From 4161dc30e6bd49ec6da00e9c227cfa00afa5914d Mon Sep 17 00:00:00 2001
From: Yi Sun <yi.sun@embl.de>
Date: Thu, 23 Oct 2025 11:45:59 +0200
Subject: [PATCH 1/2] add cellpsoe v4, with gui and gpu support

---
 cellpose/4.0.7/Dockerfile | 84 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 cellpose/4.0.7/Dockerfile

diff --git a/cellpose/4.0.7/Dockerfile b/cellpose/4.0.7/Dockerfile
new file mode 100644
index 00000000..6f16ac22
--- /dev/null
+++ b/cellpose/4.0.7/Dockerfile
@@ -0,0 +1,84 @@
+FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04
+
+LABEL base_image="nvidia/cuda:11.8.0-runtime-ubuntu22.04"
+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 <sunyi000@gmail.com>
+MAINTAINER Florian Wuennemann <flowuenne@gmail.com>
+
+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 \
+    torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --extra-index-url https://download.pytorch.org/whl/cu118 \
+    'cellpose[gui]'==$CELLPOSE_VERSION

From 935f1809640cb35dc7c934d9e28130f0d3cc45ec Mon Sep 17 00:00:00 2001
From: Yi Sun <yi.sun@embl.de>
Date: Thu, 23 Oct 2025 13:27:34 +0200
Subject: [PATCH 2/2] remove nvidia cuda

---
 cellpose/4.0.7/Dockerfile | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/cellpose/4.0.7/Dockerfile b/cellpose/4.0.7/Dockerfile
index 6f16ac22..c2fb8a8d 100644
--- a/cellpose/4.0.7/Dockerfile
+++ b/cellpose/4.0.7/Dockerfile
@@ -1,6 +1,6 @@
-FROM nvidia/cuda:11.8.0-runtime-ubuntu22.04
+FROM ubuntu:22.04
 
-LABEL base_image="nvidia/cuda:11.8.0-runtime-ubuntu22.04"
+LABEL base_image="ubuntu:22.04"
 LABEL version="1"
 LABEL software="cellpose"
 LABEL software.version="4.0.7"
@@ -80,5 +80,4 @@ RUN pip install --no-cache-dir -U pip \
     tqdm \
     tifffile \
     fastremap \
-    torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --extra-index-url https://download.pytorch.org/whl/cu118 \
     'cellpose[gui]'==$CELLPOSE_VERSION