simpleitk / tutorial

SimpleITK

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SimpleITK is an image analysis toolkit with a large number of components supporting general filtering operations, image segmentation and registration. It is built on top of the Insight Segmentation and Registration Toolkit ITK with the intent of providing a simplified interface to ITK. SimpleITK itself is written in C++ but is available for a large number of programming languages. Currently, these include:

• Python
• R
• Java
• C#
• Lua
• TCL
• Ruby

Wrapping of the C++ code is accomplished through SWIG, in principle, any language wrapped by SWIG should be applicable to SimpleITK.

Unlike ITK's support of n-dimensional spatio-temporal images, SimpleITK supports 2D, 3D and 4D images. The dimensionality refers to spatio-temporal dimensions, the voxels can be n-dimensional vectors.

SimpleITK is licensed under the Apache License.

Acknowledgments

SimpleITK development has been supported by:

• The Intramural Research Program of the National Institutes of Health, National Institute of Allergy and Infectious Diseases.

• The US National Library of Medicine under the American Recovery and Reinvestment Act (ARRA) and under the Intramural Research Program of the U.S. National Institutes of Health.

• The Insight Software Consortium and the ITK user and developer communities.

License and Copyright

The SimpleITK project is part of the Insight Software Consortium(ISC) a non-profit educational consortium dedicated to promoting and maintaining open-source, freely available software for bio-medical image analysis. The copyright is held by NumFOCUS. The SimpleITK software is distributed under the Apache License 2.0.

How to Cite

If you found SimpleITK useful in your research, support our efforts by citing the relevant publication(s):

R. Beare, B. C. Lowekamp, Z. Yaniv, "Image Segmentation, Registration and Characterization in R with SimpleITK", J Stat Software, 86(8), https://doi.org/10.18637/jss.v086.i08, 2018.

Z. Yaniv, B. C. Lowekamp, H. J. Johnson, R. Beare, "SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research", J Digit Imaging., 31(3): 290-303, https://doi.org/10.1007/s10278-017-0037-8, 2018.

B. C. Lowekamp, D. T. Chen, L. Ibáñez, D. Blezek, "The Design of SimpleITK", Front. Neuroinform., 7:45. https://doi.org/10.3389/fninf.2013.00045, 2013.

Documentation

With massive libraries like SimpleITK, good documentation is a must. The documentation for SimpleITK is split up into multiple levels:

1. API Documentation - This contains class and function documentation. The descriptions for functions and classes are primarily borrowed from the original ITK C++ classes.
2. SimpleITK Documentation - This site contains high-level guides (fundamental SimpleITK concepts, common conventions, etc.), details with respect to the toolkit's binary distributions, instructions for building the toolkit, as well as SimpleITK examples in all supported programming languages. [This site replaced the SimpleITK Wiki which is mostly of interest for historical reasons.]
3. Jupyter Notebook Repository - This repository contains a collection of Jupyter Notebooks illustrating the use of SimpleITK for educational and research activities. The notebooks demonstrate the use of SimpleITK for interactive image analysis using the Python and R programming languages. Recommended reading, if you are starting with SimpleITK.

Support

SimpleITK provides access to most of the ITK components, but not all. If you are looking for something specific and can't find it, open an issue on GitHub or ask for support on the forum.

Report and Issue or Request a Feature

Please use the issue tracker to report problems or request features.

tutorial's Issues

Not able to read image in tutorial

I am following the simpleITK tutorial and these two lines of code throw this error.

image_viewer = sitk.ImageViewer()
image_viewer.Execute(sitk.ReadImage(fetch_data(“SimpleITK.jpg”)))

Exception thrown in SimpleITK ImageFileReader_Execute: D:\a\1\sitk\Code\IO\src\sitkImageReaderBase.cxx:102:
sitk::ERROR: Unable to open “C:\Users\paral\OneDrive\Υπολογιστής\diplomatikh\TUTORIAL\data\SimpleITK.jpg” for reading.

Both the image and fiji are where they are supposed to be.

ImportError: DLL load failed while importing _SimpleITK: The specified module could not be found.

i had a problem with loading the image, so I uninstalled everything and followed the tutorial, but I get two different errors.
First, when I type
conda update anaconda
I get
PackageNotInstalledError: Package is not installed in prefix.
prefix: C:\Users\paral\anaconda3
package name: anaconda

Which can be bypassed with
conda install anaconda.

After that everything works fine until I open the notebook. When I try to import SimpleITK I get

---

ImportError Traceback (most recent call last)
Cell In[1], line 1
----> 1 import SimpleITK as sitk
2 from downloaddata import fetch_data, fetch_data_all
4 from ipywidgets import interact

File ~\anaconda3\envs\sitkpy\lib\site-packages\SimpleITK_init_.py:18
1 # ========================================================================
2 #
3 # Copyright NumFOCUS
(...)
16 #
17 # ========================================================================
---> 18 from SimpleITK.SimpleITK import *
19 from SimpleITK.extra import *
21 from SimpleITK._version import version

File ~\anaconda3\envs\sitkpy\lib\site-packages\SimpleITK\SimpleITK.py:13
11 # Import the low-level C/C++ module
12 if package or "." in name:
---> 13 from . import _SimpleITK
14 else:
15 import _SimpleITK

ImportError: DLL load failed while importing _SimpleITK: The specified module could not be found.

I have re-installed anaconda python but nothing seems to work.

Edit: The first time import simpleITK worked fine. I have no clue what I did differently.

I am new to itk.js and planning to use in my react application. Is there any tutorial/documentation/examples that I can refer?

I have been trying to check out some or any documentation on itk.js. Most of my search has led me to 404 error. Please let me know if I have missed any links that i may have missed.

environment.yml

Trying to build a conda env with the current YML file doesn't work for me. Lots of conflicts. If I change the requirement to python=3.8 it works fine.

Here is the error message for python=3.9

dave@kyloren TUTORIAL % conda env create -f environment.yml
Collecting package metadata (repodata.json): done
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Examining conflict for jupyter numpy matplotlib python scipy multiprocess pandas: : 14it [08:00Examining conflict for jupyter numpy matplotlib python scipy multiprocess pandas: : 15it [08:00Examining conflict for itkwidgets numpy matplotlib scipy pandas: : 15it [08:52, 34.26s/it] failed
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
Examining conflict for jupyter numpy matplotlib python scipy multiprocess pandas: : 14it [07:29Examining conflict for jupyter numpy matplotlib python scipy multiprocess pandas: : 15it [07:29Examining conflict for itkwidgets numpy matplotlib scipy pandas: : 15it [08:14, 26.92s/it] failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package tbb conflicts for:
scipy -> mkl[version='>=2021.4.0,<2022.0a0'] -> tbb=2021
numpy -> mkl[version='>=2021.4.0,<2022.0a0'] -> tbb=2021
simpleitk[version='>=2.2.0'] -> tbb[version='>=2021.5.0']

Package pypy3.6 conflicts for:
jupyter -> ipykernel -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2']
matplotlib -> pypy3.6[version='>=7.3.2|>=7.3.3']
pandas -> pypy3.6[version='>=7.3.1|>=7.3.2']
pandas -> bottleneck[version='>=1.3.1'] -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.3']
multiprocess -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']
numpy -> pypy3.6[version='>=7.3.1|>=7.3.2|>=7.3.3']
scipy -> numpy[version='>=1.16,<1.23'] -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.3']
scipy -> pypy3.6[version='>=7.3.1|>=7.3.2']
ipywidgets -> ipykernel[version='>=4.5.1'] -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2|>=7.3.3']
jupyter -> pypy3.6[version='>=7.3.3']
numpy -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.']
matplotlib -> tornado -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1']
multiprocess -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.|7.3.0.|7.3.1.|7.3.2.|7.3.3.']
itkwidgets -> numpy -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2|>=7.3.3']

Package numpy conflicts for:
pandas -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.|>=1.11.3,<2.0a0|>=1.12.1,<2.0a0|>=1.13.3,<2.0a0|>=1.14.6,<2.0a0|>=1.15.4,<2.0a0|>=1.16.6,<2.0a0|>=1.19.2,<2.0a0|>=1.21.5,<2.0a0|>=1.21.2,<2.0a0|>=1.20.3,<2.0a0|>=1.20.2,<2.0a0|>=1.9.3,<2.0a0|>=1.9.3,<1.10.0a0|>=1.9|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.18.4,<2.0a0|>=1.18.1,<2.0a0|>=1.9.|>=1.8|>=1.7']
matplotlib -> numpy[version='1.10.|1.11.|>=1.14.6,<2.0a0']
pandas -> bottleneck[version='>=1.3.1'] -> numpy[version='>=1.16.4,<2.0a0|>=1.21.3,<2.0a0']
scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16,<1.23|>=1.21,<1.23|>=1.21.2,<1.23.0|>=1.16.6,<1.23.0|>=1.16.6,<2.0a0|>=1.15.1,<2.0a0|>=1.9.3,<2.0a0|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9']
itkwidgets -> scipy -> numpy[version='1.10.|1.11.|1.12.|1.13.|>=1.11|>=1.11.3,<2.0a0|>=1.14.6,<2.0a0|>=1.16,<1.23|>=1.21,<1.23|>=1.21.2,<1.23.0|>=1.16.6,<1.23.0|>=1.16.6,<2.0a0|>=1.15.1,<2.0a0|>=1.9.3,<2.0a0|>=1.21.6,<2.0a0|>=1.19.5,<2.0a0|>=1.18.5,<2.0a0|>=1.21.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.19.4,<2.0a0|>=1.16.5,<2.0a0|>=1.19.2,<2.0a0|>=1.18.1,<2.0a0|>=1.9']
numpy
matplotlib -> matplotlib-base[version='>=3.5.2,<3.5.3.0a0'] -> numpy[version='>=1.11.3,<2.0a0|>=1.15.4,<2.0a0|>=1.16.6,<2.0a0|>=1.17|>=1.19.2,<2.0a0|>=1.21.5,<2.0a0|>=1.19.5,<2.0a0|>=1.21.6,<2.0a0|>=1.21.2,<2.0a0|>=1.18.5,<2.0a0|>=1.21.4,<2.0a0|>=1.17.5,<2.0a0|>=1.16.5,<2.0a0|>=1.19.4,<2.0a0|>=1.19|>=1.20.3,<2.0a0|>=1.9.3,<2.0a0']
itkwidgets -> numpy

Package ca-certificates conflicts for:
matplotlib -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
pandas -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
jupyter -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
scipy -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
python=3.9 -> openssl[version='>=1.1.1q,<1.1.2a'] -> ca-certificates
multiprocess -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
numpy -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
ipywidgets -> python -> ca-certificates
itkwidgets -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates

Package pypy3.7 conflicts for:
numpy -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
jupyter -> pypy3.7[version='>=7.3.3|>=7.3.7']
matplotlib -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
scipy -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.']
jupyter -> ipykernel -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.4|>=7.3.5']
multiprocess -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.7']
scipy -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
simpleitk[version='>=2.2.0'] -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.']
pandas -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
multiprocess -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.']
matplotlib -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.']
itkwidgets -> numpy -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.5|>=7.3.7']
numpy -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.']
ipywidgets -> ipykernel[version='>=4.5.1'] -> pypy3.7[version='7.3.3.|7.3.4.|7.3.5.|7.3.7.|>=7.3.3|>=7.3.4|>=7.3.7|>=7.3.5']
pandas -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.']

Package python conflicts for:
jupyter -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
jupyter -> ipykernel -> python[version='3.10.|3.4.|>=3.7|>=3.3|>=3.6|>=3.5|3.8.|3.9.|3.7.']
simpleitk[version='>=2.2.0'] -> python[version='>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
numpy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.']
itkwidgets -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
numpy -> python_abi=3.8[build=_cp38] -> python[version='3.10.|3.8.|3.9.|3.7.']
multiprocess -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|3.4.']
matplotlib -> tornado -> python[version='3.10.|3.6.|>=3.6|>=3.0,<=3.9|>=3.7|>=3.8|>=3|<3|3.9.|3.8.|3.7.']
scipy -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.']
multiprocess -> dill[version='>=0.2.5'] -> python[version='3.10.|>=3.5,<3.6.0a0|>=3.5|>=3.6|3.7.|3.9.|3.8.']
itkwidgets -> colorcet -> python[version='2.7.|3.5.|3.6.|>=2.7|>=3.10,<3.11.0a0|>=3.9,<3.10.0a0|>=3.5,<3.6.0a0|>=3.7|>=3.6|>=3.3|3.4.|3.7.|3.8.']
pandas -> python-dateutil[version='>=2.8.1'] -> python[version='3.10.|>=3|>=3.6|3.9.|3.8.|3.7.']
pandas -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.7.1,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.']
python=3.9
matplotlib -> python[version='2.7.|3.4.|3.5.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
scipy -> python_abi=3.10[build=_cp310] -> python[version='3.10.|3.9.|3.8.|3.7.']

Package libcxxabi conflicts for:
numpy -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|8.0.1|8.0.0|8.0.0|8.0.0|8.0.0',build='2|3|hebd6815_0|hcfea43d_1|0|4|1']
scipy -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|8.0.1|8.0.0|8.0.0|8.0.0|8.0.0',build='2|3|hebd6815_0|hcfea43d_1|0|4|1']
pandas -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|8.0.1|8.0.0|8.0.0|8.0.0|8.0.0',build='2|3|hebd6815_0|hcfea43d_1|0|4|1']
matplotlib -> libcxx[version='>=4.0.1'] -> libcxxabi[version='4.0.1|8.0.1|8.0.0|8.0.0|8.0.0|8.0.0',build='2|3|hebd6815_0|hcfea43d_1|0|4|1']

Package gdbm conflicts for:
numpy -> pypy3.8[version='>=7.3.9'] -> gdbm[version='>=1.18,<1.19.0a0']
multiprocess -> pypy3.7[version='>=7.3.7'] -> gdbm[version='>=1.18,<1.19.0a0']
jupyter -> pypy3.7[version='>=7.3.7'] -> gdbm[version='>=1.18,<1.19.0a0']
scipy -> pypy3.8[version='>=7.3.9'] -> gdbm[version='>=1.18,<1.19.0a0']
python=3.9 -> pypy3.9=7.3.9 -> gdbm[version='>=1.18,<1.19.0a0']
matplotlib -> pypy3.8[version='>=7.3.9'] -> gdbm[version='>=1.18,<1.19.0a0']
pandas -> pypy3.9[version='>=7.3.9'] -> gdbm[version='>=1.18,<1.19.0a0']

Package futures conflicts for:
jupyter -> jupyterlab -> futures
matplotlib -> tornado -> futures

Package six conflicts for:
matplotlib -> cycler[version='>=0.10'] -> six[version='>=1.5']
ipywidgets -> traitlets[version='>=4.3.1,<6.0.0'] -> six
pandas -> python-dateutil[version='>=2.8.1'] -> six[version='>=1.5']
numpy -> mkl-service[version='>=2.3.0,<3.0a0'] -> six
scipy -> mkl-service[version='>=2.3.0,<3.0a0'] -> six
itkwidgets -> six

Package tzdata conflicts for:
matplotlib -> python[version='>=3.9,<3.10.0a0'] -> tzdata
numpy -> python[version='>=3.10,<3.11.0a0'] -> tzdata
multiprocess -> python[version='>=3.10,<3.11.0a0'] -> tzdata
simpleitk[version='>=2.2.0'] -> python[version='>=3.9,<3.10.0a0'] -> tzdata
pandas -> python[version='>=3.9,<3.10.0a0'] -> tzdata
python=3.9 -> tzdata
jupyter -> python[version='>=3.9,<3.10.0a0'] -> tzdata
ipywidgets -> python -> tzdata
scipy -> python[version='>=3.9,<3.10.0a0'] -> tzdata

Package libgfortran4 conflicts for:
scipy -> libgfortran=4 -> libgfortran4
itkwidgets -> scipy -> libgfortran4[version='>=7.5.0']
numpy -> blas=[build=openblas] -> libgfortran4[version='>=7.5.0']
scipy -> libgfortran4[version='>=7.5.0']

Package ipywidgets conflicts for:
jupyter -> ipywidgets
itkwidgets -> ipywidgets[version='>=7.4.0|>=7.5.0']
ipywidgets
itkwidgets -> ipydatawidgets[version='>=4.0.1'] -> ipywidgets[version='>=5.1.5|>=6.0.0|>=7,<8|>=7,<9|>=7.6.0,<8|>=7.5.0,<8.0|>=7.6.0,<9|>=7.6.0,<8.0|>=7.0.0,<8.0|>=7.0.0']

Package notebook conflicts for:
ipywidgets -> widgetsnbextension[version='>=3.5.0,<3.6.0'] -> notebook[version='>=4.2.0|>=4.4.1|>=5.3']
ipywidgets -> notebook

Package packaging conflicts for:
pandas -> numexpr[version='>=2.7.1'] -> packaging
jupyter -> ipykernel -> packaging
matplotlib -> matplotlib-base[version='>=3.5.2,<3.5.3.0a0'] -> packaging[version='>=20.0']
ipywidgets -> ipykernel[version='>=4.5.1'] -> packaging

Package matplotlib conflicts for:
matplotlib
itkwidgets -> ipympl -> matplotlib[version='>=2.0.0|>=2.2.0']

Package python-dateutil conflicts for:
matplotlib -> python-dateutil
matplotlib -> matplotlib-base[version='>=3.5.2,<3.5.3.0a0'] -> python-dateutil[version='>=2.1|>=2.7']
pandas -> python-dateutil[version='>=2.5.*|>=2.6.1|>=2.7.3|>=2.8.1']

Package setuptools conflicts for:
python=3.9 -> pip -> setuptools
matplotlib -> setuptools
jupyter -> ipykernel -> setuptools[version='>=60']
pandas -> numexpr[version='>=2.7.1'] -> setuptools
ipywidgets -> ipykernel[version='>=4.5.1'] -> setuptools[version='>=18.5|>=60']
pandas -> setuptools[version='<60.0.0']
itkwidgets -> itk[version='>=5.1.0'] -> setuptools

Package libpng conflicts for:
itkwidgets -> itk -> libpng[version='>=1.6.27,<1.7']
simpleitk[version='>=2.2.0'] -> libpng[version='>=1.6.37,<1.7.0a0']
matplotlib -> freetype[version='>=2.8,<2.9.0a0'] -> libpng[version='1.6.*|>=1.6.21,<1.7|>=1.6.32,<1.6.35']
matplotlib -> libpng[version='>=1.6.23,<1.7|>=1.6.32,<1.7.0a0|>=1.6.34,<1.7.0a0|>=1.6.35,<1.7.0a0|>=1.6.36,<1.7.0a0|>=1.6.37,<1.7.0a0']

Package expat conflicts for:
python=3.9 -> pypy3.9=7.3.9 -> expat[version='>=2.4.7,<3.0a0|>=2.4.8,<3.0a0']
numpy -> pypy3.8[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.4.7,<3.0a0|>=2.2.9,<3.0.0a0']
pandas -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0']
matplotlib -> pypy3.8[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0']
scipy -> pypy3.8[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.2.9,<3.0.0a0']
itkwidgets -> itk -> expat=2.1
multiprocess -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0']
jupyter -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0']

Package tornado conflicts for:
matplotlib -> tornado
jupyter -> ipykernel -> tornado[version='!=6.0.0,!=6.0.1,!=6.0.2|>=4.0|>=4.2|>=4.2,<7.0|>=6.1,<7.0|>=6.1|>=5.0,<7.0|>=6.1.0|>=5.0|>=5.0,<7|>=4.1,<7|>=4,<6|>=4']
ipywidgets -> ipykernel[version='>=4.5.1'] -> tornado[version='>=4|>=4,<6|>=4.0|>=4.2|>=4.2,<7.0|>=6.1,<7.0|>=6.1|>=5.0,<7.0|>=5.0|>=5.0,<7|>=4.1,<7']

Package debugpy conflicts for:
jupyter -> ipykernel -> debugpy[version='>=1|>=1,<2.0|>=1.0.0|>=1.0.0,<2.0|>=1.0']
ipywidgets -> ipykernel[version='>=4.5.1'] -> debugpy[version='>=1|>=1,<2.0|>=1.0.0|>=1.0.0,<2.0|>=1.0']

Package scipy conflicts for:
itkwidgets -> scipy
scipy

Package llvm-openmp conflicts for:
scipy -> fftw[version='>=3.3.9,<4.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.0.1|>=11.1.0|>=13.0.1|>=14.0.4|>=12.0.1|>=4.0.1|>=8.0.0|>=9.0.1|>=9.0.0|>=8.0.1']
numpy -> libopenblas[version='>=0.3.20,<1.0a0'] -> llvm-openmp[version='>=10.0.0|>=10.0.1|>=11.0.0|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=9.0.1|>=9.0.0|>=8.0.0']

Package libtiff conflicts for:
itkwidgets -> itk -> libtiff=4.0
simpleitk[version='>=2.2.0'] -> libtiff[version='>=4.4.0,<4.5.0a0|>=4.4.0,<5.0a0']The following specifications were found to be incompatible with your system:

• feature:/osx-64::__osx==10.16=0
• feature:|@/osx-64::__osx==10.16=0
• ipywidgets -> ipykernel[version='>=4.5.1'] -> __linux
• ipywidgets -> ipykernel[version='>=4.5.1'] -> __win
• jupyter -> ipykernel -> __osx
• matplotlib -> matplotlib-base[version='>=3.6.0,<3.6.1.0a0'] -> __osx[version='>=10.12']

Your installed version is: 10.16