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Quantitative Image Analysis in C++, MATLAB and Python
https://github.com/diplib/diplib

bio-formats cpp cpp14 dipimage diplib filtering image-analysis image-processing image-viewer mathematical-morphology matlab python python3 quantification quantitative-image-analysis

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Quantitative Image Analysis in C++, MATLAB and Python

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README 

        
# *DIPlib 3*



[![Build Status](https://github.com/DIPlib/diplib/actions/workflows/cmake.yml/badge.svg?branch=master)](https://github.com/DIPlib/diplib/actions/workflows/cmake.yml)

[![CodeQL](https://github.com/DIPlib/diplib/actions/workflows/codeql.yml/badge.svg?branch=master)](https://github.com/DIPlib/diplib/security/code-scanning)



The *DIPlib* project contains:



- **[*DIPlib*](https://diplib.org/diplib-docs/)**, a C++ library for quantitative image analysis.

It has been in development at Delft University of Technology in The Netherlands since 1995.

The 3.0 release of *DIPlib* represented a complete rewrite in modern C++ of the library infrastructure,

with most of the image processing and analysis algorithms ported from the previous version,

and some of them improved significantly.

Read [the *DIPlib* documentation](https://diplib.org/diplib-docs/).



- **[*DIPimage*](https://diplib.org/DIPimage.html)**, a *MATLAB* toolbox for quantitative

image analysis. It has been in development at Delft University of Technology in The Netherlands since 1999.

Read [the *DIPimage* User Manual](https://diplib.org/diplib-docs/dipimage_user_manual.html).



- **[*PyDIP*](https://diplib.org/PyDIP.html)**, *Python* bindings to *DIPlib*.

This is currently a thin wrapper that exposes the C++ functionality with little change.

Read [the *PyDIP* User Manual](https://diplib.org/diplib-docs/pydip_user_manual.html).



- ***DIPviewer***, an interactive image display utility. It is usable from C++, *Python* and *MATLAB* programs.

Within *DIPimage* this is an optional alternative to the default *MATLAB*-native interactive display utility.

Read [the *DIPviewer* documentation](https://diplib.org/diplib-docs/dipviewer.html).



- ***DIPjavaio***, an interface to

[*OME Bio-Formats*](https://www.openmicroscopy.org/bio-formats/), a Java-based library that reads

hundreds of image file formats. This module is usable from C++ and *Python* (*DIPimage* interfaces

to *Bio-Formats* natively).

Read [the *DIPjavaio* documentation](https://diplib.org/diplib-docs/dipjavaio.html)



See [the *DIPlib* website](https://diplib.org/) for more information.



## Building and using the project



To build the library you will need a C++14 compliant compiler and *CMake*.

See [Building the *DIPlib* library](https://diplib.org/diplib-docs/building_diplib.html) for detailed instructions.



When linking against the *DIPlib* library without using *CMake*, it is important to set a few preprocessor

macros. See [Linking against the *DIPlib* library](https://diplib.org/diplib-docs/building_diplib.html#linking_diplib)

for details.



## Contributing



### Reporting a bug



We use the [issue tracker on GitHub](https://github.com/DIPlib/diplib/issues) to manage bug reports.

See [`CONTRIBUTING.md`](CONTRIBUTING.md) for instructions on how to report a bug.



### Bug fixes, algorithm improvements, new algorithms



Feel free to submit a [pull request on GitHub](https://github.com/DIPlib/diplib/pulls). Please follow

our [style guide](https://diplib.org/diplib-docs/styleguide.html) and make sure to read

[`CONTRIBUTING.md`](CONTRIBUTING.md) first.



### Documentation, tutorials



Documentation can always be improved (also, *PyDIP* has hardly any at all!). If you want to help write documentation,

or create tutorials for how to use the library, read [`CONTRIBUTING.md`](CONTRIBUTING.md), then submit a

[pull request on GitHub](https://github.com/DIPlib/diplib/pulls).



If you found an error in the documentation, we consider this a bug. See above how to report it.



## License



Copyright 2014-2024 Cris Luengo and contributors  

Copyright 1995-2014 Delft University of Technology



Licensed under the Apache License, Version 2.0 (the "License");

you may not use this library except in compliance with the License.

You may obtain a copy of the License at



   http://www.apache.org/licenses/LICENSE-2.0  

   (or see the [`LICENSE.txt`](LICENSE.txt) file in this distribution)



Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.



*DIPlib* includes the following libraries / external code:



- *Eigen 3*  

  Copyright 2008 Gael Guennebaud  

  Copyright 2007-2011 Benoit Jacob  

  Mozilla Public License Version 2.0  

  see [`dependencies/eigen3/LICENSE.txt`](dependencies/eigen3/LICENSE.txt)  

  (we do not use any of the components with more restrictive licenses)



- *DocTest* (its use can be disabled)  

  Copyright 2016-2023 Viktor Kirilov  

  MIT License  

  see [`dependencies/doctest/LICENSE.txt`](dependencies/doctest/LICENSE.txt)



- *PocketFFT*  

  Copyright 2010-2021 Max-Planck-Society  

  Copyright 2019-2020 Peter Bell  

  3-Clause BSD License  

  see [`dependencies/pocketfft/LICENSE.md`](dependencies/pocketfft/LICENSE.md)



- *PCG Random Number Generation for C++*  

  Copyright 2014-2022 Melissa O'Neill and the PCG Project contributors  

  Apache 2.0 License, or The MIT License, at your option  

  see [`include/diplib/private/pcg_*.hpp`](include/diplib/private/pcg_random.hpp)



- *robin-map*, a fast hash map and hash set  

  Copyright 2017 Thibaut Goetghebuer-Planchon  

  MIT License  

  see [`include/diplib/private/robin_*.h`](include/diplib/private/robin_map.h)



- A fast 2D labeling algorithm out of *YACCLAB*  

  Copyright 2016-2017 Costantino Grana, Federico Bolelli, Lorenzo Baraldi and Roberto Vezzani  

  3-Clause BSD License  

  see [`src/regions/labelingGrana2016.h`](src/regions/labelingGrana2016.h)



- A few color maps from *colorcet*  

  Copyright 2017 Peter Kovesi  

  1-Clause BSD-like License  

  see [`src/display/colormap.cpp`](src/display/colormap.cpp) (about half-way down the file)



- Glyph images obtained by rendering the *Open Sans* font  

  Unknown copyright, designed by Steve Matteson  

  Apache 2.0 License  

  see [`src/generation/draw_text_builtin.cpp`](src/generation/draw_text_builtin.cpp) or [Google Fonts](https://fonts.google.com/specimen/Open+Sans#about)

 

- *libics* (its use can be disabled)  

  Copyright 2015-2017 Scientific Volume Imaging Holding B.V.  

  Copyright 2000-2013 Cris Luengo and others  

  GNU Lesser General Public License, Version 2.1  

  see [`dependencies/libics/GNU_LICENSE`](dependencies/libics/GNU_LICENSE)



- *LibTIFF* (its use can be disabled)  

  Copyright 1988-1997 Sam Leffler  

  Copyright 1991-1997 Silicon Graphics, Inc.  

  2-Clause BSD-like Licence  

  see [`dependencies/libtiff/COPYRIGHT`](dependencies/libtiff/COPYRIGHT)



- *libjpeg* (its use can be disabled)  

  Copyright 1991-2018, Thomas G. Lane, Guido Vollbeding  

  Custom BSD-like Licence  

  see [`dependencies/libjpeg/README`](dependencies/libjpeg/README)



- *libspng* (its use can be disabled)  

  Copyright 2018-2023, Randy  

  2-Clause BSD-like Licence  

  see [`dependencies/libspng/LICENSE`](dependencies/libspng/LICENSE)



- *zlib* (used by *libics*, *LibTIFF* and *libspng*, its use can be disabled)  

  Copyright 1995-2022 Jean-loup Gailly and Mark Adler  

  zlib Licence  

  see [`dependencies/zlib/LICENSE`](dependencies/zlib/LICENSE)



- *pybind11* (only used in the *Python* bindings)  

  Copyright 2016 Wenzel Jakob  

  3-Clause BSD License  

  see [`dependencies/pybind11/LICENSE`](dependencies/pybind11/LICENSE)



- *python-javabridge* (only used in the *Python* bindings)  

  Copyright 2003-2009 Massachusetts Institute of Technology  

  Copyright 2009-2013 Broad Institute  

  3-Clause BSD License  

  see [`pydip/src/loadjvm.py`](pydip/src/loadjvm.py)



- A few *MATLAB* scripts from *OME Bio-Formats* (used in *DIPimage*)  

  Copyright 2012-2021 Open Microscopy Environment  

  2-Clause BSD License  

  see [`dipimage/private/bf*.m`](dipimage/private/bfGetReader.m)  

  (the full *Bio-Formats* library needs to be installed for these to be useful)



- A few Java files from *OME Bio-Formats* (used only to resolve references during the build

  process of *DIPjavaio*, not used otherwise)  

  Copyright (C) 2005 - 2017 Open Microscopy Environment  

  2-Clause BSD License  

  see [`javaio/java/bioformats/readme.md`](javaio/java/bioformats/readme.md)  

  (the full *Bio-Formats* library needs to be installed to use *DIPjavaio*)



- Modified CSS files from *dox++*, which originally came from *m.css* (for documentation)  

  Copyright 2017, 2018, 2019 Vladimír Vondruš  

  MIT License



Note that all of these have permissive open-source licenses similar in spirit

to the Apache License.



*DIPlib* also optionally links against:



- *FFTW3* (as installed on your system, not used by default)  

  Copyright 2003, 2007-14 Matteo Frigo  

  Copyright 2003, 2007-14 Massachusetts Institute of Technology  

  GNU General Public License, Version 2 (**not compatible with the Apache License**)



- *FreeType 2* (as installed on your system, not used by default)  

  Copyright 1996-2021 David Turner, Robert Wilhelm, and Werner Lemberg  

  FreeType License (BSD style)



*DIPviewer* links against the following libraries:



- *FreeGLUT* (as installed on your system, alternative to *GLFW*)  

  Copyright 1999-2000 Pawel W. Olszta  

  X-Consortium license



- *GLFW* (as installed on your system, alternative to *FreeGLUT*)  

  Copyright 2002-2006 Marcus Geelnard  

  Copyright 2006-2011 Camilla Berglund  

  BSD-like license



- *OpenGL* (as installed on your system)  

  (free from licensing requirements)



*DIPjavaio* links against:



- *JDK 8* (as installed on your system)  

  Copyright, probably Sun and/or Oracle  

  GNU General Public License, Version 2 (**not compatible with the Apache License**)



- *OME Bio-Formats* (optional, as installed on your system)  

  Copyright 2012-2017 Open Microscopy Environment  

  GNU General Public License, Version 2 (**not compatible with the Apache License**)



Note that [*OME Bio-Formats*](https://www.openmicroscopy.org/bio-formats/) is optional,

but *DIPjavaio* is currently useless without it.

The *DIPjavaio* sources provided with this project are shared under the same licence

as the rest of the project (Apache 2.0), but by linking with *Bio-Formats*, your

whole program will become GPL. This module is not suitable for use in commercial,

closed-source software.