histomicstk

Pre-release

This release is a pre-release and may not be stable for production use.

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HistomicsTK is a Python package for the analysis of digital pathology images. It can function as a stand-alone library, or as a Digital Slide Archive plugin that allows users to invoke image analysis jobs through HistomicsUI. The functionality offered by HistomicsTK can be extended using slicer cli web which allows developers to integrate their image analysis algorithms into DSA for dissemination through HistomicsUI.

Whole-slide imaging captures the histologic details of tissues in large multiresolution images. Improvements in imaging technology, decreases in storage costs, and regulatory approval of digital pathology for primary diagnosis have resulted in an explosion of whole-slide imaging data. Digitization enables the application of computational image analysis and machine learning algorithms to characterize the contents of these images, and to understand the relationships between histology, clinical outcomes, and molecular data from genomic platforms. Compared to the related areas of radiology and genomics, open-source tools for the management, visualization, and analysis of digital pathology has lagged. To address this we have developed HistomicsTK in coordination with the Digital Slide Archive (DSA), a platform for managing and sharing digital pathology images in a centralized web-accessible server, and HistomicsUI, a specialized user interface for annotation and markup of whole-slide images and for running image analysis tools and for scalable visualizing of dense outputs from image analysis algorithms. HistomicsTK aims to serve the needs of both pathologists/biologists interested in using state-of-the-art algorithms to analyze their data, and algorithm researchers interested in developing new/improved algorithms and disseminate them for wider use by the community.

HistomicsTK can be used in two ways:

As a pure Python package: enables application of image analysis algorithms to data independent of the Digital Slide Archive (DSA). HistomicsTK provides a collection of fundamental algorithms for tasks such as color normalization, color deconvolution, nuclei segmentation, and feature extraction. Read more about these capabilities here: api-docs and examples for more information.

Installation instructions on Linux:

To install HistomicsTK using PyPI:
```
$ python -m pip install histomicstk --find-links https://girder.github.io/large_image_wheels
```
To install HistomicsTK from source:
```
$ git clone https://github.com/DigitalSlideArchive/HistomicsTK/
$ cd HistomicsTK/
$ python -m pip install -e . --find-links https://girder.github.io/large_image_wheels
```
HistomicsTK uses the large_image library to read content from whole-slide and microscopy image formats. Depending on your exact system, installing the necessary libraries to support these formats can be complex. There are some non-official prebuilt libraries available for Linux that can be included as part of the installation by specifying pip install histomicstk --find-links https://girder.github.io/large_image_wheels. Note that if you previously installed HistomicsTK or large_image without these, you may need to add --force-reinstall --no-cache-dir to the pip install command to force it to use the find-links option.

The system version of various libraries are used if the --find-links option is not specified. You will need to use your package manager to install appropriate libraries (on Ubuntu, for instance, you’ll need libopenslide-dev and libtiff-dev).

To install from source on Windows:

1- Run the following:
```
$ pip install large-image
$ pip install cmake
$ git clone https://github.com/DigitalSlideArchive/HistomicsTK/
$ cd HistomicsTK/
$ python -m pip install setuptools-scm "Cython>=0.25.2" "scikit-build>=0.8.1" "cmake>=0.6.0" "numpy>=1.12.1"
```
2- Run pip install libtiff

3- Run pip install large-image-source-tiff to install typical tile sources. You may need other sources, which would require other libraries.

4- Install Visual Studio 15 2017 Community Version

5- Install C++ build tools. Under Tools > Get Tools and Features … > Desktop Development with C++, ensure that the first 8 boxes are checked.

6- Run this:
```
$ python -m pip install -e .
$ pip install girder-client
```
To install from source on OSX:

Note: This needs to be confirmed and expanded by an OSX user. There are probably assumptions made about available libraries.

Use homebrew to install libtiff and openslide or other libraries depending on your desired tile sources.

Run:
```
$ python -m pip install histomicstk large-image-source-tiff large-image-source-openslide
```
As a image-processing task library for HistomicsUI and the Digital Slide Archive: This allows end users to apply containerized analysis modules/pipelines over the web. See the Digital Slide Archive for installation instructions.

Refer to our website for more information.

Previous Versions

The HistomicsTK repository used to contain almost all of the Digital Slide Archive and HistomicsUI, and now container primarily code for image analysis algorithms and processing of annotation data. The deployment and installation code and instructions for DSA have moved to the Digital Slide Archive repository. The user interface and annotation functionality has moved to the HistomicsUI repository.

The deployment and UI code will eventually be removed from the master branch of this repository; any new development on those topics should be done in those locations.

Funding

This work is funded by the NIH grant U24-CA194362-01.

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Nov 13, 2024

1.3.15.dev2 pre-release

Nov 12, 2024

1.3.15.dev1 pre-release

Oct 24, 2024

1.3.14

Oct 22, 2024

1.3.14.dev1 pre-release

Oct 22, 2024

1.3.13

Oct 22, 2024

1.3.13.dev6 pre-release

Oct 22, 2024

1.3.13.dev5 pre-release

Oct 14, 2024

1.3.13.dev4 pre-release

Oct 14, 2024

1.3.13.dev3 pre-release

Oct 7, 2024

1.3.13.dev2 pre-release

Oct 7, 2024

1.3.13.dev1 pre-release

Sep 23, 2024

1.3.12

Sep 18, 2024

1.3.12.dev8 pre-release

Sep 17, 2024

1.3.12.dev7 pre-release

Sep 17, 2024

1.3.12.dev6 pre-release

Sep 16, 2024

1.3.12.dev5 pre-release

Sep 16, 2024

1.3.12.dev4 pre-release

Aug 23, 2024

1.3.12.dev3 pre-release

Aug 21, 2024

1.3.12.dev2 pre-release

Aug 20, 2024

1.3.12.dev1 pre-release

Aug 6, 2024

1.3.11

Aug 1, 2024

1.3.11.dev1 pre-release

Aug 1, 2024

1.3.10

Jul 15, 2024

1.3.10.dev2 pre-release

Jul 15, 2024

1.3.10.dev1 pre-release

Jul 8, 2024

1.3.9

Jul 5, 2024

1.3.9.dev4 pre-release

Jul 5, 2024

1.3.9.dev3 pre-release

Jul 2, 2024

1.3.9.dev2 pre-release

Jun 17, 2024

1.3.8

May 13, 2024

1.3.8.dev2 pre-release

May 13, 2024

1.3.8.dev1 pre-release

May 13, 2024

1.3.7.dev1 pre-release

Apr 11, 2024

1.3.6

Apr 10, 2024

1.3.6.dev5 pre-release

Apr 9, 2024

1.3.6.dev4 pre-release

Apr 4, 2024

1.3.6.dev3 pre-release

Apr 4, 2024

1.3.6.dev2 pre-release

Mar 18, 2024

1.3.6.dev1 pre-release

Feb 28, 2024

1.3.5

Feb 23, 2024

1.3.5.dev1 pre-release

Feb 21, 2024

1.3.4

Feb 19, 2024

1.3.4.dev2 pre-release

Feb 19, 2024

1.3.4.dev1 pre-release

Feb 16, 2024

1.3.3

Feb 16, 2024

1.3.3.dev3 pre-release

Feb 16, 2024

1.3.3.dev2 pre-release

Feb 16, 2024

1.3.3.dev1 pre-release

Feb 5, 2024

1.3.2

Jan 30, 2024

1.3.2.dev10 pre-release

Jan 30, 2024

1.3.2.dev9 pre-release

Jan 29, 2024

1.3.2.dev8 pre-release

Jan 25, 2024

1.3.2.dev7 pre-release

Jan 25, 2024

1.3.2.dev5 pre-release

Dec 18, 2023

1.3.2.dev2 pre-release

Dec 11, 2023

1.3.2.dev1 pre-release

Dec 11, 2023

1.3.1

Dec 6, 2023

1.3.1.dev6 pre-release

Dec 5, 2023

1.3.1.dev5 pre-release

Dec 5, 2023

1.3.1.dev4 pre-release

Dec 1, 2023

1.3.1.dev3 pre-release

Dec 1, 2023

1.3.1.dev2 pre-release

Nov 16, 2023

1.3.1.dev1 pre-release

Nov 16, 2023

1.3.0

Nov 2, 2023

1.2.11.dev9 pre-release

Nov 2, 2023

1.2.11.dev8 pre-release

Nov 2, 2023

1.2.11.dev7 pre-release

Nov 2, 2023

1.2.11.dev6 pre-release

Oct 3, 2023

1.2.11.dev5 pre-release

Sep 21, 2023

1.2.11.dev4 pre-release

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1.2.11.dev3 pre-release

Sep 19, 2023

1.2.11.dev2 pre-release

Sep 6, 2023

1.2.11.dev1 pre-release

Aug 30, 2023

1.2.10

Aug 30, 2023

1.2.10.dev9 pre-release

Aug 30, 2023

1.2.10.dev8 pre-release

Aug 30, 2023

1.2.10.dev7 pre-release

Aug 30, 2023

1.2.10.dev6 pre-release

Aug 29, 2023

1.2.10.dev5 pre-release

Aug 29, 2023

1.2.10.dev4 pre-release

Aug 29, 2023

1.2.10.dev3 pre-release

Aug 28, 2023

1.2.10.dev2 pre-release

Aug 25, 2023

1.2.10.dev1 pre-release

Aug 25, 2023

1.2.9

Aug 25, 2023

1.2.9.dev31 pre-release

Aug 24, 2023

1.2.9.dev30 pre-release

Aug 21, 2023

1.2.9.dev29 pre-release

Aug 18, 2023

1.2.9.dev28 pre-release

Aug 10, 2023

1.2.9.dev27 pre-release

Aug 10, 2023

1.2.9.dev26 pre-release

Aug 10, 2023

1.2.9.dev25 pre-release

Aug 10, 2023

1.2.9.dev24 pre-release

Aug 10, 2023

1.2.9.dev23 pre-release

Aug 7, 2023

1.2.9.dev22 pre-release

Aug 3, 2023

1.2.9.dev21 pre-release

Aug 1, 2023

1.2.9.dev20 pre-release

Aug 1, 2023

1.2.9.dev19 pre-release

Jul 28, 2023

1.2.9.dev18 pre-release

Jul 28, 2023

1.2.9.dev17 pre-release

Jul 28, 2023

1.2.9.dev16 pre-release

Jul 28, 2023

1.2.9.dev15 pre-release

Jul 28, 2023

1.2.9.dev14 pre-release

Jul 28, 2023

1.2.9.dev13 pre-release

Jul 27, 2023

1.2.9.dev12 pre-release

Jul 27, 2023

1.2.9.dev11 pre-release

Jul 27, 2023

1.2.9.dev10 pre-release

Jul 27, 2023

1.2.9.dev9 pre-release

Jul 26, 2023

1.2.9.dev8 pre-release

Jul 26, 2023

1.2.9.dev7 pre-release

Jul 26, 2023

1.2.9.dev6 pre-release

Jul 25, 2023

1.2.9.dev5 pre-release

Jul 24, 2023

1.2.9.dev4 pre-release

Jul 14, 2023

1.2.9.dev3 pre-release

Jul 14, 2023

1.2.9.dev2 pre-release

Jul 13, 2023

1.2.8

Jul 12, 2023

1.2.8.dev16 pre-release

Jul 12, 2023

1.2.8.dev15 pre-release

Jul 7, 2023

1.2.8.dev14 pre-release

Jul 6, 2023

1.2.8.dev13 pre-release

Jul 6, 2023

1.2.8.dev12 pre-release

Jun 19, 2023

1.2.8.dev8 pre-release

Jun 19, 2023

1.2.8.dev5 pre-release

Jun 1, 2023

1.2.8.dev2 pre-release

May 23, 2023

1.2.7

May 2, 2023

1.2.7.dev2 pre-release

May 2, 2023

1.2.6

Apr 27, 2023

1.2.6.dev10 pre-release

Apr 27, 2023

1.2.6.dev9 pre-release

Apr 27, 2023

1.2.6.dev7 pre-release

Apr 18, 2023

1.2.6.dev5 pre-release

Apr 17, 2023

1.2.6.dev3 pre-release

Apr 17, 2023

1.2.6.dev1 pre-release

Apr 11, 2023

1.2.5

Apr 4, 2023

1.2.5.dev5 pre-release

Apr 4, 2023

1.2.5.dev4 pre-release

Mar 6, 2023

1.2.5.dev3 pre-release

Feb 24, 2023

1.2.5.dev2 pre-release

Feb 22, 2023

1.2.5.dev1 pre-release

Feb 14, 2023

1.2.4

Feb 10, 2023

1.2.4.dev14 pre-release

Feb 8, 2023

1.2.4.dev13 pre-release

Feb 3, 2023

1.2.4.dev11 pre-release

Jan 13, 2023

1.2.4.dev10 pre-release

Jan 13, 2023

1.2.4.dev9 pre-release

Dec 20, 2022

1.2.4.dev8 pre-release

Dec 13, 2022

1.2.4.dev6 pre-release

Nov 29, 2022

1.2.4.dev5 pre-release

Nov 14, 2022

1.2.4.dev4 pre-release

Nov 10, 2022

1.2.4.dev3 pre-release

Nov 10, 2022

1.2.4.dev2 pre-release

Nov 7, 2022

1.2.4.dev1 pre-release

Sep 20, 2022

1.2.3

Sep 20, 2022

1.2.3.dev1 pre-release

Sep 20, 2022

1.2.2

Sep 16, 2022

1.2.2.dev7 pre-release

Sep 1, 2022

1.2.2.dev6 pre-release

Aug 31, 2022

1.2.2.dev5 pre-release

Aug 24, 2022

1.2.2.dev4 pre-release

Aug 23, 2022

1.2.2.dev3 pre-release

Aug 18, 2022

1.2.2.dev1 pre-release

Jul 8, 2022

1.2.1

Jun 23, 2022

1.2.1.dev17 pre-release

Jun 13, 2022

1.2.1.dev15 pre-release

May 31, 2022

1.2.1.dev12 pre-release

May 24, 2022

1.2.1.dev11 pre-release

May 17, 2022

1.2.1.dev8 pre-release

May 3, 2022

1.2.1.dev7 pre-release

Apr 21, 2022

1.2.1.dev6 pre-release

Apr 21, 2022

1.2.1.dev5 pre-release

Apr 5, 2022

1.2.1.dev4 pre-release

Mar 29, 2022

1.2.1.dev3 pre-release

Mar 22, 2022

1.2.1.dev2 pre-release

Mar 3, 2022

1.2.1.dev1 pre-release

Mar 3, 2022

1.2.0

Mar 3, 2022

1.1.1.dev51 pre-release

Mar 3, 2022

1.1.1.dev50 pre-release

Feb 28, 2022

1.1.1.dev43 pre-release

Feb 17, 2022

1.1.1.dev42 pre-release

Feb 16, 2022

1.1.1.dev41 pre-release

Feb 14, 2022

1.1.1.dev40 pre-release

Feb 10, 2022

1.1.1.dev39 pre-release

Feb 9, 2022

1.1.1.dev38 pre-release

Jan 25, 2022

1.1.1.dev37 pre-release

Dec 7, 2021

1.1.1.dev36 pre-release

Oct 26, 2021

1.1.1.dev35 pre-release

Oct 5, 2021

1.1.1.dev34 pre-release

Jun 30, 2021

1.1.1.dev31 pre-release

Jun 28, 2021

1.1.1.dev29 pre-release

Jun 23, 2021

1.1.1.dev28 pre-release

Jun 23, 2021

1.1.1.dev26 pre-release

Jun 21, 2021

1.1.1.dev22 pre-release

Jun 11, 2021

1.1.1.dev20 pre-release

Jun 11, 2021

1.1.1.dev15 pre-release

Jun 10, 2021

1.1.1.dev14 pre-release

Jun 8, 2021

1.1.1.dev13 pre-release

May 11, 2021

1.1.1.dev11 pre-release

Apr 20, 2021

1.1.1.dev10 pre-release

Apr 6, 2021

1.1.1.dev9 pre-release

Mar 26, 2021

1.1.1.dev2 pre-release

Mar 25, 2021

1.1.1.dev1 pre-release

Feb 19, 2021

1.1.0

Jan 27, 2021

1.0.8.dev23 pre-release

Jan 26, 2021

1.0.8.dev22 pre-release

Jan 11, 2021

1.0.8.dev21 pre-release

Jan 11, 2021

1.0.8.dev3 pre-release

Jan 11, 2021

1.0.8.dev2 pre-release

Jan 11, 2021

1.0.8.dev1 pre-release

Jan 8, 2021

1.0.7

Jan 8, 2021

1.0.7.dev10 pre-release

Jan 8, 2021

1.0.7.dev9 pre-release

Jan 8, 2021

1.0.7.dev8 pre-release

Jan 7, 2021

1.0.7.dev7 pre-release

Oct 22, 2020

1.0.7.dev6 pre-release

Oct 20, 2020

1.0.7.dev5 pre-release

Sep 29, 2020

1.0.7.dev2 pre-release

Jul 28, 2020

1.0.6

Jul 21, 2020

1.0.6.dev2 pre-release

Jul 21, 2020

1.0.6.dev1 pre-release

Jul 21, 2020

1.0.5

Jul 1, 2020

1.0.5.dev2 pre-release

Jun 2, 2020

1.0.5.dev1 pre-release

Jun 1, 2020

1.0.4

May 18, 2020

1.0.3.dev98 pre-release

May 18, 2020

1.0.3.dev97 pre-release

May 18, 2020

1.0.3.dev96 pre-release

Apr 30, 2020

1.0.3.dev71 pre-release

Apr 29, 2020

1.0.3.dev69 pre-release

Apr 23, 2020

1.0.3.dev68 pre-release

Apr 22, 2020

1.0.3.dev67 pre-release

Apr 22, 2020

1.0.3.dev66 pre-release

Apr 20, 2020

1.0.3.dev65 pre-release

Apr 17, 2020

1.0.3.dev64 pre-release

Apr 16, 2020

1.0.3.dev63 pre-release

Mar 5, 2020

1.0.3.dev62 pre-release

Feb 21, 2020

1.0.3.dev61 pre-release

Feb 17, 2020

1.0.3.dev60 pre-release

Jan 24, 2020

1.0.3.dev56 pre-release

Jan 23, 2020

1.0.3.dev49 pre-release

Jan 21, 2020

1.0.3.dev47 pre-release

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1.0.3.dev45 pre-release

Jan 20, 2020

1.0.3.dev39 pre-release

Jan 16, 2020

1.0.3.dev36 pre-release

Jan 16, 2020

1.0.3.dev28 pre-release

Jan 15, 2020

1.0.3.dev23 pre-release

Jan 13, 2020

1.0.3.dev17 pre-release

Jan 13, 2020

1.0.3.dev13 pre-release

Jan 13, 2020

1.0.3.dev11 pre-release

Jan 13, 2020

1.0.3.dev9 pre-release

Dec 31, 2019

1.0.3.dev7 pre-release

Dec 31, 2019

1.0.3.dev5 pre-release

Dec 10, 2019

1.0.3.dev3 pre-release

Dec 5, 2019

1.0.0.dev271 pre-release

Oct 18, 2019

1.0.0.dev262 pre-release

Oct 11, 2019

1.0.0.dev256 pre-release

Oct 10, 2019

1.0.0.dev254 pre-release

Oct 4, 2019

1.0.0.dev231 pre-release

Sep 25, 2019

1.0.0.dev212 pre-release

Sep 25, 2019

1.0.0.dev210 pre-release

Sep 24, 2019

1.0.0.dev186 pre-release

Sep 23, 2019

1.0.0.dev184 pre-release

Aug 29, 2019

1.0.0.dev175 pre-release

Aug 29, 2019

1.0.0.dev133 pre-release

Aug 27, 2019

1.0.0.dev131 pre-release

Aug 27, 2019

1.0.0.dev128 pre-release

Aug 23, 2019

1.0.0.dev44 pre-release

Aug 23, 2019

1.0.0.dev42 pre-release

Aug 22, 2019

1.0.0.dev40 pre-release

Aug 2, 2019

1.0.0.dev37 pre-release

Aug 2, 2019

1.0.0.dev35 pre-release

Aug 2, 2019

1.0.0.dev25 pre-release

May 24, 2019

1.0.0.dev11 pre-release

May 9, 2019

1.0.0.dev6 pre-release

May 9, 2019

1.0.0.dev5 pre-release

May 8, 2019

1.0.0.dev4 pre-release

May 8, 2019

1.0.0.dev3 pre-release

May 8, 2019

1.0.0.dev2 pre-release

May 8, 2019

1.0.0.dev1 pre-release

May 8, 2019

0.3.0.dev1 pre-release

May 1, 2019

0.1.5.dev142 pre-release

Dec 2, 2019

0.1.5.dev39 pre-release

Nov 20, 2019

0.1.5.dev37 pre-release

Oct 31, 2019

0.1.5.dev35 pre-release

Oct 29, 2019

0.1.5.dev32 pre-release

Oct 24, 2019

0.1.5.dev30 pre-release

Oct 24, 2019

0.1.5.dev28 pre-release

Oct 24, 2019

0.1.5.dev26 pre-release

Oct 23, 2019

0.1.5.dev16 pre-release

Oct 23, 2019

0.1.5.dev14 pre-release

Oct 23, 2019

0.1.5.dev12 pre-release

Oct 23, 2019

0.1.5.dev10 pre-release

Oct 22, 2019

0.1.5.dev8 pre-release

Oct 21, 2019

0.1.5.dev2 pre-release

Oct 21, 2019

0.0.0

Jun 2, 2025

histomicstk 1.4.1.dev58

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