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ShuTu reconstruct a single Allen neuron #12

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4 of 6 tasks

JohnTigue opened this issue Oct 15, 2019 · 1 comment

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JohnTigue commented Oct 15, 2019 •

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Latest progress is on Colab: ShuTu process Allen.

To Do:

Test if ShuTu runs on Colab (ShuTu SWC generation: probe if deploys on Colab [Yup] #4)
Demo ShuTu working on its own demo data (ShuTu SWC generator: terse demo #6)
Pick a single small neuron to reconstruct: 651806289 is 6GB (Dataset: formulate plan of attack #7)
Test downloading dataset from Wasabi to Colab
Package Allen data for ShuTu to read (ShuTu: needs a data index file to read Allen image stacks #13)
Have ShuTu do its thing on 651806289

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ShuTu: method and GUI editor app #27

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JohnTigue commented Nov 14, 2019

allensdk.morphology.validate_swc:

To be compatible with NEURON, SWC files must have the following properties:

a single root node with parent ID ‘-1’

sequentially increasing ID numbers

immediate children of the soma cannot branch

And ShuTu doesn't pick a root, which is probably why some viewers were not liking ShuTu generated SWCs.

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