spyking-circus.readthedocs.io

Welcome to the SpyKING CIRCUS’s documentation! — SpyKING CIRCUS 0.4.3 documentation

Welcome to the SpyKING CIRCUS’s documentation! Welcome to the SpyKING CIRCUS’s documentation! The SpyKING CIRCUS is a massively parallel code to perform semi automatic spike sorting on large extra-cellular recordings. Using a smart clustering and a greedy template matching approach, the code can solve the problem of overlapping spikes, and has been tested both for. In 042, we introduce the. How to get the code. Future plans and contributions. Designing your probe file. Dealing with stimulation artefacts.

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Welcome to the SpyKING CIRCUS’s documentation! — SpyKING CIRCUS 0.4.3 documentation | spyking-circus.readthedocs.io Reviews

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Welcome to the SpyKING CIRCUS’s documentation! Welcome to the SpyKING CIRCUS’s documentation! The SpyKING CIRCUS is a massively parallel code to perform semi automatic spike sorting on large extra-cellular recordings. Using a smart clustering and a greedy template matching approach, the code can solve the problem of overlapping spikes, and has been tested both for. In 042, we introduce the. How to get the code. Future plans and contributions. Designing your probe file. Dealing with stimulation artefacts.

<META> KEYWORDS

1 spyking circus

2 introduction

3 launching the code

4 using the gui

5 advanced informations

6 known issues

7 docs

8 raquo;

9 edit on github

10 in vitro

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Welcome to the SpyKING CIRCUS’s documentation! — SpyKING CIRCUS 0.4.3 documentation | spyking-circus.readthedocs.io Reviews

https://spyking-circus.readthedocs.io

Welcome to the SpyKING CIRCUS’s documentation! Welcome to the SpyKING CIRCUS’s documentation! The SpyKING CIRCUS is a massively parallel code to perform semi automatic spike sorting on large extra-cellular recordings. Using a smart clustering and a greedy template matching approach, the code can solve the problem of overlapping spikes, and has been tested both for. In 042, we introduce the. How to get the code. Future plans and contributions. Designing your probe file. Dealing with stimulation artefacts.

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spyking-circus.readthedocs.io

1

Formatting your data — SpyKING CIRCUS 0.4.3 documentation

http://spyking-circus.readthedocs.io/en/0.4.3/code/data.html

Designing your probe file. Dealing with stimulation artefacts. Input format for the code. Currently, the code only accepts plain binary data. To be more precise, suppose you have. And if you assume that (c i(t) ). Is the value of channel (c i ). Then your datafile should be a giant raw file with values. C 0(0), c 1(0), . , c N(0), c 0(1), ., c N(1), . c N(T) ]. This is simply the flatten version of your recordings matrix, with size. The values can be saved in your own format (. Documentation on Python GUI.

2

Automatic Merging — SpyKING CIRCUS 0.4.3 documentation

http://spyking-circus.readthedocs.io/en/0.4.3/code/merging.html

Designing your probe file. Dealing with stimulation artefacts. Need for an meta merging step. To automatize the procedure, we developped a so-called meta-merging step that will allow to quickly identify pairs of templates that have to be merged. To do so, first, we consider only pairs that have a similarity between their templates higher than. This allow not to considerate all the possible pairs, but only those that are likely to be the same cells, because their templates are similar. The GUI is still an...

3

Processing Several Files — SpyKING CIRCUS 0.4.3 documentation

http://spyking-circus.readthedocs.io/en/0.4.3/code/multifiles.html

Designing your probe file. Dealing with stimulation artefacts. It is often the case that, during the same recording session, the experimentalist records only some temporals chunks and not the whole experiment. However, because the neurons are the same all over the recording, it is better to process them as a single datafile. One way of doing so is to manually concatenate all those individual files into a giant one, or use the. Option of the code. If you just want to process several. Templates are then de...

4

Using the GUI — SpyKING CIRCUS 0.4.3 documentation

http://spyking-circus.readthedocs.io/en/0.4.3/GUI/index.html

Panels of the GUIs. Basis of spike sorting. Panels of the GUIs. Basis of spike sorting. Provided by Read the Docs. On Read the Docs. Free document hosting provided by Read the Docs.

5

Dealing with stimulation artefacts — SpyKING CIRCUS 0.4.3 documentation

http://spyking-circus.readthedocs.io/en/0.4.3/code/artefacts.html

Designing your probe file. Dealing with stimulation artefacts. Dealing with stimulation artefacts. Dealing with stimulation artefacts. Sometimes, because of external stimulation, you may end up having some artefacts on top of your recordings. For example, in case of optogenetic stimulation, shinning light next to your recording electrode is likely to contaminate the recording. The code has a built-in mechanism to deal with those artefacts, in the. Specifying the stimulation times. 0 100 1 500. Once those...

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Welcome to the SpyKING CIRCUS’s documentation! — SpyKING CIRCUS 0.4.3 documentation

Welcome to the SpyKING CIRCUS’s documentation! Welcome to the SpyKING CIRCUS’s documentation! The SpyKING CIRCUS is a massively parallel code to perform semi automatic spike sorting on large extra-cellular recordings. Using a smart clustering and a greedy template matching approach, the code can solve the problem of overlapping spikes, and has been tested both for. In 042, we introduce the. How to get the code. Future plans and contributions. Designing your probe file. Dealing with stimulation artefacts.

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