Introduction

To obtain reconstructed neurons from experimental brain tissue, we distinguish between

1. the ‘industrial’ approach, in which multiple neurons are labeled, a 3d high resolution volume of the brain is scanned and stored, neurons are traced in 3d (e.g. using Vaa3d), and co-registered to a reference brain using 3d contrast based warping techniques (e.g. using elastix or ANTs)

2. the 'lab scale, hypothesis-driven approach', in which one or a few neurons are labeled in a particular area of interest, the brain is sliced, additionally stained and mounted on a glass slide, axons and dendrites are traced in 2d sections (e.g. using Neurolucida), pieces of axons are stitched across sections.

The Morphology Alignment Tools are made for automating this second lab scale approach, and is described in a poster presented at the HBP Summit 2023.

Toolbox contents

The toolbox consists of

• Image preprocessing workflow.
• Image and 'pieces of neurite' alignment tool.
• Neuron morphology viewer that supports file format manipulations.
• Registration pipeline for stitched neuron and associated stack of low-resolution section images.
• Flatmap visualization tool in which the cortical distribution of the registered neuron can be shown in the Allen Mouse reference space CCF3.
• Database of long range projection neurons that have been registered to CCF3.

Target audience

The tools are created for scientists who perform lab-scale tracing experiments and who need to have their sections aligned, pieces of neuron stitched and registered to a reference atlas to enable comparison to existing data.