diff --git a/cellpose/4.0.7/Dockerfile b/cellpose/4.0.7/Dockerfile new file mode 100644 index 00000000..c2fb8a8d --- /dev/null +++ b/cellpose/4.0.7/Dockerfile @@ -0,0 +1,83 @@ +FROM ubuntu:22.04 + +LABEL base_image="ubuntu:22.04" +LABEL version="1" +LABEL software="cellpose" +LABEL software.version="4.0.7" +LABEL about.summary="A generalist algorithm for cell and nucleus segmentation." +LABEL about.home="https://github.com/MouseLand/cellpose" +LABEL about.license="BSD-3-Clause" +LABEL about.license_file="https://github.com/MouseLand/cellpose/blob/main/LICENSE" +LABEL about.documentation="https://cellpose.readthedocs.io/en/latest/" +LABEL extra.identifiers.biotools=cellpose + +MAINTAINER Yi Sun +MAINTAINER Florian Wuennemann + +ARG DEBIAN_FRONTEND="noninteractive" +ARG CELLPOSE_VERSION="4.0.7" + +ENV LANG en_US.UTF-8 \ + LC_ALL en_US.UTF-8 \ + LANGUAGE en_US:en + +ENV MPLCONFIGDIR=/tmp/mpl_cache +ENV NUMBA_CACHE_DIR=/tmp/numba_cache +ENV CELLPOSE_LOCAL_MODELS_PATH=/tmp/cellpose_models +ENV QT_PLUGIN_PATH=/usr/local/lib/python3.10/dist-packages/PyQt6/Qt6/plugins/platforms/ + +RUN apt-get update -qq && \ + apt-get install -y -q --no-install-recommends \ + gcc \ + python3-dev \ + python3-pip \ + python3-wheel \ + libblas-dev \ + liblapack-dev \ + libatlas-base-dev \ + libgl1 \ + mesa-utils \ + libxcb-cursor0 \ + libxext6 \ + libxrender1 \ + libxcb1 \ + libgl1-mesa-glx \ + libxcb-xinerama0 \ + gfortran \ + apt-utils \ + bzip2 \ + ca-certificates \ + curl \ + locales \ + gnupg \ + libfontconfig1 \ + libxkbcommon0 \ + libxkbcommon-x11-0 \ + libxcb-icccm4 \ + libxcb-keysyms1 \ + libxcb-shape0 \ + software-properties-common \ + unzip && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* + +RUN sed -i '/en_US.UTF-8/s/^# //g' /etc/locale.gen && \ + locale-gen + +RUN pip install --no-cache-dir -U pip \ + numpy \ + numba>=0.43.1 \ + wheel \ + scipy \ + pyqt6 \ + pyqt6-qt6 \ + torch>=1.6 \ + opencv-python-headless \ + pyqtgraph>=0.11.0rc0 \ + natsort \ + scikit-image matplotlib \ + scikit-learn \ + tqdm \ + tifffile \ + fastremap \ + 'cellpose[gui]'==$CELLPOSE_VERSION