Wiki source code of Morphology Alignment Tool

Version 13.1 by rbakker on 2023/07/17 12:33

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10.1	5	= Tools for morphology alignment =
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6.2	7	Align axons and dendrites traced from a sectioned brain to a reference space.
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6.4	15	= Introduction =
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6.4	17	To obtain reconstructed neurons from experimental brain tissue, we distinguish between
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6.4	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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6.4	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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11.1	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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11.1	25	== Toolbox contents ==
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	27	The toolbox consists of
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13.1	29	* [[Image preprocessing>>doc:Collabs.morphology-alignment-tool.1\. Image preprocessing.WebHome]] workflow.
10.1	30	* Image and 'pieces of neurite' [[alignment tool>>doc:.Slice alignment tool.WebHome]].
11.1	31	* [[Neuron morphology viewer>>doc:.Neuron morphology viewer.WebHome]] that supports file format manipulations.
12.1	32	* [[Registration pipeline>>doc:.Registration pipeline.WebHome]] for stitched neuron and associated stack of low-resolution section images.
6.4	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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