainrender Heatmap generation Manually segment in standard space Installation Standalone tools Silicon probe tracking For developers Contributing to cellfinder Setting up a development installation Development conventions Documentation General Getting in touch Release notes Citation Links cellfinder homepage Help forum Code repositories cellfinder amap neuro brainreg amap Introduction Installation User guide Image orientation Registration parameters Downloading files