{"id":14982591,"url":"https://github.com/insigneo/pypect2s","last_synced_at":"2026-01-22T17:07:31.478Z","repository":{"id":250876144,"uuid":"828533764","full_name":"INSIGNEO/PyPeCT2S","owner":"INSIGNEO","description":"A GUI built to provide a contained base for the automation of the CT2S pipeline. With specific focus on paediatric applications. Utilising ANSYS and other FEM solver tools. 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align=\"center\"\u003e\n  \u003cdiv\u003e\n    \u003ca href=\"https://insigneo.org/\"\u003e\n    \u003cimg src=\"icons/big_logo.svg\" alt=\"PyPeCT2S\" width=\"100%\" alt=\"PyPeCT2S Logo\"\u003e\n    \u003c/a\u003e\n  \u003c/div\u003e\n\u003c/h1\u003e\n\n\u003ch2 align=\"center\"\u003e\n  Pythonic Paediatric Computed Tomography to Strength\n\u003c/h2\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://figshare.com/articles/software/PyPeCT2S/26425591\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/DOI-10.6084/m9.figshare.26425591-brightgreen\" alt=\"DOI\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://www.sheffield.ac.uk\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/-The%20University%20of%20Sheffield-blue.svg?colorA=ffffff\u0026colorB=009fe3\u0026logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAA4AAAAOCAMAAAAolt3jAAABsFBMVEUAAABmZplVVYBLPHheUYZJPXlSR3pCOnNgWIdoYI9FPnVMQXc0JGM0KmhEOXI0MW8xMW2Ph6yYkrOWj6%2BOiayinLqWkbIcWJkdWJezrsW2sciclrWmoL0cWpkbXJuCfqQVba4Vba2tqsKBgKWXkbGgm7ioo7%2Bln7umobyppcClob0RdrgSd7ikoLuXkbEeeKwieqmYkrKkn7sAneAAn%2BMBnN8Dn%2BIEj9IEkNQEoOMFi88GicwHnuAInuAVaqkVgrEWa6sWiskYj84ek88mk8wmqOInqOIqhrA4qd45qd87kaA8q988q%2BA9qN0%2Fk51Aqd1CqdxCqd1JnqtNnc9OnKVPnItSmsZUmqZVlsFVnYZVns1bst9ds99ftN9isNtitN9joa1msdtnveZqoaRqrNZqvuZsrdZvk2lylWR0nKZ2oJx%2BfKOBf6WEn5eGr3iIr3eduNWfmbifmrifudWim6mjnKmloLymrz2psTuuqb6uqsOwq8C0taG2tqS4tqy4tra6uTC6ui6%2FsCK%2FsCPBvdHDv9LFwtfGwtjOy9rPzdvUlaHmkpb%2B%2FPz%2B%2Fv7%2F%2FPz%2F%2F%2F9OZpcfAAAAM3RSTlMABQYRExUZHyAgJS8xMTFTVFleZmiJkpOTmp2oqba9wsTFxcfO0dPX3OLj5%2Bf19v39%2Fv4kncL4AAAAvElEQVR4AWNgYBIQV9Q20NdRkOBnZGBg4DExTQ9taIzMMDbhA3PdzMqbmyosXaHc4kCvvHy%2FgAIINzElvL%2B%2FvzcoLQ7E5bX1TOhq624P8bDhBnLZTEwye%2Fr7%2BpNNTFgYgMApJreuprY%2BK94RyOGSlEv19XZx9vFPkpViZ1BRZ7WKdq%2Bsto%2B1ZtZQYhAp1FS2iCopDTaX1yoSZmDgkNHrsAuLcOjUleZkAAGxqtbsnJYyUQYoEFIzMlQVBLEA%2FZgsl9iPrB4AAAAASUVORK5CYII%3D\" alt=\"TUoS\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://insigneo.org/\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/-INSIGNEO-red.svg?colorA=ffffff\u0026colorB=cf2020\u0026logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAA4AAAAOCAMAAAAolt3jAAABC1BMVEUAAAD%2FAAC%2FAADMGhrRFxfSHh7VHBzJGxvTISHKICDMHx%2FOHR3RJCTTIyPOISHPICDMHR3NIyPNICDRISHQHx%2FQHx%2FOHx%2FQISHOICDQICDQHx%2FOHx%2FPISHQISHQICDOICDQISHOICDQICDPISHPICDQISHPICDPICDOHx%2FPISHPISHQISHPICDPISHPISHQICDOICDOICDPHx%2FPICDPICDOICDPICDPICDPICDPHx%2FPICDPICDQICDPICDPHx%2FQISHOICDPICDPICDPICDPICDPHx%2FMISHOICDPICDQICDPICDPISHPHx%2FPICDPICDPICDPICDPICDPICDOICDPHx%2FPICDPICDPICDPICDi8V76AAAAWHRSTlMAAgQKCxESExcYGRocHR8gIyRITVFSU1ZYYWJjZGZnaWxucXV5fH%2BAg4SFjI%2BUlZeYqKuusbK2ubrDxcbHycvMzdHU2Nrb4uLl5%2Bnq6%2Bzt7u%2F09vf7%2FP3%2B%2FHERCQAAAKVJREFUeAEdx%2BVCg2AAhtHHAANDMQRD7ECwO7DDjViM7b3%2FK9n4zr9Dxdk6jjc4s02si46kK7tMLGDuW%2Fq%2FvdxZlt5shh7VWhsGTqWvTVYll0q4PjMyy7VuYHQ7nIL98oVMAey183sI9EtNPpzXfz7BV8aHIpi%2Fe3ch1iuHysYxnFxHTDf1bD7xpMKBxa6Kk6WVKFXPY8BLZTQWMMYOHvK%2FZHcS6AOapR0V%2FpSSVQAAAABJRU5ErkJggg%3D%3D\" alt=\"INSIGNEO\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://opensource.org/licenses/GPL-3.0\"\u003e\n    \u003cimg src=\"https://img.shields.io/badge/License-GPL%203.0-blue.svg\" alt=\"License GNU GPL 3.0\"\u003e\n  \u003c/a\u003e\n  \u003cimg alt=\"GitHub all releases\" src=\"https://img.shields.io/github/downloads/INSIGNEO/PyPeCT2S/total\"\u003e\n    \u003cimg alt=\"GitHub commits since latest release (by date) for a branch\" src=\"https://img.shields.io/github/commits-since/INSIGNEO/PyPeCT2S/latest\"\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://github.com/INSIGNEO/PyPeCT2S/releases/latest\"\u003eDownload\u003c/a\u003e |\n  \u003ca href=\"https://insigneo.github.io/PyPeCT2S/\"\u003eDocumentation\u003c/a\u003e |\n  \u003ca href=\"mailto:GHAllison1@sheffield.ac.uk\"\u003eContact\u003c/a\u003e\n\u003c/p\u003e\n\n**Authors:** George H Allison\u003csup\u003e1,2\u003c/sup\u003e\n\n**Affiliation:** \n\u003csup\u003e1\u003c/sup\u003e [INSIGNEO Institute, University of Sheffield, United Kingdom](https://www.sheffield.ac.uk/insigneo); \n\u003csup\u003e2\u003c/sup\u003e [School of Mechanical, Aerospace \u0026 Civil Engineering, University of Sheffield, United Kingdom](https://www.sheffield.ac.uk/mecheng)\n\n**Contact:** \nGHA ([Email](mailto:GHAllison1@sheffield.ac.uk) | [LinkedIn](https://www.linkedin.com/in/george-h-allison/)), \nDr X. Li ([Email](mailto:xinshan.li@sheffield.ac.uk))\n\n## INTRODUCTION\n\nThis work uses techniques and tools developed by the [INSIGNEO Institute](https://www.sheffield.ac.uk/insigneo) for the [CT2S](https://ct2s.insigneo.org/ct2s/) pipeline.\n\nThe goal of this work is to automate the [CT2S](https://ct2s.insigneo.org/ct2s/) pipeline steps, to use them in a modern setting in a repeatable and\nuser-friendly manner; with high adaptability and extensibility.\n\nUse of this tool has resulted in pipeline time reductions of up to 70 %.\n\nScripts, methods, and work contained in this repository have been heavily based on works by \n[Dr Xinshan Li](https://scholar.google.co.uk/citations?user=T3t8XdcAAAAJ\u0026hl=en) and \n[Dr Zainab Altai](https://scholar.google.com/citations?user=VaL--SsAAAAJ\u0026hl=en).\n\nSpecific works of importance to this repository are: \u003cref\u003e[1](#ref1), [2](#ref2), [3](#ref3), [4](#ref4)\u003c/ref\u003e\n\nIf you use this software in your work, please cite the following: [CITATION](CITATION.cff)\n\nDetailed documentation can be found in the project page or in the application itself under the `HELP` \nlink at the bottom. [Documentation](https://insigneo.github.io/PyPeCT2S/)\n\nIf you find this software useful, please consider starring the repository.\n\n\n## USAGE\n\n**_Please only run the scripts if you are comfortable running Python scripts._**\n\nIt is recommended to use the latest release available under: [Releases](https://github.com/INSIGNEO/PyPeCT2S/releases/latest)\n\nYou can run each tab individually, or run the entire pipeline from the start. \n(e.g. You may want to stop after the material assignment step and take that file to your own solving software. This is\npossible and just requires you to use the first two tabs.)\n\nFill in blank fields and press button to run. Information will display in the log window. Repeat for each tab required.\n\n## REQUIREMENTS\n\n\u003e[!IMPORTANT]\n\u003e \n\u003e\u003cspan style=\"color:red\"\u003e**An ANSYS install is required to run ANSYS based scripts**\u003c/span\u003e\n\u003e \n\u003e Make Sure you are connected to a licensing server before running.\n\u003e\n\u003eANSYS scripts require a minimum ANSYS version (2021R2) to function correctly. 2023R2 and above is recommended, and the \n\u003e systems have been tested on 2021R2 up.\n\nIf you are looking to use automatic Bonemat-based material assignment, you will need to have the **_rolling_** version\nof [Bonemat](https://ior-bic.github.io/software/bonemat/) available on your system and copy the `BonematCLI.exe` in \nto the Bonemat folder. We will not distribute a copy of Bonemat with is software.\n\nPlease keep in mind the limits of the software this GUI interfaces with. _We cannot solve issues that arise for errors \nin software we do not control._ However, if you think there is an issue with the GUI, please raise an issue on the repo.\n\n### Python Requirements\n\n- [See requirements file](requirements.txt)\n\n- Set up an environment as follows:\n  - `pip install -r requirements.txt`\n\n### File / Model / Input Requirements\n\nYou can start the process at any step by jumping to that tab.\n\nIf you wish to start fresh you require the following files:\n- DICOM image scans contained in a `*.VTK` file.\n- Segmented 3D `*.STL` model of the bone. (_**It is important you check the quality of segmentation, meshing will fail \nif there are external floating elements in the model.**_)\n- Configuration file for material application, based on the specific CT scanner used.\n\n## CONTACT\n\nBatch and pool processing are currently unavailable in the public release.\n\nSideways and STANCE are currently unavailable in the public release.\n\nIf you are interested in any of these features, please contact the authors.\n\nGHA ([Email](mailto:GHAllison1@sheffield.ac.uk) | [LinkedIn](https://www.linkedin.com/in/george-h-allison/)), \nDr X. Li ([Email](mailto:xinshan.li@sheffield.ac.uk))\n\n## DISCLAIMER\n\nThis software has been designed for research purposes only and has not been reviewed or approved by medical device \nregulation bodies.\n\nThis software is not to be used alone or in combination, for human beings for one or more of the following specific \nmedical purposes:\n- diagnosis, prevention, monitoring, prediction, prognosis, treatment or alleviation of disease.\n- diagnosis, monitoring, treatment, alleviation of, or compensation for, an injury or disability.\n- investigation, replacement or modification of the anatomy or of a physiological or pathological process or\nstate.\n- providing information by means of _in vitro_ examination of specimens derived from the human body, including\norgan, blood and tissue donations.\n\n## FEEDBACK AND DEVELOPMENT\n\nThis software is in active development and will likely remain for the next few years. If you have any feedback, \nplease raise an issue or open a discussion on the repository.\n\nIf you want to include your custom scripts, please raise an issue, open a discussion, or create a pull request \non the repository. Alternatively, you can contact the authors directly.\n\nPull requests are welcome, but please ensure you have tested your changes before submitting.\n\n## REFERENCES\n\n\u003ca id='ref1'\u003e1\u003c/a\u003e: Altai, Z., Viceconti, M., Offiah, A.C. et al. Investigating the mechanical response of paediatric \nbone under bending and torsion using finite element analysis. Biomechanics and Modeling in Mechanobiology 17, 1001–1009 \n(2018). [DOI](https://doi.org/10.1007/s10237-018-1008-9)\n\n\u003ca id='ref2'\u003e2\u003c/a\u003e: Altai, Z., Muhammad, Q., Li, X. et al. The effect of boundary and loading conditions on patient \nclassification using finite element predicted risk of fracture. Clinical Biomechanics 68, 137–143 \n(2019). [DOI](https://doi.org/10.1016/j.clinbiomech.2019.06.004)\n\n\u003ca id='ref3'\u003e3\u003c/a\u003e: Li, X., Viceconti, M., Cohen, M.C. et al. Developing CT based computational models of pediatric \nfemurs. Journal of Biomechanics 48, 2034–2040 \n(2015). [DOI](https://doi.org/10.1016/j.jbiomech.2015.03.027)\n\n\u003ca id='ref4'\u003e4\u003c/a\u003e: Viceconti, M., Muhammad, Q., Bhattacharya, P. et al. Are CT-Based Finite Element Model Predictions \nof Femoral Bone Strengthening Clinically Useful? Current Osteoporosis Reports 16, 216–223 \n(2018). [DOI](https://doi.org/10.1007/s11914-018-0438-8)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsigneo%2Fpypect2s","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsigneo%2Fpypect2s","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsigneo%2Fpypect2s/lists"}