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Systems Neuro Browser (SNUB)

Systems Neuro Browser (SNUB) - Published in JOSS (2024)

https://github.com/calebweinreb/snub

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Sociology Social Sciences - 87% confidence
Artificial Intelligence and Machine Learning Computer Science - 62% confidence
Last synced: 4 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: calebweinreb
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 32.9 MB
Statistics
  • Stars: 28
  • Watchers: 4
  • Forks: 5
  • Open Issues: 1
  • Releases: 17
Created about 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License

README.md

Systems Neuro Browser (SNUB)

DOI

Read the documentation!

SNUB is a visual interface for systems neuroscience. Using a set of linked data-views, users can explore relationships between raw video, 3D animal pose, behavior annotations, neural activity, or any other relevant time-series data.

Installation

Create and activate a new conda environment with python≥3.8 and install via pip conda create -n snub python=3.8 conda activate snub pip install systems-neuro-browser

Note: Python version 3.8 is required for Linux. For Windows and MacOS, any version ≥3.8 should work.

To speed up selections, pip install ncls. To install optional developer dependencies, pip install systems-neuro-browser[dev]. The docs include more detailed installation instructions.

Getting Started

  • Download the example project.
  • Launch SNUB from the command line with the command snub.
  • Go to File > Open Project, navigate to the project directory, and hit Choose with the directory selected.
  • Alternatively, launch SNUB directly with the project path snub /path/to/project/directory.

Browse your own data

Loading data is simple with the snub.io module. For example the following code creates a new project with paired electrophysiology and video data. See the Tutorial for more details.

``` import snub.io

project_directory = 'path/to/new/project'

snub.io.project.createproject(projectdirectory, duration=1800) snub.io.project.addvideo(projectdirectory, 'path/to/myvideo.avi', name='IRcamera') snub.io.project.addsplikeplot(projectdirectory, 'myephysdata', spiketimes, spikelabels) ```

Convert an NWB file

We provide a rudimentary tool for automatically generating SNUB datasets from Neurodata Without Borders (NWB) files, which contain raw and processed data from neuroscience recordings. The data in NWB files are stored hierarchically, and each component of the hierarchy has a specific neurodata type that reflects the measurement modality (e.g, "Units" for spike trains, "ImageSeries" for video). Our conversion tool generates a SNUB display element for each supported neurodata type. Users can optionally restrict this process to a subset of the NWB hierarchy (e.g., include pose tracking while excluding electrophysiology, or include just a subset of electrophysiology measurements). Here's an example:

```

Run from the command line

Download NWB file

dandi download https://api.dandiarchive.org/api/dandisets/000540/versions/0.230515.0530/assets/94307bee-459c-424e-b3a0-1e86b23f04b2/download/

Download associated video and create directory for it

dandi download https://api.dandiarchive.org/api/dandisets/000540/versions/0.230515.0530/assets/942b0806-2c8b-4289-a072-9e965884fcb6/download/ mkdir sub-SLR087ses-20180706obj-14ua2bsbehavior+image mv 9557b48e-46f0-45f2-a700-a2e15318c5bcexternalfile0.avi sub-SLR087ses-20180706obj-14ua2bs_behavior+image/ ```

```

Run in python

import os, snub

Define paths

nwbfile = "sub-SLR087ses-20180706obj-14ua2bsbehavior+image.nwb" name = os.path.splitext(os.path.basename(nwbfile))[0] projectdirectory = os.path.join(os.path.dirname(nwb_file), f"SNUB-{name}")

Make SNUB plot that includes video and torso tracking

snub.io.createprojectfromnwb(projectdirectory, nwbfile, branches=['torsodlc', 'ImageSeries']) ```

Owner

  • Name: Caleb Weinreb
  • Login: calebweinreb
  • Kind: user

JOSS Publication

Systems Neuro Browser (SNUB)
Published
March 24, 2024
DOI
Volume 9, Issue 95, Page 6187
Authors
Caleb Weinreb ORCID
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
Mohammed Abdal Monium Osman ORCID
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
Maya Jay ORCID
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
Sandeep Robert Datta ORCID
Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
Editor
Elizabeth DuPre ORCID
Tags
neuroscience animal behavior graphical user interface
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GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 2
  • Pull request event: 1
  • Fork event: 1

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 191
  • Total Committers: 3
  • Avg Commits per committer: 63.667
  • Development Distribution Score (DDS): 0.016
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Caleb Weinreb c****w@g****m 188
Mohammed m****6@g****m 2
Ralph Emilio Peterson r****n 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 27
  • Total pull requests: 17
  • Average time to close issues: 30 days
  • Average time to close pull requests: about 5 hours
  • Total issue authors: 10
  • Total pull request authors: 4
  • Average comments per issue: 2.11
  • Average comments per pull request: 0.18
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 35 minutes
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • vigji (9)
  • niksirbi (7)
  • NeuTTH (2)
  • sneakers-the-rat (1)
  • kir0ul (1)
  • jonahpearl (1)
  • lucasmiranda42 (1)
  • ralphpeterson (1)
  • vickerse1 (1)
  • danielpollak (1)
Pull Request Authors
  • calebweinreb (27)
  • NeuTTH (2)
  • yarikoptic (2)
  • ralphpeterson (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 1
pypi.org: systems-neuro-browser

Systems Neuro Browser

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 15 Last month
Rankings
Dependent packages count: 9.9%
Average: 37.8%
Dependent repos count: 65.7%
Maintainers (1)
calebweinreb
Last synced: 4 months ago

Dependencies

.github/workflows/draft-pdf.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v1 composite
  • openjournals/openjournals-draft-action master composite
docs/requirements.txt pypi
  • snub *
  • sphinx ==4.4.0
  • sphinx_rtd_theme ==1.0.0
setup.py pypi
  • PyQt5 *
  • cmapy *
  • imageio *
  • imageio-ffmpeg *
  • interlap *
  • ipykernel *
  • networkx *
  • numba *
  • numpy *
  • opencv-python-headless *
  • pyqtgraph *
  • rastermap *
  • scikit-learn *
  • tqdm *
  • umap-learn *
  • vidio >=0.0.3
  • vispy *
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite