scivision
scivision: a framework for scientific image analysis
Science Score: 85.0%
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
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
4 of 23 committers (17.4%) from academic institutions -
✓Institutional organization owner
Organization alan-turing-institute has institutional domain (turing.ac.uk) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.7%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
scivision: a framework for scientific image analysis
Basic Info
- Host: GitHub
- Owner: alan-turing-institute
- License: bsd-3-clause
- Language: JavaScript
- Default Branch: main
- Homepage: https://sci.vision/
- Size: 45.5 MB
Statistics
- Stars: 104
- Watchers: 10
- Forks: 40
- Open Issues: 68
- Releases: 24
Topics
Metadata Files
README.md
If you are new to Scivision, start with the website.
The Scivision project is building:
- A community of computer vision practitioners in the sciences and humanities (join the community on Slack)
- A catalog of community-curated computer vision models and datasets from the sciences and humanities
- A software ecosystem of interoperable tools and utilities for working with computer vision models and data, including:
- Scivision.Py, a Python package for conveniently downloading and using the computer vision models and datasets from Python (Scivision on PyPI)
- Pixelflow, a tool for extracting information about the characteristics of objects in images
Example use cases for these tools can be found in the gallery of notebooks using Scivision models and datasets
The Scivision project was founded by the Alan Turing Institute.
Repository contents
This main project repository on GitHub hosts
- development of the Python package (in the root directory)
- development of the website (in frontend)
- the documentation sources (in docs)
Get involved
Submit a bug or feature request here.
If you would like a link to a model or datasource to be listed in the catalog, such a contribution would be gratefully received. These can be submitted through the Scivision website. See the Contributing Guide for more details on how to format your model / data.
Pull requests for code changes are also welcome.
Getting Started with Scivision.Py
A quick overview of using the Scivision.Py python package.
Install Scivision.Py
sh
$ pip install scivision
Load a Scivision model
```python from scivision import loadpretrainedmodel
resnet18 = loadpretrainedmodel( # The model URL "https://github.com/alan-turing-institute/scivision_classifier",
# A Scivision model can contain several variants -- below we select the one to use
model_selection='resnet18',
# Allow the model and its dependencies to be installed if they are not already
# (including tensorflow in this example)
allow_install=True
) ```
We can give an image as input to the model. Any image data compatible with numpy (an 'Array_like') is accepted. We can obtain some image data by loading a Scivision datasource.
Load a Scivision datasource
```python from scivision import loadpretrainedmodel
dataset = load_dataset('https://github.com/alan-turing-institute/scivision-test-data')
'dataset' provides several named arrays. This datasource provides one named 'test_image':
the keys can be looked up with list(dataset) (or by consulting the datasource documentation)
testimage = dataset['testimage'].read() ```
Optionally, inspect the image (with matplotlib, for example): ```python import matplotlib.pyplot as plt
plt.imshow(test_image) ```
Run a Scivision model
python
resnet18.predict(test_image)
Output: koala : 99.78%
Query the model and datasource catalogs
```python from scivision import default_catalog
The datasource catalog as a Pandas dataframe
defaultcatalog.datasources.todataframe()
Similarly for the model catalog
defaultcatalog.models.todataframe() ```
Output:
| | name | description | tasks | url | pkgurl | format | scivisionusable | pretrained | labelsrequired | institution | tags |
|---:|:---------|:---------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------|:----------------------------------------------------|:---------|:-------------------|:-------------|:------------------|:--------------------|:--------------------------------------------------------------------------------------------------------------------------------------|
| 0 | stardist | Single class object detection and segementation of star-convex polygons | (<TaskEnum.objectdetection: 'object-detection'>,
The catalogs are browsable online: - model catalog - datasource catalog
Contributors
Thanks goes to these wonderful people (emoji key):
This project follows the all-contributors specification. Contributions of any kind welcome!
Owner
- Name: The Alan Turing Institute
- Login: alan-turing-institute
- Kind: organization
- Email: info@turing.ac.uk
- Website: https://turing.ac.uk
- Repositories: 477
- Profile: https://github.com/alan-turing-institute
The UK's national institute for data science and artificial intelligence.
Citation (CITATION.cff)
cff-version: 1.2.0
title: scivision
message: "If you use this software, please cite it using the metadata from this file."
type: software
authors:
- given-names: Sebastian
family-names: Ahnert
- given-names: Meghna
family-names: Asthana
orcid: 'https://orcid.org/0000-0002-6101-8904'
- given-names: Edward Jonathan
family-names: Chalstrey
orcid: 'https://orcid.org/0000-0003-2560-1294'
- given-names: Alejandro
family-names: Coca-Castro
orcid: 'https://orcid.org/0000-0002-9264-1539'
- given-names: Alden
family-names: Conner
orcid: 'https://orcid.org/0000-0003-0927-2267'
- given-names: Evangeline Mae
family-names: Corcoran
orcid: 'https://orcid.org/0000-0003-0321-009X'
- given-names: Beatriz
family-names: Costa-Gomes
orcid: 'https://orcid.org/0000-0002-1073-8442'
- given-names: Isabel S.
family-names: Fenton
orcid: 'https://orcid.org/0000-0001-7174-0725'
- given-names: J. Scott
family-names: Hosking
orcid: 'https://orcid.org/0000-0002-3646-3504'
- given-names: Alan R
family-names: Lowe
orcid: 'https://orcid.org/0000-0002-0558-3597'
- given-names: Oliver
family-names: Strickson
orcid: 'https://orcid.org/0000-0002-8177-5582'
- given-names: Samuel
family-names: Tonks
orcid: 'https://orcid.org/0009-0008-1408-1493'
repository-code: 'https://github.com/alan-turing-institute/scivision'
url: 'https://sci.vision/'
identifiers:
- type: doi
value: '10.5281/zenodo.10792860'
keywords:
- computer vision
- image analysis
license: BSD-3-Clause
GitHub Events
Total
- Watch event: 8
- Push event: 846
- Pull request event: 2
- Create event: 1
Last Year
- Watch event: 8
- Push event: 846
- Pull request event: 2
- Create event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ed Chalstrey | e****y@g****m | 181 |
| ots22 | o****2 | 67 |
| Alejandro © | a****c@g****m | 42 |
| Isabel Fenton | I****n | 41 |
| quantumjot | c****e@a****k | 36 |
| Evangeline Corcoran | 8****n | 28 |
| allcontributors[bot] | 4****] | 24 |
| kasra-hosseini | k****i@t****k | 18 |
| Scott Hosking | j****g@g****m | 17 |
| Aida Mehonic | 4****c | 11 |
| Miquel Massot | m****t@g****m | 4 |
| Samuel Tonks | 6****4 | 4 |
| vimode | 3****e | 4 |
| mooniean | b****s@g****m | 4 |
| Meghna Asthana | 3****a | 3 |
| Alden Conner | a****r@t****k | 2 |
| Marjan Famili | 4****i | 2 |
| Aaron Lapworth | 1****n | 1 |
| AlexGregory96 | 4****1 | 1 |
| Arianna | a****i@g****m | 1 |
| James Parkhurst | j****t@d****k | 1 |
| John Francis | j****3@u****u | 1 |
| Mateusz Konieczny | m****z@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 138
- Total pull requests: 144
- Average time to close issues: 8 months
- Average time to close pull requests: 12 days
- Total issue authors: 13
- Total pull request authors: 17
- Average comments per issue: 1.88
- Average comments per pull request: 0.55
- Merged pull requests: 108
- Bot issues: 0
- Bot pull requests: 4
Past Year
- Issues: 1
- Pull requests: 21
- Average time to close issues: 3 days
- Average time to close pull requests: 10 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ots22 (50)
- edwardchalstrey1 (32)
- evangeline-corcoran (14)
- IFenton (11)
- acocac (9)
- quantumjot (4)
- scotthosking (4)
- asthanameghna (3)
- miquelmassot (1)
- Tonks684 (1)
- LittleAri (1)
- aldenc (1)
- phinate (1)
Pull Request Authors
- IFenton (76)
- ots22 (34)
- acocac (9)
- aldenc (9)
- evangeline-corcoran (9)
- Tonks684 (5)
- allcontributors[bot] (5)
- asthanameghna (4)
- edwardchalstrey1 (3)
- quantumjot (3)
- vimode (3)
- johnfrancis13 (2)
- marjanfamili (2)
- LapworthAaron (2)
- mooniean (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 31 last-month
- Total dependent packages: 0
- Total dependent repositories: 3
- Total versions: 23
- Total maintainers: 5
pypi.org: scivision
Scivision
- Homepage: https://sci.vision
- Documentation: https://scivision.readthedocs.io/
- License: BSD 3-Clause License Copyright (c) 2021, The Alan Turing Institute All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Latest release: 0.7.4
published over 1 year ago
Rankings
Dependencies
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