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Welcome to neuPrint, a set of tools for analyzing neural connectomes based on electron microscopy data. This forum is for users and developers of the neuPrint connectome analysis tools. Also, please note any issues with regards to our public datasets hosted through neuPrint (e.g., https://neuprint.janelia.org).

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Xin Zhong, Berg, Stuart5

12/17/25

Pin data of medulla for left optic lobe

❤️ Xin Zhong reacted via Gmail On Tue, Dec 9, 2025 at 12:46 AM Berg, Stuart <be...@janelia.hhmi.

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Pin data of medulla for left optic lobe

❤️ Xin Zhong reacted via Gmail On Tue, Dec 9, 2025 at 12:46 AM Berg, Stuart <be...@janelia.hhmi.

12/17/25

8/19/25

Is neuprint server down?

We tested with two different accounts, neither could see those datasets options. Accessing data

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Is neuprint server down?

We tested with two different accounts, neither could see those datasets options. Accessing data

8/19/25

6/30/25

No access to the datasets

Dear all, I'm interested in browsing the data (after being linked through a paper - Eckstein et

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No access to the datasets

Dear all, I'm interested in browsing the data (after being linked through a paper - Eckstein et

6/30/25

Jan Clemens, Jasper Phelps3

2/19/25

Download tables for latest MANC version 1.2.1

Hi, turns out one can fetch the tables using python: https://connectome-neuprint.github.io/neuprint-

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Download tables for latest MANC version 1.2.1

Hi, turns out one can fetch the tables using python: https://connectome-neuprint.github.io/neuprint-

2/19/25

Samuele Tatullo

7/31/24

fetch_adjacencies Error

Hello, I am new of neuPrint, hence I started from the QueryTutorial. However, whenever I run the

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fetch_adjacencies Error

Hello, I am new of neuPrint, hence I started from the QueryTutorial. However, whenever I run the

7/31/24

Anirudh Sivarajan, … Lou Scheffer5

7/20/24

Connections issue

Hey Lou, Thanks so much for the insight! I am truly grateful for this information. I had a follow-up

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Connections issue

Hey Lou, Thanks so much for the insight! I am truly grateful for this information. I had a follow-up

7/20/24

5/14/24

Function for getting compartment of a given coordinate

Hello, I'm having trouble finding a function in neuprint python that can, given a coordinate,

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Function for getting compartment of a given coordinate

Hello, I'm having trouble finding a function in neuprint python that can, given a coordinate,

5/14/24

Miranda D, Berg, Stuart3

3/13/24

AssertionError: Since you listed nonprimary rois ({'g1(R)'}), please specify include_nonprimary=True

Hi again Miranda, Sorry, I misunderstood the problem. I'm working on a fix. Please keep an eye on

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AssertionError: Since you listed nonprimary rois ({'g1(R)'}), please specify include_nonprimary=True

Hi again Miranda, Sorry, I misunderstood the problem. I'm working on a fix. Please keep an eye on

3/13/24

Sarah Pugliese, Berg, Stuart2

10/27/23

Difference between "downstream" property and result of fetch_adjacencies()

Hi Sarah, What is the difference between what is measured by the "downstream" property of a

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Difference between "downstream" property and result of fetch_adjacencies()

Hi Sarah, What is the difference between what is measured by the "downstream" property of a

10/27/23

Miranda D, stuar...@gmail.com2

10/22/23

Fetching synapses but excluding certain neurons

I am fetching synapses from KC neurons and creating 3d plots of the pre and post synapse locations on

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Fetching synapses but excluding certain neurons

I am fetching synapses from KC neurons and creating 3d plots of the pre and post synapse locations on

10/22/23

Peter Raffaele Hasenhuetl Sarnataro

9/18/23

Hello, Is there a way to avoid the timeout (via batching?) on neuprint explorer when running queries

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Hello, Is there a way to avoid the timeout (via batching?) on neuprint explorer when running queries

9/18/23

Benjamin Midler, … Peter Raffaele Hasenhuetl Sarnataro3

9/18/23

Large Query Timeout

Hi! Did anyone manage to solve the timeout issue? On Monday, 23 January 2023 at 13:17:38 UTC PRATEEK

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Large Query Timeout

Hi! Did anyone manage to solve the timeout issue? On Monday, 23 January 2023 at 13:17:38 UTC PRATEEK

9/18/23

7/25/23

Re: Dataset just got deleted??

Sorry, neuprint was down today from 2-2:45 for scheduled maintenance. Looks like you caught it at a

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Re: Dataset just got deleted??

Sorry, neuprint was down today from 2-2:45 for scheduled maintenance. Looks like you caught it at a

7/25/23

7/5/23

Fetching neuron ID/name by coordinate

Dear all, I located a neuron of interest in the neuroglancer so basically I have the coordinate(s) of

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Fetching neuron ID/name by coordinate

Dear all, I located a neuron of interest in the neuroglancer so basically I have the coordinate(s) of

7/5/23

Jordan Imani Kalai, … Philipp Schlegel3

6/23/23

Trouble Fetching Generalized Group of Neurons + General Question

Hi Jordan. I might be able to help you with navis. If you send me a private message with your email

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Trouble Fetching Generalized Group of Neurons + General Question

Hi Jordan. I might be able to help you with navis. If you send me a private message with your email

6/23/23

1/31/23

How to find where a neuron's cell body resides?

Dear all, The roi info for any neuron gives the regions its axons and dendrites span, right? So, I

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How to find where a neuron's cell body resides?

Dear all, The roi info for any neuron gives the regions its axons and dendrites span, right? So, I

1/31/23

PRATEEK YADAV, Greg Jefferis3

1/23/23

Trouble with understanding body

Dear Dr. Jefferis, Thank you for your response. I am confused. Aren't all objects in the data

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Trouble with understanding body

Dear Dr. Jefferis, Thank you for your response. I am confused. Aren't all objects in the data

1/23/23

1/20/23

Timeout experienced

Dear all, I am new to Neuprint so I was just playing around with the database to get a feel for it. I

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Timeout experienced

Dear all, I am new to Neuprint so I was just playing around with the database to get a feel for it. I

1/20/23

Chris Liu, Berg, Stuart5

7/12/22

How to calculate the cross-sectional area of each neuron slice？

Hi Stuart, I think it will be very helpful, and I will have a try. Thank you again for your generous

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How to calculate the cross-sectional area of each neuron slice？

Hi Stuart, I think it will be very helpful, and I will have a try. Thank you again for your generous

7/12/22

Joel Butterwick, … Farzaan Salman6

7/7/22

download mesh for entire hemibrain

Hello, Do you know if it is possible to add this mesh as a layer in neuroglancer? On Friday, October

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download mesh for entire hemibrain

Hello, Do you know if it is possible to add this mesh as a layer in neuroglancer? On Friday, October

7/7/22

Peter Jenny, Pratyush Kandimalla2

6/29/22

Difficulty with the neuron ROI property

Hi, ROI names need a back-tic. The following update to your query pulls neurons with innervation in

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Difficulty with the neuron ROI property

Hi, ROI names need a back-tic. The following update to your query pulls neurons with innervation in

6/29/22

6/17/22

Need help understanding connections between cells

Hi All, I need help in understanding the connections between GF (Giant Fiber) neurons (R68A04) and 1)

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Need help understanding connections between cells

Hi All, I need help in understanding the connections between GF (Giant Fiber) neurons (R68A04) and 1)

6/17/22

Garrett Sager, … Berg, Stuart4

5/17/22

Yes, mito size is expressed in voxels. Each voxel is 8nm wide (isotropic), so multiply by 8^3 to

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Yes, mito size is expressed in voxels. Each voxel is 8nm wide (isotropic), so multiply by 8^3 to

5/17/22

Miranda D, Berg, Stuart2

5/17/22

Render skeleton of neuron with mitochondria and synapses

Not yet. Would you mind opening an issue for this feature request on the github repo? From: neuprint@

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Render skeleton of neuron with mitochondria and synapses

Not yet. Would you mind opening an issue for this feature request on the github repo? From: neuprint@

5/17/22

Luka Blagojevic, … Berg, Stuart3

5/11/22

How are skeletons created from original mapping? Skeletonization procedure details?

Hi Luka and Chris, The skeletons are generated using an implementation of the TEASAR skeletonization

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How are skeletons created from original mapping? Skeletonization procedure details?

Hi Luka and Chris, The skeletons are generated using an implementation of the TEASAR skeletonization

5/11/22

Markus Pleijzier, … Stuart Berg3

4/3/22

fetch_synapse_connections time out: markdown render found here https://github.com/connectome-neuprint/neuprint-python/issues/27

Hi Chris, I have the same problem. And it's just searching for connections between two neurons

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fetch_synapse_connections time out: markdown render found here https://github.com/connectome-neuprint/neuprint-python/issues/27

Hi Chris, I have the same problem. And it's just searching for connections between two neurons

4/3/22

Ryosuke Tanaka, Stuart Berg2

2/17/22

Definition of "pre" property of :Neuron

Hi Ryosuke I just came to realize that "pre" property of a :Neuron can be much smaller than

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Definition of "pre" property of :Neuron

Hi Ryosuke I just came to realize that "pre" property of a :Neuron can be much smaller than

2/17/22

Letícia Batista, … Greg Jefferis3

2/14/22

ROIs coordinates

Dear Letícia, Just to note that thread Stuart mentions provides a good way to map arbitrary XYZ

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ROIs coordinates

Dear Letícia, Just to note that thread Stuart mentions provides a good way to map arbitrary XYZ

2/14/22

Lydia Elaine Hamburg

12/1/21

No info for certain "partner" bodyids

Hi all, Sometimes when I search for synaptic partners in neuPrint, I see bodyids for which there is

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No info for certain "partner" bodyids

Hi all, Sometimes when I search for synaptic partners in neuPrint, I see bodyids for which there is

12/1/21

Joel Butterwick, Stuart Berg3

11/30/21

fetch_shortest_paths intermediate_criteria

Thank you so much for the quick fix Stuart! I can confirm that the updated neuprint-python (0.4.16)

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fetch_shortest_paths intermediate_criteria

Thank you so much for the quick fix Stuart! I can confirm that the updated neuprint-python (0.4.16)

11/30/21

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