Changes for page Morphology Alignment Tool

Last modified by rbakker on 2023/07/17 12:44
From version 9.1
edited by rbakker
on 2023/07/17 11:08
Change comment: There is no comment for this version
To version 12.1
edited by rbakker
on 2023/07/17 12:19
Change comment: There is no comment for this version

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2 2  (((
3 3  (% class="container" %)
4 4  (((
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.
8 8  )))
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20 20  
21 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 22  
23 -The Morphology Alignment Tools are made for automating this second lab scale approach, and consists of
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 24  
25 +== Toolbox contents ==
26 +
27 +The toolbox consists of
28 +
25 25  * [[Image preprocessing>>doc:.Image preprocessing.WebHome]] workflow.
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.
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.
29 29  * Flatmap visualization tool in which the cortical distribution of the registered neuron can be shown in the Allen Mouse reference space CCF3.
30 30  * Database of long range projection neurons that have been registered to CCF3.
31 31