Statistical Region Merging

Statistical Region Merging (SRM) is a method for image segmentation. The labeled image is initialized such that each pixel (or voxel) corresponds to one region. A statistical test on neighboring regions determines whether the mean intensities are similar enough to be merged.

This library is an adaptation of the SRM plugin to Fiji/ImageJ and is based on the algorithm proposed in Nock and Nielsen (2004). Our contribution was to translate the original algorithm to C++ and wrap it in Python. We provide this package under the Digital Porous Media (DPM) organization.

Installation:

dpm_srm is packaged on pypi and can be installed with pip. pip install dpm-srm.

If installing from source, this package requires a C++ compiler.

Usage Example:

This implementation of SRM expects a 2D or 3D grayscale (single color channel) image of type uint8, uint16, or uint32 and a value for Q, which is used as a merging criterion. Roughly speaking, Q is an estimate of the number of expected regions, though this is not strictly adhered to. The larger the Q value, the more regions are produced. The algorithm will return a labeled image of the same shape and datatype as the input image.

Note that the algorithm performs bucket sorting, where the number of buckets correspond to the maximum allowable value for the particular datatype. Therefore, it's important that intensity values of the input image are scaled over the entire range of the datatype. For example, if the input image is uint8, the image should be scaled such that the minimum intensity value is 0, and the maximum is 255. If the input image is uint16 or uint32, the minimum values should be 0 and the maximum should be 65535 (or 4294967295) respectively.

We wrapped each version (2D vs. 3D, dtype) of the template class into individual class instances. The nomenclature is: SRM[2(or 3)]D_unumber_of_bits (e.g. SRG2D_u8(), SRG3D_u32()).

Python Example:

import dpm_srm
import numpy as np

np.random.seed(130621)
image = np.random.randint(0, 256, size=(100, 200, 200), dtype=np.uint8)

srm_obj = dpm_srm.SRM3D_u8(image, Q=5.0)
srm_obj.segment()
segmentation = srm_obj.get_result()

Acknowledgements

This project includes code adapted from Statistical Region Merging by Johannes Schindelin, which is licensed under the BSD 2-Clause License.

The original code can be found here

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for bchang from gravatar.com bchang

Credits

Author: Digital Porous Media

License

BSD License (BSD License)

Requires

Python >=3.8

Classifiers

Report project as malware

Metadata

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for bchang from gravatar.com bchang

Credits

Author: Digital Porous Media

License

BSD License (BSD License)

Requires

Python >=3.8

Classifiers

Report project as malware

Release files for dpm-srm 0.1.9

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Built distributions (wheels)

Table of built distributions (wheels) for dpm-srm 0.1.9
File
dpm_srm-0.1.9-cp314-cp314t-win_amd64.whl 110.3 kB CPython 3.14 CPython 3.14 free-threading Windows x86-64 Details
dpm_srm-0.1.9-cp314-cp314t-win32.whl 98.7 kB CPython 3.14 CPython 3.14 free-threading Windows x86-32 Details
dpm_srm-0.1.9-cp314-cp314t-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp314-cp314t-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp314-cp314t-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 130.4 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
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dpm_srm-0.1.9-cp314-cp314-win_amd64.whl 100.4 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
dpm_srm-0.1.9-cp314-cp314-win32.whl 91.6 kB CPython 3.14 CPython 3.14 Windows x86-32 Details
dpm_srm-0.1.9-cp314-cp314-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp314-cp314-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 128.3 kB CPython 3.14 CPython 3.14 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
dpm_srm-0.1.9-cp314-cp314-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 122.0 kB CPython 3.14 CPython 3.14 Linux glibc 2.27+ ARM64, Linux glibc 2.28+ ARM64 Details
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dpm_srm-0.1.9-cp313-cp313-win_amd64.whl 97.7 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
dpm_srm-0.1.9-cp313-cp313-win32.whl 89.4 kB CPython 3.13 CPython 3.13 Windows x86-32 Details
dpm_srm-0.1.9-cp313-cp313-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp313-cp313-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 128.2 kB CPython 3.13 CPython 3.13 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details
dpm_srm-0.1.9-cp313-cp313-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 121.5 kB CPython 3.13 CPython 3.13 Linux glibc 2.28+ ARM64, Linux glibc 2.27+ ARM64 Details
dpm_srm-0.1.9-cp313-cp313-macosx_11_0_arm64.whl 257.4 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp313-cp313-macosx_10_13_x86_64.whl 242.3 kB CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
dpm_srm-0.1.9-cp312-cp312-win_amd64.whl 97.6 kB CPython 3.12 CPython 3.12 Windows x86-64 Details
dpm_srm-0.1.9-cp312-cp312-win32.whl 89.5 kB CPython 3.12 CPython 3.12 Windows x86-32 Details
dpm_srm-0.1.9-cp312-cp312-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp312-cp312-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 128.2 kB CPython 3.12 CPython 3.12 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details
dpm_srm-0.1.9-cp312-cp312-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 121.3 kB CPython 3.12 CPython 3.12 Linux glibc 2.28+ ARM64, Linux glibc 2.27+ ARM64 Details
dpm_srm-0.1.9-cp312-cp312-macosx_11_0_arm64.whl 257.3 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp312-cp312-macosx_10_13_x86_64.whl 242.1 kB CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
dpm_srm-0.1.9-cp311-cp311-win_amd64.whl 96.5 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
dpm_srm-0.1.9-cp311-cp311-win32.whl 88.6 kB CPython 3.11 CPython 3.11 Windows x86-32 Details
dpm_srm-0.1.9-cp311-cp311-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp311-cp311-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 126.5 kB CPython 3.11 CPython 3.11 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
dpm_srm-0.1.9-cp311-cp311-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 120.7 kB CPython 3.11 CPython 3.11 Linux glibc 2.27+ ARM64, Linux glibc 2.28+ ARM64 Details
dpm_srm-0.1.9-cp311-cp311-macosx_11_0_arm64.whl 255.7 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp311-cp311-macosx_10_9_x86_64.whl 240.5 kB CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
dpm_srm-0.1.9-cp310-cp310-win_amd64.whl 95.9 kB CPython 3.10 CPython 3.10 Windows x86-64 Details
dpm_srm-0.1.9-cp310-cp310-win32.whl 87.6 kB CPython 3.10 CPython 3.10 Windows x86-32 Details
dpm_srm-0.1.9-cp310-cp310-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp310-cp310-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 125.7 kB CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
dpm_srm-0.1.9-cp310-cp310-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 119.7 kB CPython 3.10 CPython 3.10 Linux glibc 2.27+ ARM64, Linux glibc 2.28+ ARM64 Details
dpm_srm-0.1.9-cp310-cp310-macosx_11_0_arm64.whl 254.7 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp310-cp310-macosx_10_9_x86_64.whl 239.6 kB CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details
dpm_srm-0.1.9-cp39-cp39-win_amd64.whl 95.9 kB CPython 3.9 CPython 3.9 Windows x86-64 Details
dpm_srm-0.1.9-cp39-cp39-win32.whl 87.5 kB CPython 3.9 CPython 3.9 Windows x86-32 Details
dpm_srm-0.1.9-cp39-cp39-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp39-cp39-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.9 CPython 3.9 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 126.0 kB CPython 3.9 CPython 3.9 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
dpm_srm-0.1.9-cp39-cp39-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 120.7 kB CPython 3.9 CPython 3.9 Linux glibc 2.27+ ARM64, Linux glibc 2.28+ ARM64 Details
dpm_srm-0.1.9-cp39-cp39-macosx_11_0_arm64.whl 255.0 kB CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp39-cp39-macosx_10_9_x86_64.whl 239.8 kB CPython 3.9 CPython 3.9 macOS 10.9+ x86-64 Details
dpm_srm-0.1.9-cp38-cp38-win_amd64.whl 95.5 kB CPython 3.8 CPython 3.8 Windows x86-64 Details
dpm_srm-0.1.9-cp38-cp38-win32.whl 87.5 kB CPython 3.8 CPython 3.8 Windows x86-32 Details
dpm_srm-0.1.9-cp38-cp38-musllinux_1_2_x86_64.whl 1.2 MB CPython 3.8 CPython 3.8 Linux musl 1.2+ x86-64 Details
dpm_srm-0.1.9-cp38-cp38-musllinux_1_2_aarch64.whl 1.1 MB CPython 3.8 CPython 3.8 Linux musl 1.2+ ARM64 Details
dpm_srm-0.1.9-cp38-cp38-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 125.5 kB CPython 3.8 CPython 3.8 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
dpm_srm-0.1.9-cp38-cp38-manylinux_2_27_aarch64.manylinux_2_28_aarch64.whl 120.1 kB CPython 3.8 CPython 3.8 Linux glibc 2.27+ ARM64, Linux glibc 2.28+ ARM64 Details
dpm_srm-0.1.9-cp38-cp38-macosx_11_0_arm64.whl 254.7 kB CPython 3.8 CPython 3.8 macOS 11.0+ ARM64 Details
dpm_srm-0.1.9-cp38-cp38-macosx_10_9_x86_64.whl 239.5 kB CPython 3.8 CPython 3.8 macOS 10.9+ x86-64 Details

Total release size: 25.6 MB

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0.1.9 This release

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