Error when plotting neurons in FCWB template

[Xiyang Sun]

Hi Dr. Jefferis,

I am trying to visualize neurons in FlyCircuit database.

Here are the programs:

    library(flycircuit)
    library(nat.flybrains)

    fc.ids = fc_get_ids()
    fcn_1000 <- fc_read_neurons(fc.ids[1:1000],xform=FALSE)
    plot3d(fcn_1000)
    plot3d(FCWB, alpha=0.1)

    I also tried xform_brain() to bridge neurons into FCWB template, but it shows the error "Transforming neurons using the sequence: chiangm->FCWB".

    Currently, I can only obtain the result like the following figure, where neurons and FCWB template are not overlapped.

    Thanks for your kind response.

Best regards

Xiyang

[Greg Jefferis]

Dear Xiyang,

On 19 Aug 2022, at 11:54, Xiyang Sun <xiyan...@gmail.com> wrote:

    fcn_1000 <- fc_read_neurons(fc.ids[1:1000],xform=FALSE)

Unchecked but I am fairly sure the problem is here. The documentation says

xform

Whether or not to tranform neurons from their original space to the FCWB template space.

If you do not specify that argument (or explicitly set it to TRUE, the default) then everything should work:

 fcn_1000 <- fc_read_neurons(fc.ids[1:1000])

Re this:

    I also tried xform_brain() to bridge neurons into FCWB template, but it shows the error "Transforming neurons using the sequence: chiangm->FCWB".

This is a message not an error.

All the best,

Greg.

PS Here with 10 ids.

[Xiyang Sun]

Dear Gerg

Thanks very much for your kind response.

I reinstalled the CMTK, and now everything is okay for the visualization. 

(The previous version without CMTK cannot run the fc_read_neuron successfully, only when xform is set as FALSE.)

Thanks again.

Best regards

Xiyang