Wiki source code of Morphology Alignment Tool

Version 9.1 by rbakker on 2023/07/17 11:08

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6.2	5	= Morphology alignment tools =
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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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8.1	23	The Morphology Alignment Tools are made for automating this second lab scale approach, and consists of
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9.1	25	* [[Image preprocessing>>doc:.Image preprocessing.WebHome]] workflow.
6.4	26	* Image and 'pieces of neurite' alignment tool.
	27	* Neuron morphology viewer that supports file format manipulations.
	28	* Registration pipeline for stitched neuron and associated stack of low-resolution section images.
	29	* Flatmap visualization tool in which the cortical distribution of the registered neuron can be shown in the Allen Mouse reference space CCF3.
	30	* Database of long range projection neurons that have been registered to CCF3.
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	32	== Target audience ==
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	34	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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	40	{{box title="Contents"}}
	41	{{toc/}}
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