segmentation
Boonelab segmentation for microscopy images
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Keywords
Repository
Boonelab segmentation for microscopy images
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 3
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
Fast Mixture Model Segmentation
Fast mixture model segmentation used in Boone and Andrews labs
Python requirements
- Numpy
- Cython
- scikit-image
Installation
Create a virtual environment (optional)
sh
$ virtualenv -ppython3 segmentation-env
$ source segmentation-env/bin/activate
Install python requirements (needed to build the package)
sh
$ pip install numpy cython
Install our library (pulls in all other dependencies)
sh
$ pip install segmentation
Usage example
Programmatically:
```python from segmentation import segmentation from segmentation import watershed from skimage.io import imread
image = imread('./image.tiff', plugin='tifffile')[1] # Read channel 1 of a tiff/flex im = segmentation.blurframe(image) # gaussian blur segmented, _ = segmentation.mixturemodel(im, debug=True) # second return argument is currently unused labels = watershed(im, segmented) ```
Command line
```sh $ segment -h # for usage information
$ segment -o segmented.data image.tiff ```
Output is a memmaped labels array. You can read it like this:
python
from numpy import memmap
labels = memmap('segmented.data', dtype='int32', shape=(1010, 1346)) # shape is same as input image
Owner
- Name: Boone-Andrews Lab
- Login: BooneAndrewsLab
- Kind: organization
- Location: Toronto, Canada
- Website: http://sites.utoronto.ca/boonelab/
- Repositories: 3
- Profile: https://github.com/BooneAndrewsLab
Donnelly Centre, University of Toronto
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| usajusaj | u****j@u****g | 19 |
| usajusaj | u****j@g****m | 5 |
| Matej Usaj | u****j | 4 |
| Nil Sahin | n****n | 1 |
| Matej Usaj | m****j@u****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 2
- Total pull requests: 2
- Average time to close issues: 1 day
- Average time to close pull requests: 1 minute
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- leesin9527 (1)
- pdavis39 (1)
Pull Request Authors
- usajusaj (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- cython
- gcc_linux-64
- numpy
- scikit-image
- cython *
- numpy *
- scikit-image *
- scipy *
- numpy *
- scikit-image *
- scipy *