02 Input files

Barrio relies on two data files as input. The surfaces meshes of all neuronal structures and the volume of the original imaging data.

Surface meshes

The input file format must be one wavefront file containing triangulated surface meshes. The name of each object (o object_name) in the .obj must follow a strict naming convention.

structure	naming convention	explanation	example
Dendrites	DendriteXXX	dendrite followed by a 3 digit number	Dendrite023
Axons	AxonXXX	axon followed by a 3 digit number	Axon123
Dendritic Mitochondria	Mito_DXXX_YY	mito number YY of dendrite XXX	Mito_D001_01
Axonal Mitochondria	Mito_AXXX_YY	mito number YY of axon XXX	Mito_A015_02
Inhibitory Synapses	Syn_DXXXSYYAZZZBKK_I	inhibitory synapse between DendriteXXX SpineYY and AxonZZZ BoutonKK	Syn_D023S01A054B01_I
Excitatory Synapses	Syn_AXXXSYYAZZZBKK_E	excitatory synapse between DendriteXXX SpineYY and AxonZZZ BoutonKK	Syn_D023S01A054B01_E

Remarks:

• all names are case insensitive
• anything additional connected to the object name separated with a _ will be ignored in the names
• if meshes are exported as .obj files with blender, make sure that only these export options are set: Forward: X, Up: -Z, Apply Modifiers, Include Edges, Triangulate Faces, Objects as OBJ Objects.

Image data (EM or light microscopy)

Must be specified in the .raw file format. Use ImageJ to convert a stack of (.png, .tiff) images into a .raw volume.