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https://github.com/psteinb/b3get
a python module to download Broad Bioimage Benchmark Collection images
https://github.com/psteinb/b3get
Last synced: 7 days ago
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a python module to download Broad Bioimage Benchmark Collection images
- Host: GitHub
- URL: https://github.com/psteinb/b3get
- Owner: psteinb
- License: bsd-3-clause
- Created: 2019-02-15T16:33:10.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2019-03-15T14:44:49.000Z (almost 6 years ago)
- Last Synced: 2024-10-07T20:17:49.496Z (3 months ago)
- Language: Python
- Size: 162 KB
- Stars: 24
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE
Awesome Lists containing this project
README
# b3get [](https://travis-ci.com/psteinb/b3get) [](https://codecov.io/gh/psteinb/b3get)
A python module to download [Broad Bioimage Benchmark Collection](https://data.broadinstitute.org/bbbc/image_sets.html) images.
## Usage
### As a python module
``` python
import b3get
images, labels = b3get.to_numpy(6)
```
The call illustrated above creates 2 python lists. Each list contains a set of `numpy.ndarray` objects which yield the images of the dataset (`images`) or the labels (`labels`).
If you like the idea for this repo, please drop me a star. Due to time constraints, I will concentrate on dataset [06](https://data.broadinstitute.org/bbbc/BBBC006/), [24](https://data.broadinstitute.org/bbbc/BBBC024/) and [27](https://data.broadinstitute.org/bbbc/BBBC027/). If your dataset is not among those, please consider contributing.
### From the Command-line
- to list available datasets
``` shell
$ b3get list
BBBC006 Human U2OS cells (out of focus)
BBBC008 Human HT29 colon-cancer cells
BBBC024 3D HL60 Cell Line (synthetic data)
BBBC027 3D Colon Tissue (synthetic data)
```
- to show the URLS for a given dataset
``` shell
$ b3get show 08
https://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_images.zip
https://data.broadinstitute.org/bbbc/BBBC008/BBBC008_v1_foreground.zip
```