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15		-= What can I find here? =
	15	+= Introduction =
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17		-* Notice how the table of contents on the right
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	17	+To obtain reconstructed neurons from experimental brain tissue, we distinguish between
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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/]])
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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**.
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	23	+The Morphology Alignment Tools are made for automating the lab scale approach, and consists of
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	25	+* Image preprocessing 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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