Wiki source code of Morphology Alignment Tool
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| 5 | = Morphology alignment tools = | ||
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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 consists of | ||
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| 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. | ||
| 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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