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83 changes: 83 additions & 0 deletions cellpose/4.0.7/Dockerfile
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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 <[email protected]>
MAINTAINER Florian Wuennemann <[email protected]>

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