Changes for page Morphology Alignment Tool

Last modified by rbakker on 2023/07/17 12:44
From version 6.3
edited by rbakker
on 2023/07/17 10:25
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To version 15.1
edited by rbakker
on 2023/07/17 12:44
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2 2  (((
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5 -= Morphology alignment tools =
5 += Tools for morphology alignment =
6 6  
7 7  Align axons and dendrites traced from a sectioned brain to a reference space.
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15 -= What can I find here? =
15 += Introduction =
16 16  
17 -* Notice how the table of contents on the right
18 -* is automatically updated
19 -* to hold this page's headers
17 +To obtain reconstructed neurons from experimental brain tissue, we distinguish between
20 20  
21 -= Who has access? =
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/]])
22 22  
23 -Describe the audience of this collab.
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**.
22 +
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.
24 +
25 +== Toolbox contents ==
26 +
27 +The toolbox consists of
28 +
29 +* [[Image preprocessing>>doc:Collabs.morphology-alignment-tool.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>>doc:.Flatmap visualization.WebHome]] 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>>doc:.Neuron database.WebHome]] that have been registered to CCF3.
35 +
36 +== Target audience ==
37 +
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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