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)
$ virtualenv -ppython3 segmentation-env
$ source segmentation-env/bin/activate
Install python requirements (needed to build the package)
$ pip install numpy cython
Install our library (pulls in all other dependencies)
$ pip install segmentation
Usage example
import segmentation as seg
from skimage.io import imread
image = imread('./001001000.tiff', plugin='tifffile')[1] # Read channel 1 of a tiff/flex
im = seg.blur_frame(image) # gaussian blur
segmented, _ = seg.mixture_model(im, debug=True) # second return argument is currently unused
labels = seg.watershed(im, segmented)
1 maintainer
Metadata
1 maintainer
Release files for segmentation 0.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| segmentation-0.2.2.tar.gz | 133.0 kB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| segmentation-0.2.2-cp39-cp39-manylinux2010_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.12+ x86-64 | Details |
| segmentation-0.2.2-cp39-cp39-manylinux1_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.5+ x86-64 | Details |
| segmentation-0.2.2-cp38-cp38-manylinux2010_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.12+ x86-64 | Details |
| segmentation-0.2.2-cp38-cp38-manylinux1_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.5+ x86-64 | Details |
| segmentation-0.2.2-cp37-cp37m-manylinux2010_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| segmentation-0.2.2-cp37-cp37m-manylinux1_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.5+ x86-64 | Details |
| segmentation-0.2.2-cp36-cp36m-manylinux2010_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.12+ x86-64 | Details |
| segmentation-0.2.2-cp36-cp36m-manylinux1_x86_64.whl | CPython 3.6 | CPython 3.6 pymalloc | Linux glibc 2.5+ x86-64 | Details |
Total release size: 3.9 MB
Release files / segmentation-0.2.2.tar.gz
| Download URL | segmentation-0.2.2.tar.gz |
|---|---|
| Size | 133.0 kB |
| Tags | Source |
|
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Release files / segmentation-0.2.2-cp39-cp39-manylinux2010_x86_64.whl
| Download URL | segmentation-0.2.2-cp39-cp39-manylinux2010_x86_64.whl |
|---|---|
| Size | 475.4 kB |
| Tags | CPython 3.9 Linux glibc 2.12+ x86-64 |
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Release files / segmentation-0.2.2-cp39-cp39-manylinux1_x86_64.whl
| Download URL | segmentation-0.2.2-cp39-cp39-manylinux1_x86_64.whl |
|---|---|
| Size | 475.4 kB |
| Tags | CPython 3.9 Linux glibc 2.5+ x86-64 |
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Release files / segmentation-0.2.2-cp38-cp38-manylinux2010_x86_64.whl
| Download URL | segmentation-0.2.2-cp38-cp38-manylinux2010_x86_64.whl |
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| Size | 491.2 kB |
| Tags | CPython 3.8 Linux glibc 2.12+ x86-64 |
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Release files / segmentation-0.2.2-cp38-cp38-manylinux1_x86_64.whl
| Download URL | segmentation-0.2.2-cp38-cp38-manylinux1_x86_64.whl |
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| Size | 491.2 kB |
| Tags | CPython 3.8 Linux glibc 2.5+ x86-64 |
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Release files / segmentation-0.2.2-cp37-cp37m-manylinux2010_x86_64.whl
| Download URL | segmentation-0.2.2-cp37-cp37m-manylinux2010_x86_64.whl |
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| Size | 449.8 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.12+ x86-64 |
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Release files / segmentation-0.2.2-cp37-cp37m-manylinux1_x86_64.whl
| Download URL | segmentation-0.2.2-cp37-cp37m-manylinux1_x86_64.whl |
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| Size | 449.8 kB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.5+ x86-64 |
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Release files / segmentation-0.2.2-cp36-cp36m-manylinux2010_x86_64.whl
| Download URL | segmentation-0.2.2-cp36-cp36m-manylinux2010_x86_64.whl |
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| Tags | CPython 3.6 CPython 3.6 pymalloc Linux glibc 2.12+ x86-64 |
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Release files / segmentation-0.2.2-cp36-cp36m-manylinux1_x86_64.whl
| Download URL | segmentation-0.2.2-cp36-cp36m-manylinux1_x86_64.whl |
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