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15		-= Introduction =
	15	+= What can I find here? =
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17		-To obtain reconstructed neurons from experimental brain tissue, we distinguish between
	17	+* Notice how the table of contents on the right
	18	+* is automatically updated
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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/]])
	21	+= Who has access? =
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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 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.
31		-
32		-== Target audience ==
33		-
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.
	23	+Describe the audience of this collab.
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