Export neurons

Export to SWC or HOC

To export neuron reconstructions to a SWC or HOC file, click File > Export > Neuron Objects or run the Export Neuron Objects command from the search bar. The exported neuron file can be used in other neuron analysis software for additional analyses.

Export in Aivia format

Neuron reconstructions can be exported for later use in Aivia as .neurons files. (Neuron reconstructions are also saved with images when images are saved as Aivia TIFFs.) To export Aivia Neurons, click on the Export Neurons icon in the neuron group's row of the Object Set Settings panel and then on the Export Neurons in Aivia Format option. 

 

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Export Neurons menu in Object Set Settings

 

Export to mask

Neuron groups can be exported as 16-bit labelled masks in TIFF format. Labelled neuron masks are images with the same spatial dimensions as the image from which they are exported with voxel intensities corresponding to the neuron objects that contain the voxels. To export a neuron object group as a labelled mask, click on the Export Neurons icon in the neuron group's row of the Object Set Settings panel and then on the Export Neurons to a 16 Bit Labelled Mask option.

Soma sets, dendrite sets, and spine sets can each be exported as 8-bit binary masks or 16- or 32-bit labelled masks. Labelled masks of dendrite sets have unique labels for each dendrite segment. Labelled masks of spine sets have unique labels for each spine head and spine neck, so the head and neck of a spine are not given the same label. To export a labelled or binary mask for a soma set, dendrite set, or spine set, click on the Export Objects to a Mask icon in the row of the object set in the Object Set Settings panel and then choose the desired export option.

 

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Export Objects to a Mask menu for a dendrite set

 

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