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Welcome to the forum to discuss tips and problems with the NeuroAnatomy Toolbox (aka natverse), a suite of R packages and related web applications including NBLAST neuron search.

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Paul Dampenon, Greg Jefferis4

Feb 20

Missing annotation file

Hi Greg, It fixed it! Thank you so much, and apologies for not creating an issue back then. Best,

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Missing annotation file

Hi Greg, It fixed it! Thank you so much, and apologies for not creating an issue back then. Best,

Feb 20

anhd...@gmail.com, … andy cole7

12/19/23

Analyze connectivity of FlyWire objects using natverse

Unfortunately, I this method didn't work. I assume it's because we're exporting as binary

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Analyze connectivity of FlyWire objects using natverse

Unfortunately, I this method didn't work. I assume it's because we're exporting as binary

12/19/23

Sean Chen

12/11/23

Issues installing natverse

Hello, When installing natverse with natmanager::install('natverse') I have been facing

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Issues installing natverse

Hello, When installing natverse with natmanager::install('natverse') I have been facing

12/11/23

Max Max, Ibrahim Taştekin2

11/28/23

Suitable parameters for setting the view of JFRC2

Dear Xun, You can use nview3d function for this Best Ibo Sal, 28/11/2023, saat 04:54 tarihinde Max

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Suitable parameters for setting the view of JFRC2

Dear Xun, You can use nview3d function for this Best Ibo Sal, 28/11/2023, saat 04:54 tarihinde Max

11/28/23

Xiyang Sun, Greg Jefferis2

11/22/23

Access to the new FlyCircuit dataset

Dear Xiyang, The error message is not very helpful, but I am afraid the problem is quite simple. The

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Access to the new FlyCircuit dataset

Dear Xiyang, The error message is not very helpful, but I am afraid the problem is quite simple. The

11/22/23

Takuro Ohashi

11/16/23

Averaging multiple brains

Dear Dr. JefferisI am Takuro Ohashi, a postdoc at Nagoya University. I'm currently trying to

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Averaging multiple brains

Dear Dr. JefferisI am Takuro Ohashi, a postdoc at Nagoya University. I'm currently trying to

11/16/23

Xiyang Sun, Gregory Jefferis2

10/20/23

Obtain 2d neuropil coordinates from the 3D FlyCircuit brain template

Dear Xiyang, could you clarify which brain template? Flycircuit released a typical female and typical

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Obtain 2d neuropil coordinates from the 3D FlyCircuit brain template

Dear Xiyang, could you clarify which brain template? Flycircuit released a typical female and typical

10/20/23

Greg Jefferis, Zhihua Liu2

9/22/23

Re: [nat-user] How to use `natverse` to match neurons in confocal and fly EM data?

Dear Dr. Greg Jefferis, I appreciate your prompt and helpful response! You have given me a lot of

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Re: [nat-user] How to use `natverse` to match neurons in confocal and fly EM data?

Dear Dr. Greg Jefferis, I appreciate your prompt and helpful response! You have given me a lot of

9/22/23

Ibrahim Taştekin, Greg Jefferis3

9/1/23

error with flywire_partner_summary

Thanks a lot Greg! method ='cave' solved the problem! On Fri, Sep 1, 2023 at 11:56 AM Greg

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error with flywire_partner_summary

Thanks a lot Greg! method ='cave' solved the problem! On Fri, Sep 1, 2023 at 11:56 AM Greg

9/1/23

Dr Gregory Jefferis

8/9/23

Re: Request for information on the Innervation pattern of Local Interneurons

Dear Prateek, The neuprint API provides information about glomerular innervation. You can access this

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Re: Request for information on the Innervation pattern of Local Interneurons

Dear Prateek, The neuprint API provides information about glomerular innervation. You can access this

8/9/23

Amanda Abusaif, … Greg Jefferis3

8/1/23

Error when running NBLAST

Dear Both, NBLAST assumes 1. that all your neurons are in the same space 2. that they have been

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Error when running NBLAST

Dear Both, NBLAST assumes 1. that all your neurons are in the same space 2. that they have been

8/1/23

shuo cao, Gregory Jefferis2

7/26/23

How to fetch neurotransmitter type prediction from hemibrain with neuprintr?

Dear Shuo, it is not available in hemibrain neuprint yet as there are a couple of other updates

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How to fetch neurotransmitter type prediction from hemibrain with neuprintr?

Dear Shuo, it is not available in hemibrain neuprint yet as there are a couple of other updates

7/26/23

Margo SLVTR, Gregory Jefferis3

7/18/23

Cloudvolume error

It worked, I don't get this error anymore! Thanks! Best On Tuesday, July 18, 2023 at 10:07:08 PM

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Cloudvolume error

It worked, I don't get this error anymore! Thanks! Best On Tuesday, July 18, 2023 at 10:07:08 PM

7/18/23

Li Guo, … Gregory Jefferis11

5/9/23

R session aborted

Hi you need python >= 3.7. Unfortunately the python 3.6 you have is too old. Recent versions of

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R session aborted

Hi you need python >= 3.7. Unfortunately the python 3.6 you have is too old. Recent versions of

5/9/23

Emine Ozen, Greg Jefferis3

2/6/23

3D Template Registration via natverse

Dear Emine, Thanks for the additional information. Registering a calcium indicator dataset is a bit

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3D Template Registration via natverse

Dear Emine, Thanks for the additional information. Registering a calcium indicator dataset is a bit

2/6/23

Jiajun Zhang, Greg Jefferis3

1/17/23

contradictory data - interpretation

Hi Greg, Thank you very much for your quick reply and patient explanation! Cheers, Jiajun 在2023年1月17日

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contradictory data - interpretation

Hi Greg, Thank you very much for your quick reply and patient explanation! Cheers, Jiajun 在2023年1月17日

1/17/23

Nilay Yapici, Greg Jefferis3

1/17/23

Issues reading meshes from Flywire in R with fafbseg library.

Great! On Sunday, November 13, 2022 at 11:28:56 PM UTC ny...@cornell.edu wrote: I actually fixed this

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Issues reading meshes from Flywire in R with fafbseg library.

Great! On Sunday, November 13, 2022 at 11:28:56 PM UTC ny...@cornell.edu wrote: I actually fixed this

1/17/23

Sanja Jasek, Greg Jefferis2

1/17/23

catmaid_remove_annotations_for_skeletons strange behavior

Dear Sanja, It seems i missed a few messages from a while back. I hope you have figured out your

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catmaid_remove_annotations_for_skeletons strange behavior

Dear Sanja, It seems i missed a few messages from a while back. I hope you have figured out your

1/17/23

Samra Hami, Greg Jefferis2

1/17/23

conda envirement

Dear Samra, I'm sorry I missed this message at the time. When you run R, what does py_config()

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conda envirement

Dear Samra, I'm sorry I missed this message at the time. When you run R, what does py_config()

1/17/23

Ibrahim Taştekin, Greg Jefferis10

9/15/22

meshparty_skeletonize not working

That's great, Ibo. I have added (I hope) a slightly more general fix based on what you found.

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meshparty_skeletonize not working

That's great, Ibo. I have added (I hope) a slightly more general fix based on what you found.

9/15/22

Liangyu Tao, … Greg Jefferis6

9/15/22

natmanager installation issue (not on CRAN)

Just to note that natmanager is back to normal on CRAN. On Tuesday, July 5, 2022 at 8:29:56 PM UTC+1

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natmanager installation issue (not on CRAN)

Just to note that natmanager is back to normal on CRAN. On Tuesday, July 5, 2022 at 8:29:56 PM UTC+1

9/15/22

Geonil Kim, Greg Jefferis4

9/15/22

Access failing problem with fafbseg

On Tuesday, September 6, 2022 at 2:14:45 PM UTC+1 gktmf...@gmail.com wrote: By any chance, is it

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Access failing problem with fafbseg

On Tuesday, September 6, 2022 at 2:14:45 PM UTC+1 gktmf...@gmail.com wrote: By any chance, is it

9/15/22

Xiyang Sun, Greg Jefferis3

8/19/22

Error when plotting neurons in FCWB template

Dear Gerg Thanks very much for your kind response. I reinstalled the CMTK, and now everything is okay

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Error when plotting neurons in FCWB template

Dear Gerg Thanks very much for your kind response. I reinstalled the CMTK, and now everything is okay

8/19/22

andy cole, … Gregory Jefferis3

6/22/22

With RGL 0.108.xx, center of rotation no longer pivot on visualized objects

Thanks, Art. Andy, although I can't rule out a change in rgl, I haven't had any other reports

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With RGL 0.108.xx, center of rotation no longer pivot on visualized objects

Thanks, Art. Andy, although I can't rule out a change in rgl, I haven't had any other reports

6/22/22

artx...@gmail.com

6/22/22

Error running CMTK streamxform!

Hi Greg, i got this error Error in cmtk.streamxform(points, reg, direction, transformtype) : Error

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Error running CMTK streamxform!

Hi Greg, i got this error Error in cmtk.streamxform(points, reg, direction, transformtype) : Error

6/22/22

Dr Gregory Jefferis, … Kai-Yi Hsu8

6/14/22

Re: problem about nblast

Dear Dr.Greg, I will run the code, thank you very much. Best regards, Kai-Yi jeff...@gmail.com 在 2022

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Re: problem about nblast

Dear Dr.Greg, I will run the code, thank you very much. Best regards, Kai-Yi jeff...@gmail.com 在 2022

6/14/22

Ibrahim Taştekin, Gregory Jefferis3

5/30/22

simple_python meshparty and creating dotprops from skeletons created by using skeletor

Hi Greg, Thanks a lot for the answers. It was a speed issue with creating dotprops. As you guessed it

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simple_python meshparty and creating dotprops from skeletons created by using skeletor

Hi Greg, Thanks a lot for the answers. It was a speed issue with creating dotprops. As you guessed it

5/30/22

Florian Freitag, … Greg Jefferis7

5/17/22

dr_fafbseg returns error in py_call_impl

Happy to hear that fixed your problem. Best, Greg. On 11 May 2022, at 21:31, Farzaan Salman <

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dr_fafbseg returns error in py_call_impl

Happy to hear that fixed your problem. Best, Greg. On 11 May 2022, at 21:31, Farzaan Salman <

5/17/22

Ibrahim Taştekin, Gregory Jefferis3

4/21/22

error with skeletor

Thanks a lot Greg Both options work! I think it is my bad. The neuron I tried to skeletonize is a

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error with skeletor

Thanks a lot Greg Both options work! I think it is my bad. The neuron I tried to skeletonize is a

4/21/22

Amanda Abusaif, Gregory Jefferis2

2/24/22

Using SWC files and comparing specific neurons in NBLAST

Dear Amanda, Thanks for your messsge. This mailing list is focussed on the R natverse packages but it

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Using SWC files and comparing specific neurons in NBLAST

Dear Amanda, Thanks for your messsge. This mailing list is focussed on the R natverse packages but it

2/24/22