"Heal" multiple neurons

[Jiajun Zhang]

Dear all,

I am trying to do NBLASTing of my light level data against the whole FlyEM dataset. As I understood from previous posts, the precedure would be:

1. download the whole skeletons data

2. transform them to required template

3. heal, prun and convert the swc to dotprops

4. read my query and run nblast

I have tried the procedure with one query against one of those skeleton and thing went well. However, when I tried with one against two skeletons, I got a problem. The function stitch_neurons_mst() return a neuron object rather than a neuronlist of two neurons.

May I ask for some advice on that problem? Thank you in advance!

Best,

Jiajun

[Greg Jefferis]

Dear Jiajun,

You can use:

neuprintr::neuprint_read_neurons

To heal and read at the same time. If you already have the neurons downloaded in a neuronlist then do

nl.healed=nlappy(nl, stitch_neurons_mst)

In general any function that can be applied to one neuron can be applied to a neuronlist with the function nlapply

http://natverse.org/nat/reference/nlapply.html

All the best,

Greg.

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