visiomode
A rodent touchscreen-based visuomotor behaviour platform
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Repository
A rodent touchscreen-based visuomotor behaviour platform
Basic Info
- Host: GitHub
- Owner: DuguidLab
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://www.visiomode.org
- Size: 9.64 MB
Statistics
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 23
- Releases: 9
Metadata Files
README.md
Visiomode is an open-source platform for rodent touchscreen-based visuomotor tasks. It has been designed to promote the use of touchscreens as an accessible option for implementing a variety of visual task paradigms, with low-cost and ease-of-use as a priority. Visiomode is implemented on the popular Raspberry Pi computer, and provides the user with an intuitive web interface to design and manage experiments. It can be deployed as a stand-alone cognitive testing solution in both freely-moving and head-restrained environments.
Installation
Raspberry Pi OS (recommended)
The recommended way to install Visiomode is by using pipx (https://pypa.github.io/pipx/). pipx will create an isolated python environment from which Visiomode will run, leaving the system python alone. This is the recommended way to install Visiomode, as it will not interfere with any other python packages you may have installed on your system.
First, make sure that your Raspberry Pi OS is up-to-date.
bash
sudo apt update && sudo apt upgrade
Visiomode runs on SDL 2.0. To make sure all system dependencies are present, run
bash
sudo apt install -y libhdf5-dev libsdl2-mixer-2.0-0 libsdl2-image-2.0-0 libsdl2-2.0-0 libsdl2-ttf-2.0-0
Install pipx using
bash
sudo apt install pipx
And finally, install Visiomode using pipx:
bash
pipx install visiomode
Linux / MacOS
While Visiomode primarily targets the Raspberry Pi OS, it can be installed on any Linux or MacOS machine, which can be useful for trying out the software before deployment, or for testing. Please note that only the Raspberry Pi OS is officially supported - your milage with any other Linux distribution or MacOS in production may vary.
The recommended way to install Visiomode is via pipx (https://pypa.github.io/pipx/).
bash
pipx install visiomode
Usage
To launch Visiomode, open a terminal and run
bash
visiomode
If running over ssh, you will need to prepend DISPLAY=:0 to the visiomode command to run the behaviour window on the primary display.
bash
DISPLAY=:0 visiomode
This will launch the behaviour window (what the animal sees). The web interface can be accessed from any machine connected on the same network as the Raspberry Pi running Visiomode at http://<YOUR-PI-HOSTNAME>.local:5000, where <YOUR-PI-HOSTNAME> is the hostname of your Raspberry Pi. If you're unsure on what this is, run hostname in a terminal window.
Upgrading
Use pipx to upgrade visiomode:
bash
pipx upgrade visiomode
Contributing
Visiomode is currently closed to PRs, except bugfixes. Please open an issue if you wish to contribute.
Funders
Owner
- Name: Duguid Lab
- Login: DuguidLab
- Kind: organization
- Website: www.duguidlab.com
- Repositories: 3
- Profile: https://github.com/DuguidLab
Neural Circuits & Motor Behaviour
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Eleftheriou"
given-names: "Constantinos"
orcid: "https://orcid.org/0000-0002-8506-2504"
- family-names: "Clarke"
given-names: "Thomas"
orcid: "https://orcid.org/0000-0001-6987-3545"
- family-names: "Poon"
given-names: "V"
- family-names: "Zechner"
given-names: "Marie"
- family-names: "Duguid"
given-names: "Ian"
orcid: "https://orcid.org/0000-0001-6966-2641"
title: "Visiomode"
version: 0.5.1
doi: 10.5281/zenodo.1234
date-released: 2023-03-10
url: "https://github.com/DuguidLab/visiomode"
preferred-citation:
type: article
authors:
- family-names: "Eleftheriou"
given-names: "Constantinos"
orcid: "https://orcid.org/0000-0002-8506-2504"
- family-names: "Clarke"
given-names: "Thomas"
orcid: "https://orcid.org/0000-0001-6987-3545"
- family-names: "Poon"
given-names: "V"
- family-names: "Zechner"
given-names: "Marie"
- family-names: "Duguid"
given-names: "Ian"
orcid: "https://orcid.org/0000-0001-6966-2641"
doi: "10.1016/j.jneumeth.2022.109779"
journal: "Journal of Neuroscience Methods"
month: 2
title: "Visiomode: An open-source platform for building rodent touchscreen-based behavioral assays"
volume: 386
year: 2023
GitHub Events
Total
- Issues event: 9
- Delete event: 8
- Issue comment event: 8
- Push event: 55
- Pull request event: 14
- Pull request review event: 5
- Pull request review comment event: 2
- Create event: 7
Last Year
- Issues event: 9
- Delete event: 8
- Issue comment event: 8
- Push event: 55
- Pull request event: 14
- Pull request review event: 5
- Pull request review comment event: 2
- Create event: 7
Committers
Last synced: about 3 years ago
All Time
- Total Commits: 965
- Total Committers: 4
- Avg Commits per committer: 241.25
- Development Distribution Score (DDS): 0.004
Top Committers
| Name | Commits | |
|---|---|---|
| Constantinos Eleftheriou | C****u@e****k | 961 |
| Constantinos Eleftheriou | c****u@e****k | 2 |
| mcol | m****l@p****t | 1 |
| dependabot[bot] | 4****]@u****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 124
- Total pull requests: 72
- Average time to close issues: 8 months
- Average time to close pull requests: 20 days
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 1.1
- Average comments per pull request: 0.49
- Merged pull requests: 68
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 14
- Pull requests: 14
- Average time to close issues: about 1 month
- Average time to close pull requests: 17 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.21
- Average comments per pull request: 0.57
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- celefthe (109)
- olivierdelree (10)
- m-col (3)
- v31415 (2)
Pull Request Authors
- celefthe (55)
- olivierdelree (35)
- m-col (3)
- dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 20 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 13
- Total maintainers: 1
pypi.org: visiomode
An open-source platform for touchscreen-based visuomotor tasks in rodents.
- Documentation: https:/docs.visiomode.org
- License: MIT License Copyright (c) 2019 Constantinos Eleftheriou Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.6.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- actions/stale v3 composite
- Flask ~=2.0.3
- PyYAML ~=6.0
- numpy >=1.22
- pygame ==2.0.1
- pyserial ~=3.5
- actions/cache v3 composite
- actions/checkout v4 composite
- actions/setup-python v4 composite