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SpyKING CIRCUS

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Welcome to the SpyKING CIRCUS forum!

This forum is meant to be a way to keep in touch with the users of the software, in order to interact and get feedback. This is also a place where people could share ideas/views on what are the features they would like to be implemented. To know more about what is and how to install/use the software, please have a look at the online documentation http://spyking-circus.rtfd.org

Note that a publication about the software is available on eLife with the following link https://elifesciences.org/articles/34518, and the repository is hosted on Github, open access, now without any credentials.

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6/17/19

Release of 0.8.0

Dear all We've just pushed a 0.8.0 release, and I would suggest you to update your installations

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Release of 0.8.0

Dear all We've just pushed a 0.8.0 release, and I would suggest you to update your installations

6/17/19

5/10/17

Dear all We've just pushed a 0.5.7 release, including some minor bug fixes and improvements. An

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Dear all We've just pushed a 0.5.7 release, including some minor bug fixes and improvements. An

5/10/17

2/16/17

Release Candidate for 0.5: time to update from 0.4.XX

Dear all I just want to let you know that we pushed yesterday a release candidate for our 0.5 version

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Release Candidate for 0.5: time to update from 0.4.XX

Dear all I just want to let you know that we pushed yesterday a release candidate for our 0.5 version

2/16/17

View more pinned conversations

Cornelia, Pierre Yger3

12/20/24

Detection of a spike only on subset of channels

Thanks a lot for your fast reply! It indeed seems to be a display issue in phy. Attached here is an

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Detection of a spike only on subset of channels

Thanks a lot for your fast reply! It indeed seems to be a display issue in phy. Attached here is an

12/20/24

7/3/24

Ignoring other channels during sorting

Hi everyone! First, thanks for a super convenient sorting algorithm! I'm using Spyking Circus on

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Ignoring other channels during sorting

Hi everyone! First, thanks for a super convenient sorting algorithm! I'm using Spyking Circus on

7/3/24

4/29/24

Time duration mismatch in Open Ephys and Spyking Circus

Hi all, I recently encounter a problem with Open Ephys. I notice a time duration mismatch for the

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Time duration mismatch in Open Ephys and Spyking Circus

Hi all, I recently encounter a problem with Open Ephys. I notice a time duration mismatch for the

4/29/24

3/27/23

File format numpy is not supported by phy. TraceView disabled.

Hi. I can run some files and all works perfectly. But with other data pre-filtered by me It doesn

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File format numpy is not supported by phy. TraceView disabled.

Hi. I can run some files and all works perfectly. But with other data pre-filtered by me It doesn

3/27/23

2/10/23

help fine-tuning parameters

and another that circus considered a single unit but klustakwik resolved. I am considering running

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help fine-tuning parameters

and another that circus considered a single unit but klustakwik resolved. I am considering running

2/10/23

1/31/23

issue with libtiff.5.dylib

I followed your instructions while installing spyking-circus in conda while running it with my data I

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issue with libtiff.5.dylib

I followed your instructions while installing spyking-circus in conda while running it with my data I

1/31/23

Joachim Grimstvedt, Pierre Yger4

12/22/22

Problems trying to assign reference channels to tetrode recordings

Yes, you can do that, put everything in a single shank and design a geometry such that channels will

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Problems trying to assign reference channels to tetrode recordings

Yes, you can do that, put everything in a single shank and design a geometry such that channels will

12/22/22

5/31/22

Strange voltage pulses after filtering MaxOne h5 file

There is a typo in my last email. The attached figure is from the dataset in Google Drive. Sorry

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Strange voltage pulses after filtering MaxOne h5 file

There is a typo in my last email. The attached figure is from the dataset in Google Drive. Sorry

5/31/22

Matheus Oliveira, Pierre Yger4

3/16/22

Using phy for the first time

What do you mean? After manually sorting the data with phy? Then everything is saved as python arrays

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Using phy for the first time

What do you mean? After manually sorting the data with phy? Then everything is saved as python arrays

3/16/22

3/12/22

Two bugs in use

Dear Pierre, I've got two problems in using the spike sorter. 1. when executing the code,

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Two bugs in use

Dear Pierre, I've got two problems in using the spike sorter. 1. when executing the code,

3/12/22

Stephan Boltzmann, Pierre Yger3

2/16/22

Optimizing settings for spike detection/fitting

Hi Pierre, Thanks a lot for your support. I kept changing and adapting the parameters starting from

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Optimizing settings for spike detection/fitting

Hi Pierre, Thanks a lot for your support. I kept changing and adapting the parameters starting from

2/16/22

Fukuaki Kinoshita

2/8/22

noisy spikes in phy

Dear Pierre, Thank you for your support always. I have seen the results in the phy and found that

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noisy spikes in phy

Dear Pierre, Thank you for your support always. I have seen the results in the phy and found that

2/8/22

Fukuaki Kinoshita, Pierre Yger2

2/2/22

minimizing the influence of drifts

Dear Fukuaki The data are in vivo I supposed? I would first strongly encourage you to activate the

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minimizing the influence of drifts

Dear Fukuaki The data are in vivo I supposed? I would first strongly encourage you to activate the

2/2/22

Mo Hask, Pierre Yger3

12/7/21

Threshold determined

Dear Pierre, Thank you very much for the fast response and sorry for the delayed answer. It would be

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Threshold determined

Dear Pierre, Thank you very much for the fast response and sorry for the delayed answer. It would be

12/7/21

Azar Ghahari, Pierre Yger2

10/26/21

path/mydata.params

Dear Azar The names here are only for indication purposes... You must provide the path/names of your

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path/mydata.params

Dear Azar The names here are only for indication purposes... You must provide the path/names of your

10/26/21

Fukuaki Kinoshita, Pierre Yger3

10/17/21

The problem in analysis of 400 electrodes' recording

Dear Pierre Thank you for your concern. I tried threshold 6, clustering sensitivity 2. I could obtain

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The problem in analysis of 400 electrodes' recording

Dear Pierre Thank you for your concern. I tried threshold 6, clustering sensitivity 2. I could obtain

10/17/21

Fukuaki Kinoshita

9/28/21

About template matching algorithm

Dear Pierre, I have a question about template matching. Would you tell me that after obtain templates

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About template matching algorithm

Dear Pierre, I have a question about template matching. Would you tell me that after obtain templates

9/28/21

Fukuaki Kinoshita

9/26/21

template.npy file in merged.GUI folder

To whom it may concern, Now, I'm trying to analyze template.npy created in the mydata_0-merged.

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template.npy file in merged.GUI folder

To whom it may concern, Now, I'm trying to analyze template.npy created in the mydata_0-merged.

9/26/21

tens.r...@gmail.com

9/15/21

spyKING circus run time

I'm trying to get an intuition as to what parameters might be relaxed in spyking circus to speed

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spyKING circus run time

I'm trying to get an intuition as to what parameters might be relaxed in spyking circus to speed

9/15/21

Gergely Komlósi

9/1/21

clustering error

Hi Pierre, I've just recently installed spyking circus, and my process fails at the clustering

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clustering error

Hi Pierre, I've just recently installed spyking circus, and my process fails at the clustering

9/1/21

Ashley Kees, Gergely Komlósi2

8/31/21

error at the clustering step

Hi Ashley, Have you found any solution for this problem? I've just ran into the same one:

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error at the clustering step

Hi Ashley, Have you found any solution for this problem? I've just ran into the same one:

8/31/21

Fukuaki Kinoshita

8/17/21

problem with GUI

I'm Sorry for causing you concern. Now I'm trying to view my data in GUI with phy2.0. After

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problem with GUI

I'm Sorry for causing you concern. Now I'm trying to view my data in GUI with phy2.0. After

8/17/21

Barbara Genocchi, … Pierre Yger3

8/5/21

Problems with .h5 files

Dear Alice I already answered to Barbara, see below and hope this helps Best Pierre Ok, then you

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Problems with .h5 files

Dear Alice I already answered to Barbara, see below and hope this helps Best Pierre Ok, then you

8/5/21

Gergely Komlósi, Pierre Yger2

8/5/21

installation problem

Hi Can you start again, in a fresh new conda env, and remove the -c intel flag everywhere, in all the

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installation problem

Hi Can you start again, in a fresh new conda env, and remove the -c intel flag everywhere, in all the

8/5/21

tens.r...@gmail.com, Pierre Yger3

7/21/21

small amplitude cluster blocking detection of another?

Hi Pierre, >> It is hard to see on your png plots, but the missed big spike in the "error.

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small amplitude cluster blocking detection of another?

Hi Pierre, >> It is hard to see on your png plots, but the missed big spike in the "error.

7/21/21

Stephen Whitmarsh, … Pierre Yger8

6/7/21

large differences in spike amplitudes within clusters

Oh, great! I'll just set it to False in my analyses, that way I'm sure. Cheers, Stephen Op ma

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large differences in spike amplitudes within clusters

Oh, great! I'll just set it to False in my analyses, that way I'm sure. Cheers, Stephen Op ma

6/7/21

abhijithk...@gmail.com, Pierre Yger2

4/7/21

Spike sorting Retnal wave data.

Default parameters should work fine for retina. Can you maybe share a small dataset with us, and/or

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Spike sorting Retnal wave data.

Default parameters should work fine for retina. Can you maybe share a small dataset with us, and/or

4/7/21

Steven Ceto, … Pierre Yger7

3/22/21

Spikes sorted during dead_Times

Hi Pierre, So the circus-artefacts script worked, but for some reason it converts my dead times from

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Spikes sorted during dead_Times

Hi Pierre, So the circus-artefacts script worked, but for some reason it converts my dead times from

3/22/21

Mohamed Ouardouz, Pierre Yger2

3/11/21

converting neuralynx .ncs file to rwa-binary file

SC should be able to load .ncs files, you simply need to say neuralynx for the file format, and the .

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converting neuralynx .ncs file to rwa-binary file

SC should be able to load .ncs files, you simply need to say neuralynx for the file format, and the .

3/11/21

ashle...@gmail.com, Mariela Escande3

2/22/21

issue with installation

Hi Pierre, Just wanted to see whether you saw the response from Mariela (she is my colleague and it

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issue with installation

Hi Pierre, Just wanted to see whether you saw the response from Mariela (she is my colleague and it

2/22/21

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