Wiki source code of Morphology Alignment Tool
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| 5 | = Tools for morphology alignment = | ||
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| 7 | Align axons and dendrites traced from a sectioned brain to a reference space. | ||
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| 15 | = Introduction = | ||
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| 17 | To obtain reconstructed neurons from experimental brain tissue, we distinguish between | ||
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| 19 | ~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>>https://home.penglab.com/proj/vaa3d/home/index.html]]), and co-registered to a reference brain using 3d contrast based warping techniques (e.g. using [[elastix>>https://elastix.lumc.nl/]] or [[ANTs>>https://stnava.github.io/ANTs/]]) | ||
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| 21 | 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>>https://www.mbfbioscience.com/products/neurolucida/]]), pieces of axons are **stitched across sections**. | ||
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| 23 | The Morphology Alignment Tools are made for automating this second lab scale approach, and is [[described in a poster>>https://www.scienceopen.com/document/read?vid=6fa9ee94-4ad7-484e-a321-3b46c5f64f15]] presented at the HBP Summit 2023. | ||
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| 25 | == Toolbox contents == | ||
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| 27 | The toolbox consists of | ||
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| 29 | * [[Image preprocessing>>doc:Collabs.morphology-alignment-tool.1\. Image preprocessing.WebHome]] workflow. | ||
| 30 | * Image and 'pieces of neurite' [[alignment tool>>doc:.Slice alignment tool.WebHome]]. | ||
| 31 | * [[Neuron morphology viewer>>doc:.Neuron morphology viewer.WebHome]] that supports file format manipulations. | ||
| 32 | * [[Registration pipeline>>doc:.Registration pipeline.WebHome]] for stitched neuron and associated stack of low-resolution section images. | ||
| 33 | * Flatmap visualization tool in which the cortical distribution of the registered neuron can be shown in the Allen Mouse reference space CCF3. | ||
| 34 | * Database of long range projection neurons that have been registered to CCF3. | ||
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| 36 | == Target audience == | ||
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| 38 | 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. | ||
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| 44 | {{box title="**Contents**"}} | ||
| 45 | {{toc/}} | ||
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