Open Behavior Wiki - User contributions [en]

Analysis

2021-03-29T21:03:38Z

Jonny:

{{#ask:
[[Category:Tools]]
[[Category:Software]]
[[In Software Category::Analysis]]
|?Has Repository
|?Programmed In Language
|?Has Modality
}}

Analysis

2021-03-29T21:03:33Z

Jonny:

{{#ask:
[[Category:Tools]]
[[Category:Software]]
[[In Software Category::Analysis]]
|?Has Repository
|?Programmed In Language
|?Has Modality
}}

a

Tools

2021-03-29T21:03:10Z

Jonny:

== Software ==

'''Categories''':

* [[Analysis]]
* [[Behavior Measurement]]
* [[Video Recording and Analysis]]
* [[Neural Modulation]]

{{#ask:
[[Category:Tools]]
[[Category:Software]]
|?In Software Category
|?Has Repository
|?Programmed In Language
|?Has Modality
|sort=In Software Category
|order=asc
}}

== Hardware ==

B-SoID

2021-03-29T19:16:49Z

Jonny:

{{ Software
| language = Python
| homepage_url = https://github.com/YttriLab/B-SOID
| repository_url = https://github.com/YttriLab/B-SOID
| paper_doi = https://doi.org/10.1101/770271
| authors = Alexander I. Hsu; Eric A. Yttri
| category = Analysis
| modalities = video; unsupervised classification
| uses_tools = DeepLabCut
|}}

B-soID: unsupervised behavior analysis

Jan 16, 2020
B-SOiD-1

Eric Yttri from Carnegie Mellon University has shared the following about B-SOiD, an open source unsupervised algorithm for discovery of spontaneous behaviors:

“Capturing the performance of naturalistic behaviors remains a tantalizing but prohibitively difficult field of study – current methods are difficult, expensive, low temporal resolution, or all of the above. Recent machine learning applications have enabled localization of limb position; however, position alone does not yield behavior. To provide a high temporal resolution bridge from positions to actions and their kinematics, we developed Behavioral Segmentation of Open-field In DeepLabCut, or B-SOiD. B-SOiD is an unsupervised learning algorithm that discovers and classifies actions based on the inherent statistics of the data points of the data points provided (including any marker or markerless system, not just deeplabcut). Our algorithm enables the automated segregation of different, sub-second behaviors with a single bottom-up perspective video camera – and does so without considerable effort or potential bias from the user. This open-source platform opens the door to the efficient study of spontaneous behavior and its neural mechanisms. It also readily provides critical behavioral metrics that historically have been difficult to quantify, such as grooming and stride-length in OCD and stroke research.”

Template:Software

2021-03-29T19:14:25Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Uses Tool=
|mainlabel=-
}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By=
|mainlabel=-
}}
|}

[[Category:Tools]] [[Category:Software]]

B-SoID

2021-03-29T19:13:12Z

Jonny:

B-SoID

2021-03-29T19:11:55Z

Jonny:

B-SoID

2021-03-29T19:11:44Z

Jonny: Created page with "{{ Software | language = Python | homepage_url = https://github.com/YttriLab/B-SOID | repository_url = https://github.com/YttriLab/B-SOID | paper_doi = https://doi.org/10.1101..."

Template:Software

2021-03-29T19:09:02Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Uses Tool=
|mainlabel=-
}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By=
|mainlabel=-
}}
|}

[[Category:Tools]] [[Category:Software]]

Tools

2021-03-29T19:06:46Z

Jonny:

Analysis

2021-03-29T19:05:07Z

Jonny:

{{#ask:
[[Category:Tools]]
[[Category:Software]]
[[In Software Category::Analysis]]
|?Has Repository
|?Programmed In Language
|?Has Modality
}}

Tools

2021-03-29T19:02:06Z

Jonny:

== Software ==

{{#ask:
[[Category:Tools]]
[[Category:Software]]
|?In Software Category
|?Has Repository
|?Programmed In Language
|?Has Modality
|sort=In Software Category
}}

== Hardware ==

== [[Analysis]] ==

== [[Behavior Measurement]] ==

== [[Video Recording and Analysis]] ==

== [[Behavior Apparatus]] ==

== [[Neural Recording]] ==

== [[Neural Modulation]] ==

Tools

2021-03-29T19:01:23Z

Jonny:

== Software ==

{{#ask:
[[Category:Tools]]
[[Category:Software]]
|?In Software Category
|?Has Homepage
|?Has Repository
|?Has DOI
|?Programmed In Language
|sort=In Software Category
}}

== Hardware ==

== [[Analysis]] ==

== [[Behavior Measurement]] ==

== [[Video Recording and Analysis]] ==

== [[Behavior Apparatus]] ==

== [[Neural Recording]] ==

== [[Neural Modulation]] ==

Tools

2021-03-29T19:00:40Z

Jonny:

== Software ==

{{#ask:
[[Category:Tools]]
[[Category:Software]]
|?In Software Category
|?Has Homepage
|?Has Repository
|?Has DOI
|?Programmed In Language
|?sort=In Software Category
}}

== Hardware ==

== [[Analysis]] ==

== [[Behavior Measurement]] ==

== [[Video Recording and Analysis]] ==

== [[Behavior Apparatus]] ==

== [[Neural Recording]] ==

== [[Neural Modulation]] ==

Template:Software

2021-03-29T18:53:50Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By=
|mainlabel=-
}}
|}

[[Category:Tools]] [[Category:Software]]

Template:Software

2021-03-29T18:53:33Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By=-
|mainlabel=-
}}
|}

[[Category:Tools]] [[Category:Software]]

Template:Software

2021-03-29T18:52:45Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By
|mainlabel=-
}}
|}

[[Category:Tools]] [[Category:Software]]

Template:Software

2021-03-29T18:52:24Z

Jonny: |

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By
|mainlabel=-
|format=ul
}}
|}

[[Category:Tools]] [[Category:Software]]

DeepLabCut

2021-03-29T18:51:12Z

Jonny:

{{ Software
| language = Python
| homepage_url = http://www.mackenziemathislab.org/deeplabcut
| repository_url = https://github.com/DeepLabCut/DeepLabCut
| paper_doi = https://doi.org/10.1038/s41593-018-0209-y
| authors = Mackenzie Mathis; Alexander Mathis; Pranav Mamidanna; Kevin M. Cury; Taiga Abe; Venkatesh N. Murthy; Matthias Bethge
| category = analysis
| modalities = video; pose tracking; machine learning
| uses_tools = h5py; matplotlib; numpy; pandas; scikit-image; scikit-learn; scipy; pytables; moviepy
|}}

== Overview ==

Researchers from the [https://www.mathislab.org/ Mathis Group] & [http://www.mousemotorlab.org/home Mathis Lab] at [[Associated With Institution::EPFL]]/[[Associated With Institution::Harvard]] have collaboratively developed DeepLabCut, an open source software package for markerless pose estimation. This software features a robust and fast algorithm for transfer learning with deep neural networks which allows for pose estimation with minimal training data from pre-recorded [[Has Modality::video]] files. The graphical user interface and documentation for this project make it straightforward for users without extensive coding experience and has been applied to video datasets of multiple species, including those commonly studied in neuroscience research labs. DeepLabCut ahs been implemented in a number of other open source paradigms for non-invasive behavior tracking, including projects like [[Used By::B-SoID]], [[Used By::Stytra]], and [[Used By::Kinemouse Wheel]].

We would *highly* encourage anyone interested in video tracking, particularly markerless tracking of subjects in behavioral paradigms to check out the DeepLabCut website, as their documentation, how-to guides, example applications, and descriptions of their software are quite informative. Here you will also find up to date information about their DeepLabCut related projects, including a DLC blog and the Model Zoo, which contains pre-trained models for different species, including Cute Cats, aDorable Dogs, and perhaps more relevant for neuroscience, Mighty Mice. Furhtermore, for more technical details about the computational power of the DeepLabCut algorithm, be sure to check out their GitHub repository (specifically the “Why Use DeepLabCut?” portion).

== See Also ==

Template:Software

2021-03-29T18:50:46Z

Jonny:

<noinclude>
Some example of a software tool!!!

'''Syntax:'''

<pre>
{{ Software
| language =
| homepage_url =
| repository_url =
| paper_doi =
| authors = charles barkley; a big dog t shirt; dune buggin
| category = analysis (or whatever other categories you want to have)
| modalities = video; pose; tracking
| uses_tools = sklearn; etc.
|}}
</pre>

</noinclude>

{| style="border: 1px solid; width:90%; float: center; font-size: 90%; padding: 1rem; margin: auto;"
|-
|colspan="2" style="text-align: center;"| '''{{PAGENAME}}'''
|-
! [[Property:Programmed In Language | Language]]
| [[Programmed In Language::{{{language}}}]]
|-
! [[Property:Has Homepage | Homepage]]
| [[Has Homepage::{{{homepage_url}}}]]
|-
! [[Property:Has Repository | Repository]]
| [[Has Repository::{{{repository_url}}}]]
|-
! [[Property:Has DOI | DOI]]
| [[Has DOI::{{{paper_doi}}}]]
|-
! [[Property:Has Author | Authors]]
| {{#set:Has Author={{{Authors|{{{authors|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:In Software Category | Software Category]]
| [[In Software Category::{{{category}}}]]
|-
! [[Property:Has Modality | Modalities]]
| {{#set:Has Modality={{{Modalities|{{{modalities|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Uses Tool | Uses Tool]]
| {{#set:Uses Tool={{{Uses Tools|{{{uses_tools|}}}}}}|+sep=;|template=LinkToAskQueryForParameter}}
|-
! [[Property:Used By | Used By]]
| {{#ask:
[[Category:Tools]]
[[Uses Tool::{{FULLPAGENAME}}]] ||
|format=ul
}}
{{#ask:
[[{{FULLPAGENAME}}]]
|?Used By
|format=ul
}}
|}

[[Category:Tools]] [[Category:Software]]

Property:Used By

2021-03-29T18:41:03Z