Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/astrazeneca/lung-tumour-mice-mri

https://github.com/astrazeneca/lung-tumour-mice-mri

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AstraZeneca
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Size: 3.61 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

Lung tumour segmentation using 2D and 3D MR images of mice

This the codebase for Lung tumour segmentation using 2D and 3D MR images of mice paper.

diagram summarizing the work

Abstract

Accurate lung tumour segmentation is an important step for assessing tumour size and its progression in cancer patients. While deep learning models have been developed to automate this process, the focus has predominantly been on human subjects, neglecting the pivotal role of animal models in preclinical drug development. In our study, we explore various approaches for segmenting lung tumours in MRI scans of mice. Unlike the prior approach that involves the combined segmentation of lungs and tumours within the lungs, our work achieves state-of-the-art results using only lung tumour annotations. Furthermore, we demonstrate that the nnU-Net framework outperforms models such as U-Net, U-Net3+ and DeepMeta. Most importantly, we achieve better results with nnU-Net 3D framework than 2D framework, indicating the importance of spatial context in the field of MRI. This study demonstrates the importance of 3D input over 2D input images for lung tumour segmentation in MRI scans. This work is an important step in automating pre-clinical animal studies to quantify the efficacy of experimental drugs, particularly in assessing tumour changes in animal models.

Setup

Before running any of the experiments, ensure to set up the virtual environment correctly. ~~~ conda env create -f environment.yml conda activate condaenv ~~~ Note that setting up conda might take a long time, alternatively you can use mamba ~~~ mamba create -n condaenv python=3.9 mamba env update -n conda_env --file environment.yml ~~~

Reproduction

reproduction diagram

If you want to reproduce all experiments, run the following commands ~~~ python -m src.setup python -m src.preparedata python -m src.runtrain python -m src.run_eval ~~~ These scripts are wrappers which will execute each experiment one-after-one (note that it will take a long time to execute all experiments with as many epochs as stated in the publication). For detailed codebase and instructions how to execute a specific expriment only, see docs

Owner

  • Name: AstraZeneca
  • Login: AstraZeneca
  • Kind: organization
  • Location: Global

Data and AI: Unlocking new science insights

GitHub Events

Total
Last Year

Dependencies

src/nnunet/nnUNet/pyproject.toml pypi
  • SimpleITK >=2.2.1
  • acvl-utils >=0.2,<0.3
  • batchgenerators >=0.25
  • batchgeneratorsv2 *
  • dicom2nifti *
  • dynamic-network-architectures >=0.3.1,<0.4
  • einops *
  • graphviz *
  • imagecodecs *
  • matplotlib *
  • nibabel *
  • numpy *
  • pandas *
  • requests *
  • scikit-image >=0.19.3
  • scikit-learn *
  • scipy *
  • seaborn *
  • tifffile *
  • torch >=2.1.2
  • tqdm *
  • yacs *
src/nnunet/nnUNet/setup.py pypi
src/setup.py pypi
environment.yml conda
  • _libgcc_mutex 0.1
  • _openmp_mutex 4.5
  • aiohttp 3.9.5
  • aiohttp-retry 2.8.3
  • aiosignal 1.3.1
  • alsa-lib 1.2.10
  • amqp 5.2.0
  • annotated-types 0.7.0
  • antlr-python-runtime 4.9.3
  • aom 3.6.1
  • appdirs 1.4.4
  • astroid 3.1.0
  • async-timeout 4.0.3
  • asyncssh 2.14.1
  • atk-1.0 2.38.0
  • atpublic 3.0.1
  • attr 2.5.1
  • attrs 23.2.0
  • backports.zoneinfo 0.2.1
  • billiard 4.2.0
  • blas 1.0
  • blosc 1.21.5
  • brotli 1.0.9
  • brotli-bin 1.0.9
  • brotli-python 1.0.9
  • brunsli 0.1
  • bzip2 1.0.8
  • c-ares 1.27.0
  • c-blosc2 2.13.2
  • ca-certificates 2024.6.2
  • cairo 1.18.0
  • celery 5.3.5
  • certifi 2024.2.2
  • cffi 1.16.0
  • cfitsio 4.2.0
  • charls 2.4.2
  • charset-normalizer 3.3.2
  • click 8.1.7
  • click-didyoumean 0.3.1
  • click-plugins 1.1.1
  • click-repl 0.3.0
  • colorama 0.4.6
  • configobj 5.0.8
  • contourpy 1.2.0
  • cryptography 42.0.8
  • cuda-cudart 11.8.89
  • cuda-cupti 11.8.87
  • cuda-libraries 11.8.0
  • cuda-nvrtc 11.8.89
  • cuda-nvtx 11.8.86
  • cuda-runtime 11.8.0
  • cudatoolkit 11.3.1
  • cycler 0.12.1
  • dav1d 1.2.1
  • dbus 1.13.18
  • decorator 5.1.1
  • dictdiffer 0.9.0
  • dill 0.3.8
  • diskcache 5.6.3
  • distro 1.9.0
  • dpath 2.1.6
  • dulwich 0.22.1
  • dvc-data 3.9.0
  • dvc-http 2.32.0
  • dvc-objects 3.0.6
  • dvc-render 1.0.2
  • dvc-studio-client 0.20.0
  • dvc-task 0.4.0
  • entrypoints 0.4
  • expat 2.5.0
  • ffmpeg 4.3
  • filelock 3.13.1
  • flake8 7.0.0
  • flatten-dict 0.4.2
  • flufl.lock 7.1
  • font-ttf-dejavu-sans-mono 2.37
  • font-ttf-inconsolata 3.000
  • font-ttf-source-code-pro 2.038
  • font-ttf-ubuntu 0.83
  • fontconfig 2.14.2
  • fonts-conda-ecosystem 1
  • fonts-conda-forge 1
  • fonttools 4.49.0
  • freetype 2.12.1
  • fribidi 1.0.10
  • frozenlist 1.4.1
  • fsspec 2022.11.0
  • funcy 2.0
  • future 1.0.0
  • gdk-pixbuf 2.42.10
  • gettext 0.21.1
  • giflib 5.2.1
  • gitdb 4.0.11
  • gitpython 3.1.43
  • glib 2.78.4
  • glib-tools 2.78.4
  • gmp 6.3.0
  • gmpy2 2.1.2
  • gnutls 3.6.13
  • grandalf 0.7
  • graphite2 1.3.13
  • graphviz 9.0.0
  • gst-plugins-base 1.14.1
  • gstreamer 1.14.1
  • gtk2 2.24.33
  • gto 1.6.2
  • gts 0.7.6
  • harfbuzz 8.3.0
  • hydra-core 1.3.2
  • icu 73.2
  • idna 3.6
  • imagecodecs 2023.1.23
  • imageio 2.34.0
  • importlib-metadata 7.1.0
  • importlib-resources 6.1.1
  • importlib_resources 6.1.1
  • intel-openmp 2022.1.0
  • isort 5.13.2
  • iterative-telemetry 0.0.8
  • jinja2 3.1.3
  • joblib 1.3.2
  • jpeg 9e
  • jxrlib 1.1
  • keyutils 1.6.1
  • kiwisolver 1.4.5
  • kombu 5.3.3
  • krb5 1.20.1
  • lame 3.100
  • lazy_loader 0.3
  • lcms2 2.15
  • ld_impl_linux-64 2.40
  • lerc 4.0.0
  • libaec 1.1.2
  • libavif 0.11.1
  • libavif16 1.0.1
  • libblas 3.9.0
  • libbrotlicommon 1.0.9
  • libbrotlidec 1.0.9
  • libbrotlienc 1.0.9
  • libcap 2.69
  • libcblas 3.9.0
  • libclang 14.0.6
  • libclang13 14.0.6
  • libcublas 11.11.3.6
  • libcufft 10.9.0.58
  • libcufile 1.8.1.2
  • libcups 2.3.3
  • libcurand 10.3.4.107
  • libcurl 8.1.2
  • libcusolver 11.4.1.48
  • libcusparse 11.7.5.86
  • libdeflate 1.17
  • libedit 3.1.20191231
  • libev 4.33
  • libevent 2.1.12
  • libexpat 2.5.0
  • libffi 3.4.2
  • libflac 1.4.3
  • libgcc-ng 13.2.0
  • libgcrypt 1.10.3
  • libgd 2.3.3
  • libgfortran-ng 13.2.0
  • libgfortran5 13.2.0
  • libgit2 1.7.2
  • libglib 2.78.4
  • libgomp 13.2.0
  • libgpg-error 1.47
  • libiconv 1.17
  • libjpeg-turbo 2.0.0
  • liblapack 3.9.0
  • libllvm14 14.0.6
  • libllvm15 15.0.7
  • libnghttp2 1.58.0
  • libnpp 11.8.0.86
  • libnsl 2.0.1
  • libnvjpeg 11.9.0.86
  • libogg 1.3.4
  • libopenblas 0.3.26
  • libopus 1.3.1
  • libpng 1.6.42
  • libpq 12.17
  • librsvg 2.56.3
  • libsndfile 1.2.2
  • libsqlite 3.45.1
  • libssh2 1.11.0
  • libstdcxx-ng 13.2.0
  • libsystemd0 255
  • libtiff 4.5.0
  • libuuid 2.38.1
  • libvorbis 1.3.7
  • libwebp-base 1.3.2
  • libxcb 1.15
  • libxcrypt 4.4.36
  • libxkbcommon 1.6.0
  • libxml2 2.12.5
  • libzlib 1.2.13
  • libzopfli 1.0.3
  • llvm-openmp 15.0.7
  • lz4-c 1.9.4
  • markdown-it-py 3.0.0
  • markupsafe 2.1.5
  • matplotlib 3.8.3
  • matplotlib-base 3.8.3
  • mccabe 0.7.0
  • mdurl 0.1.2
  • mkl 2022.1.0
  • mpc 1.3.1
  • mpfr 4.2.1
  • mpg123 1.32.4
  • mpmath 1.3.0
  • multidict 6.0.5
  • munkres 1.1.4
  • mysql 5.7.20
  • mysql-common 8.0.33
  • mysql-libs 8.0.33
  • nanotime 0.5.2
  • ncurses 6.4
  • nettle 3.6
  • networkx 3.2.1
  • nibabel 5.2.1
  • nspr 4.35
  • nss 3.98
  • numpy 1.26.4
  • omegaconf 2.3.0
  • openh264 2.1.1
  • openjpeg 2.5.0
  • openssl 3.3.1
  • orjson 3.10.3
  • packaging 23.2
  • pandas 2.2.0
  • pango 1.50.14
  • pathlib2 2.3.7.post1
  • pathspec 0.12.1
  • pcre2 10.42
  • pillow 10.2.0
  • pip 24.0
  • pixman 0.43.2
  • platformdirs 3.11.0
  • ply 3.11
  • progressbar 2.5
  • prompt-toolkit 3.0.46
  • prompt_toolkit 3.0.46
  • psutil 5.9.8
  • pthread-stubs 0.4
  • pulseaudio-client 16.1
  • pycodestyle 2.11.1
  • pycparser 2.22
  • pydantic 2.7.3
  • pydantic-core 2.18.4
  • pydot 2.0.0
  • pyflakes 3.2.0
  • pygit2 1.14.1
  • pygments 2.18.0
  • pygtrie 2.5.0
  • pylint 3.1.0
  • pyopenssl 24.0.0
  • pyparsing 3.1.1
  • pyqt 5.15.4
  • pyqt5-sip 12.9.0
  • pysocks 1.7.1
  • python 3.9.18
  • python-dateutil 2.8.2
  • python-gssapi 1.8.2
  • python-tzdata 2024.1
  • python_abi 3.9
  • pytorch 1.12.1
  • pytorch-cuda 11.8
  • pytorch-mutex 1.0
  • pytz 2024.1
  • pywavelets 1.4.1
  • pywin32-on-windows 0.1.0
  • pyyaml 6.0.1
  • qt-main 5.15.2
  • rav1e 0.6.6
  • readline 8.2
  • requests 2.31.0
  • rich 13.7.1
  • ruamel.yaml 0.18.6
  • ruamel.yaml.clib 0.2.8
  • scikit-image 0.22.0
  • scikit-learn 1.4.1.post1
  • scipy 1.12.0
  • scmrepo 2.1.1
  • semver 3.0.2
  • setuptools 69.1.0
  • shellingham 1.5.4
  • shortuuid 1.0.13
  • shtab 1.7.1
  • sip 6.5.1
  • six 1.16.0
  • smmap 5.0.0
  • snappy 1.1.10
  • sqlite 3.45.1
  • sqltrie 0.11.0
  • svt-av1 1.7.0
  • sympy 1.12
  • tabulate 0.9.0
  • threadpoolctl 3.3.0
  • tifffile 2023.8.12
  • tk 8.6.13
  • toml 0.10.2
  • tomli 2.0.1
  • tomlkit 0.12.4
  • torchaudio 0.12.1
  • torchtriton 2.2.0
  • torchvision 0.13.1
  • tornado 6.3.3
  • tqdm 4.66.4
  • typer 0.12.3
  • typer-slim 0.12.3
  • typer-slim-standard 0.12.3
  • typing 3.10.0.0
  • typing-extensions 4.9.0
  • typing_extensions 4.9.0
  • tzdata 2024a
  • unicodedata2 15.1.0
  • urllib3 2.2.1
  • vine 5.1.0
  • voluptuous 0.14.2
  • wcwidth 0.2.13
  • wheel 0.42.0
  • xcb-util 0.4.0
  • xcb-util-image 0.4.0
  • xcb-util-keysyms 0.4.0
  • xcb-util-renderutil 0.3.9
  • xcb-util-wm 0.4.1
  • xkeyboard-config 2.41
  • xorg-kbproto 1.0.7
  • xorg-libice 1.1.1
  • xorg-libsm 1.2.4
  • xorg-libx11 1.8.7
  • xorg-libxau 1.0.11
  • xorg-libxdmcp 1.1.3
  • xorg-libxext 1.3.4
  • xorg-libxrender 0.9.11
  • xorg-renderproto 0.11.1
  • xorg-xextproto 7.3.0
  • xorg-xf86vidmodeproto 2.3.1
  • xorg-xproto 7.0.31
  • xz 5.2.6
  • yaml 0.2.5
  • yarl 1.9.4
  • zc.lockfile 3.0.post1
  • zfp 1.0.1
  • zipp 3.17.0
  • zlib 1.2.13
  • zlib-ng 2.0.7
  • zstd 1.5.5