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5		-= Tools for morphology alignment =
	5	+= Morphology alignment tools =
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7	7	Align axons and dendrites traced from a sectioned brain to a reference space.
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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**.
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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 the 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>>doc:.Slice alignment tool.WebHome]].
27		-* [[Neuron morphology viewer>>https://neuroinformatics.nl/HBP/morphology-viewer-dev/]] that supports file format manipulations.
	25	+* Image preprocessing workflow.
	26	+* Image and 'pieces of neurite' alignment tool.
	27	+* Neuron morphology viewer that supports file format manipulations.
28	28	* Registration pipeline 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.