Table 5. Major processing scripts used in the pipeline.

Script name	Description
kn_pipeline_meso_get_t2n.py	Converts 2D STPT sections to Nifti stacks
kn_pipeline_meso_reg2TCstd_org.py	Register STPT image stacks to STPT template
kn_pipeline_meso_inj_seg.py	Rough localization of the injection site
kn_pipeline_meso_NN_cells.py	Single-cell detection in the injection site using a DNN
kn_pipeline_meso_NN_cells_3D.py	Computing cell density images for the injection site
kn_pipeline_meso_NN_tracerseg.py	DNN-based anterograde tracer segmentation
kn_pipeline_meso_NN_tracerseg_3D.py	3D image stack generation
kn_pipeline_meso_norm_tracer.py	Anterograde tracer normalization
kn_pipeline_meso_NISSL_2D.py	Registering the Nifti images and creating stacks
kn_pipeline_meso_apply_trafos_TC.py	Moving all images to the STPT/BMA/MBMv2+3 image spaces
kn_pipeline_meso_map_pts2std.py	Moving point data to the STPT image space
kn_pipeline_meso_flatmap.py	Mapping data to the BMA and MBM flatmaps
kn_pipeline_meso_flatmap_stack.py	Mapping to flatmap stacks
kn_pipeline_meso_DWI.py	Creating streamline density maps for the injection site
kn_pipeline_meso_map_highres.py	Mapping image data to high-resolution template space

STPT, serial two-photon tomography.