From a26f998b94f1d746125c0bf50db835732f96cc78 Mon Sep 17 00:00:00 2001 From: iback Date: Wed, 23 Sep 2026 06:41:41 +0000 Subject: [PATCH] added paper and other badges, added paper citation to README and added CITATION.cff --- CITATION.cff | 62 ++++++++++++++++++++++++++++++++++++ README.md | 90 +++++++++++++--------------------------------------- 2 files changed, 84 insertions(+), 68 deletions(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..f2655a9 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,62 @@ +cff-version: 1.2.0 +title: "TPTBox: Torso Processing ToolBox" +message: "If you use this software, please cite both the software and the accompanying paper (see preferred-citation)." +type: software +authors: + - family-names: "Möller" + given-names: "Hendrik" + email: "hendrik.moeller@tum.de" + affiliation: "Technical University of Munich" + - family-names: "Graf" + given-names: "Robert" + email: "robert.graf@tum.de" + affiliation: "Technical University of Munich" + - family-names: "Lerchl" + given-names: "Tanja" + affiliation: "Technical University of Munich" + - family-names: "Rueckert" + given-names: "Daniel" + affiliation: "Technical University of Munich" + - family-names: "Kirschke" + given-names: "Jan S." + affiliation: "Technical University of Munich" +repository-code: "https://github.com/Hendrik-code/TPTBox" +url: "https://tptbox.readthedocs.io" +abstract: >- + The Torso Processing ToolBox (TPTBox) is a Python package for processing + BIDS-compliant medical imaging datasets (CT, MRI), with a focus on torso and + spine analysis. It provides NIfTI I/O, reorientation and resampling, Points of + Interest computation for vertebrae, 2D and 3D snapshots, registration, + stitching, and segmentation integrations. +keywords: + - medical imaging + - BIDS + - NIfTI + - spine + - segmentation + - registration + - computed tomography + - magnetic resonance imaging +license: Apache-2.0 +version: 1.0.0 +date-released: "2026-09-07" +preferred-citation: + type: article + title: "TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging" + authors: + - family-names: "Möller" + given-names: "Hendrik" + - family-names: "Graf" + given-names: "Robert" + - family-names: "Lerchl" + given-names: "Tanja" + - family-names: "Rueckert" + given-names: "Daniel" + - family-names: "Kirschke" + given-names: "Jan S." + journal: "SoftwareX" + year: 2026 + start: 103055 + issn: "2352-7110" + doi: "10.1016/j.softx.2026.103055" + url: "https://www.sciencedirect.com/science/article/pii/S2352711026005467" diff --git a/README.md b/README.md index 1343a0f..a2ff1b2 100755 --- a/README.md +++ b/README.md @@ -3,12 +3,14 @@
-[![PyPI version tptbox](https://badge.fury.io/py/tptbox.svg)](https://pypi.python.org/pypi/tptbox/) -[![Python Versions](https://img.shields.io/pypi/pyversions/tptbox)](https://pypi.org/project/tptbox/) +[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.softx.2026.103055-B31B1B)](https://doi.org/10.1016/j.softx.2026.103055) [![Stable Version](https://img.shields.io/pypi/v/tptbox?label=stable)](https://pypi.python.org/pypi/tptbox/) +[![Python Versions](https://img.shields.io/pypi/pyversions/tptbox)](https://pypi.org/project/tptbox/) +[![Downloads](https://img.shields.io/pepy/dt/tptbox?label=downloads)](https://pepy.tech/project/tptbox) [![tests](https://github.com/Hendrik-code/TPTBox/actions/workflows/tests.yml/badge.svg)](https://github.com/Hendrik-code/TPTBox/actions/workflows/tests.yml) [![codecov](https://codecov.io/gh/Hendrik-code/TPTBox/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/Hendrik-code/TPTBox) [![Documentation](https://readthedocs.org/projects/tptbox/badge/?version=latest)](https://tptbox.readthedocs.io/en/latest/) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

@@ -20,6 +22,24 @@ The Torso Processing ToolBox (TPTBox) is a multi-functional package to handle any sort of bids-conform dataset (CT, MRI, ...) +## Publication + +This is the official repository of "TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging" + +If you use this toolbox, please cite our publication: https://doi.org/10.1016/j.softx.2026.103055 +``` +@article{MollerGraf2026TPTBox, + title = {TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging}, + journal = {SoftwareX}, + pages = {103055}, + year = {2026}, + issn = {2352-7110}, + doi = {https://doi.org/10.1016/j.softx.2026.103055}, + url = {https://www.sciencedirect.com/science/article/pii/S2352711026005467}, + author = {Hendrik Möller and Robert Graf and Tanja Lerchl and Daniel Rueckert and Jan S. Kirschke}, +} +``` + ## Features - **Dataset Handling**: Loop over datasets, search query, and find images and their corresponding derivatives @@ -114,69 +134,3 @@ Each sub-package has its own README with API tables and examples. Click on the n | [`mesh3D`](https://tptbox.readthedocs.io/en/latest/modules/mesh3d/) | 3D surface mesh generation and rendering from segmentation volumes | | [`stitching`](https://tptbox.readthedocs.io/en/latest/modules/stitching/) | Multi-station NIfTI stitching for whole-body or long-spine acquisitions | | [`logger`](https://tptbox.readthedocs.io/en/latest/modules/logger/) | Structured, consistent logging for medical image processing pipelines | - - - -# Publications - -An incomplete list of publications that actively used TPTBox: - -1. **Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation**; Graf, Robert; -Schmitt, Joachim; Schlaeger, Sarah; Möller, Hendrik Kristian; Sideri-Lampretsa, Vasiliki; Sekuboyina, Anjany; Krieg, Sandro Manuel; -Wiestler, Benedikt; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan; **European Radiology Experimental, 2023** - -2. **Modeling the acquisition shift between axial and sagittal MRI for di usion super-resolution to enable axial spine segmentation**; Graf, Robert; Möller, Hendrik; McGinnis, Julian; Rühling, Sebastian; Weihrauch, Maren; Atad, Matan; Shit, -Suprosanna; Menze, Bjoern; Mühlau, Mark; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **Proceedings of Machine Learning Research, 2024** - -3. **Detecting unforeseen data properties with diffusion autoencoder embeddings using spine MRI data**; Graf, Robert; Hunecke, Florian; Pohl, Soeren; Atad, Matan; Möller, Hendrik; Starck, Sophie; Kröncke, Thomas; Bette, Stefanie; Bamberg, -Fabian; Pischon, Tobias; Niendorf, Thoralf; Schmidt, Carsten; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024** - -4. **SPINEPS—automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation**; Möller, Hendrik; Graf, Robert; Schmitt, Joachim; Keinert-Weth, Benjamin; -Schön, Hanna; Atad, Matan; Sekuboyina, Anjany; Streckenbach, Felix; Kofler, Florian; -Kroencke, Thomas; Bette, Stefanie; Willich, Stefan N.; Keil, Thomas; Niendorf, Thoralf; -Pischon, Tobias; Endemann, Beate; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; -**European Radiology, 2025** - -5. **VIBESegmentator: full body MRI segmentation for the NAKO and UK Biobank**; -Graf, Robert; Platzek, Paul; Riedel, Evamaria Olga; Ramschütz, Constanze; Starck, Sophie; Möller, Hendrik K.; Atad, Matan; Völzke, -Henry; Bülow, Robin; Schmidt, Carsten Oliver; Rüdebusch, Julia; Jung, Matthias; Reisert, Marco; Weiss, Jakob; Lö ler, Maximilian T.; -Bamberg, Fabian; Wiestler, Benedikt; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **European Radiology, 2025** - -6. **Generating synthetic high-resolution spinal STIR and T1w images from T2w FSE and low-resolution axial Dixon**; Graf, Robert; Platzek, Paul-Sören; Riedel, Evamaria Olga; Kim, Su Hwan; Lenhart, Nicolas; Ramschütz, Constanze; Paprottka, -Karolin Johanna; Kertels, Olivia Ruriko; Möller, Hendrik Kristian; Atad, Matan; Bülow, Robin; Werner, Nicole; Völzke, Henry; Schmidt, -Carsten Oliver; Wiestler, Benedikt; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **European Radiology, 2025** - -7. **MAGO-SP: detection and correction of water-fat swaps in magnitude-only VIBE MRI**; -Graf, Robert; Möller, Hendrik; Starck, Sophie; Atad, Matan; Braun, Philipp; Stelter, Jonathan; Peters, Annette; Krist, Lilian; Willich, -Stefan N.; Völzke, Henry; Bülow, Robin; Pischon, Tobias; Niendorf, Thoralf; Paetzold, Johannes C.; Karampinos, Dimitrios; Rueckert, -Daniel; Kirschke, Jan S.; **International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025** - -8. **Automated Thoracolumbar Stump Rib Detection and Analysis in a Large CT Cohort**; -Möller, Hendrik; Dima, Alina; Keinert-Weth, Benjamin; Graf, Robert; Atad, Matan; Paetzold, -Johannes; Jungmann, Friederike; Braren, Rickmer; Kofler, Florian; Menze, Bjoern; Rueckert, -Daniel; Kirschke, Jan S.; Schön, Hanna; **MDPI AI, 2026** - -9. **PARASIDE: An automatic paranasal sinus segmentation and structure analysis tool for magnetic resonance imaging**; Möller, Hendrik; -Krautschick, Lukas; Graf, Robert; Atad, Matan; Busch, Chia-Jung; Beule, Achim Georg; -Scharf, Christian; Kaderali, Lars; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; -Paperlein, Fabian; **Computers in Biology and Medicine, 2026** - -10. **One Sequence to Segment Them All: Efficient Data Augmentation for CT and MRI Cross-Domain 3D Spine Segmentation;** Molinier, -Nathan*; Möller, Hendrik*; Dagonneau, Thomas; Curto-Vilalta, Anna; Graf, Robert; Atad, -Matan; Rueckert, Daniel; Kirschke, Jan S.; Cohen-Adad, Julien; **International Conference on -Medical Image Computing and Computer-Assisted Intervention (MICCAI) , 2026** - -11. **VERIDAH: Solving Enumeration Anomaly Aware Vertebra -Labeling across Imaging Sequences;** Möller, Hendrik; Schön, Hanna; Graf, Robert; -Atad, Matan; Molinier, Nathan; Sekuboyina, Anjany; Budai, Bettina; Bamberg, Fabian; -Ringhof, Steffen; Schlett, Christopher; Pischon, Tobias; Niendorf, Thoralf; Decker, Josua; -Weber, Marc-André; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; **European -Radiology (under review), 2026** - -12. **Rule-based key-point extraction for MR-guided biomechanical digital twins of the spine**; Graf, Robert; Lerchl, -Tanja; Nispel, Kati; Möller, Hendrik; Atad, Matan; McGinnis, Julian; Watrinet, Julius Maria; Paetzold, Johannes C.; Rueckert, Daniel; -Kirschke, Jan S.; **International Workshop on Digital Twin for Healthcare (DT4H), 2025** - -13. **VERPEX: Anatomical Landmark Extraction on 3D Vertebrae exploiting Segmentation Masks**; Möller, Hendrik; Wang, Alissa Yuxuan; Graf, Robert; -Nispel, Kati; Atad, Matan; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; Lerchl, Tanja; -**International Workshop on Digital Twin for Healthcare (DT4H), 2026**