nat-user

Contact owners and managers

1–24 of 188

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.

0 selected

George Yerou, Greg Jefferis2

8/6/20

Q&A

xform

Dear George, The error messages are not very clear, but I am afraid that there is currently no

unread,

Dear George, The error messages are not very clear, but I am afraid that there is currently no

8/6/20

Arthur Zhao, … Gregory Jefferis4

5/4/20

Q&A

resample and strahler order

Dear Arthur, glad things are working ok. Marcel, resample is a fundamentally destructive operation as

unread,

nat

Q&A

resample and strahler order

Dear Arthur, glad things are working ok. Marcel, resample is a fundamentally destructive operation as

5/4/20

Pasha Davoudian, Gregory Jefferis8

5/4/20

Q&A

Calculating geodesic distances in hemibrain dataset

The factor of / 125 is the product of 8 / 1000. This is because neurons in the hemibrain are in a raw

unread,

bridging

nat

Q&A

Calculating geodesic distances in hemibrain dataset

The factor of / 125 is the product of 8 / 1000. This is because neurons in the hemibrain are in a raw

5/4/20

Asphodel H, Greg Jefferis2

4/20/20

Q&A

mouselightr: running example failed

Sorry, Tina. I missed this at the time. There is a bug in this demo script. I hope its author will

unread,

mouselightr: running example failed

Sorry, Tina. I missed this at the time. There is a bug in this demo script. I hope its author will

4/20/20

Arthur Zhao, Gregory Jefferis2

10/29/19

Q&A

editing neuron skeletons generated in rgl.plot3d

I always generate pngs with plot3d / snapshot3d. You have to watch out for antialias settings for

unread,

nat

Q&A

editing neuron skeletons generated in rgl.plot3d

I always generate pngs with plot3d / snapshot3d. You have to watch out for antialias settings for

10/29/19

Arthur Zhao, Greg Jefferis4

7/31/19

Q&A

fetch volumes from CATMAID

👍 On Wednesday, July 31, 2019 at 5:22:04 PM UTC-4, Greg Jefferis wrote: Hi Arthur, I will follow up

unread,

catmaid

nat

Q&A

fetch volumes from CATMAID

👍 On Wednesday, July 31, 2019 at 5:22:04 PM UTC-4, Greg Jefferis wrote: Hi Arthur, I will follow up

7/31/19

Arthur Zhao, Gregory Jefferis4

7/9/19

Q&A

cable lengh

Actually this already returns the physical distance if you make the ngraph object with weights=T. If

unread,

nat

Q&A

cable lengh

Actually this already returns the physical distance if you make the ngraph object with weights=T. If

7/9/19

Shruthi Ravindranath, Gregory Jefferis3

6/17/19

Q&A

Append to neuronlist with rbind()?

Thanks a lot for the help. read.neurons() works well for my purpose. On Friday, June 14, 2019 at 9:02

unread,

nat

Q&A

Append to neuronlist with rbind()?

Thanks a lot for the help. read.neurons() works well for my purpose. On Friday, June 14, 2019 at 9:02

6/17/19

Arthur Zhao, Greg Jefferis5

5/23/19

Q&A

connector counting discrepancy between CATMAID and NAT

On Wed, May 22, 2019 at 8:03 PM Greg Jefferis <jeff...@gmail.com> wrote: On Wednesday, May 22,

unread,

catmaid

nat

Q&A

connector counting discrepancy between CATMAID and NAT

On Wed, May 22, 2019 at 8:03 PM Greg Jefferis <jeff...@gmail.com> wrote: On Wednesday, May 22,

5/23/19

Isabel D'Alessandro, … Greg Jefferis4

5/22/19

Q&A

How do you generate a neuron object based on the flycircuit identifier?

Dear Shruthi, Thanks for your interest. The best approach depends somewhat on what template space you

unread,

flycircuit_neurons

nat

Q&A

How do you generate a neuron object based on the flycircuit identifier?

Dear Shruthi, Thanks for your interest. The best approach depends somewhat on what template space you

5/22/19

matsut...@gmail.com, Greg Jefferis4

1/10/19

Q&A

How do you trace neurons?

Dear matsutakehoyo, We have tried ImageJ for tracing, and I was hoping your tools offered something

unread,

nat

Q&A

How do you trace neurons?

Dear matsutakehoyo, We have tried ImageJ for tracing, and I was hoping your tools offered something

1/10/19

Jingpeng Wu, Gregory Jefferis2

10/30/18

Q&A

what to do if the distance or absolute dot product is outside of the scoremat?

On 30 Oct 2018, at 15:22, Jingpeng Wu <jingp...@gmail.com> wrote: I see you have a score

unread,

nat

nblast

Q&A

what to do if the distance or absolute dot product is outside of the scoremat?

On 30 Oct 2018, at 15:22, Jingpeng Wu <jingp...@gmail.com> wrote: I see you have a score

10/30/18

Jingpeng Wu, Greg Jefferis3

10/23/18

Q&A

error while saving neurons as swc format

thanks for the help, your solution works! On Monday, October 22, 2018 at 6:36:33 PM UTC-4, Greg

unread,

nat

nblast

Q&A

error while saving neurons as swc format

thanks for the help, your solution works! On Monday, October 22, 2018 at 6:36:33 PM UTC-4, Greg

10/23/18

Jingpeng Wu, Gregory Jefferis3

10/15/18

Q&A

what is the proper way to save the distance matrix?

thanks a lot, that works perfectly! On Monday, October 15, 2018 at 11:24:05 AM UTC-4, Greg Jefferis

unread,

nat

nblast

Q&A

what is the proper way to save the distance matrix?

thanks a lot, that works perfectly! On Monday, October 15, 2018 at 11:24:05 AM UTC-4, Greg Jefferis

10/15/18

Jingpeng Wu, Gregory Jefferis7

10/13/18

Q&A

How to transform neurons to a list of dotprops?

Great! Happy to try and answer additional queries or to give comments offline if you want to get

unread,

How to transform neurons to a list of dotprops?

Great! Happy to try and answer additional queries or to give comments offline if you want to get

10/13/18

Greg Jefferis

6/8/17

Q&A

anyone (interested in) using nat+CMTK on Windows

Dear All, If anyone is (interested in) using the nat R package in conjunction with the CMTK

unread,

anyone (interested in) using nat+CMTK on Windows

Dear All, If anyone is (interested in) using the nat R package in conjunction with the CMTK

6/8/17

Meredith Peterson, Gregory Jefferis3

11/15/16

Q&A

reading/plotting hxsurf and amiramesh files

On 15 Nov 2016, at 17:14, Meredith Peterson <smer....@gmail.com> wrote: Thanks so much! It

unread,

image-processing

nat

Q&A

reading/plotting hxsurf and amiramesh files

On 15 Nov 2016, at 17:14, Meredith Peterson <smer....@gmail.com> wrote: Thanks so much! It

11/15/16

mke...@ucla.edu, Greg Jefferis6

2/3/16

Q&A

Searching registered brains for neuron similarity

I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in

unread,

Searching registered brains for neuron similarity

I was wondering if it would be possible to search a trace (or a neuron ID from flycircuit) in

2/3/16

Joses Ho, Gregory Jefferis5

8/5/15

Q&A

Flipping Flycircuit neurons

Hi, The "mirror" function works perfectly, just had to use the sum of the bounding box for

unread,

Flipping Flycircuit neurons

Hi, The "mirror" function works perfectly, just had to use the sum of the bounding box for

8/5/15

Joses Ho, Gregory Jefferis5

8/13/15

Q&A

Importing skeletonised neurons into NAT

Will give your suggestions a go! Thanks a lot. Regards, Joses On Thu, Aug 13, 2015 at 2:26 PM,

unread,

nat

upload_neuron

Q&A

Importing skeletonised neurons into NAT

Will give your suggestions a go! Thanks a lot. Regards, Joses On Thu, Aug 13, 2015 at 2:26 PM,

8/13/15

Dr Gregory Jefferis

6/29/15

Re: CMTK statistics question

Hi Mike, cmtk.statistics calculates the image statistics within a labelled region. n refers to the

unread,

image-processing

nat

Re: CMTK statistics question

Hi Mike, cmtk.statistics calculates the image statistics within a labelled region. n refers to the

6/29/15

Dr Gregory Jefferis

6/29/15

image thresholds (with e.g. for Janelia GMR lines)

Calculating Thresholds ====================== Calculating thresholds for image expression patterns is

unread,

image-processing

nat

image thresholds (with e.g. for Janelia GMR lines)

Calculating Thresholds ====================== Calculating thresholds for image expression patterns is

6/29/15

Ajayrama Kumaraswamy, Greg Jefferis2

5/6/15

Q&A

Applying NBLAST on SWC files

Dear Ajay, Many thanks for your interest in this work. As a general comment, I think you might find

unread,

nat

nblast

Q&A

Applying NBLAST on SWC files

Dear Ajay, Many thanks for your interest in this work. As a general comment, I think you might find

5/6/15

Gregory Jefferis, … Greg Jefferis9

10/24/15

Re: Adding new traced neurons to myneurons

Dear Sonia, On Friday, October 23, 2015 at 8:04:40 PM UTC+1, Sonia Chin wrote: The bridging code you

unread,

nat

Re: Adding new traced neurons to myneurons

Dear Sonia, On Friday, October 23, 2015 at 8:04:40 PM UTC+1, Sonia Chin wrote: The bridging code you

10/24/15