Merge pull request #19 from BIOP/update_desktop

biop-desktop to 0.1.0

docker/Dockerfile-base

@@ -107,13 +107,24 @@ RUN mkdir -p /home/biop/Desktop && chown -R biop:biop /home/biop/Desktop \
     && chown -R biop:biop /home/biop \
     && chmod -R a+rwx /home/biop/
 
-
 #################################################################
 # Install Inkscape 
 RUN sudo apt-get update -y \
     && sudo apt-get install inkscape -y 
 
 
+################################################################# 
+# OpenCL for clij ...
+RUN apt-get update \
+    && apt-get install -y nvidia-opencl-dev \
+    && apt remove -y libnvidia-compute-550-server \
+    && apt-get autoremove --purge \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && rm -rf /tmp/* \
+    && find /var/log -type f -exec cp /dev/null \{\} \;
+
+#################################################################
 RUN chown -R biop:biop /home/biop/ \
     && chmod -R a+rwx /home/biop/ 
 

docker/Dockerfile-ms

@@ -1,22 +1,23 @@
-ARG BASE_IMAGE=0.0.3
+ARG BASE_IMAGE=0.1.0
 
 ARG ALIAS=biop/
 
 # because COPY --from= doesn't support build-arg (https://github.com/docker/for-mac/issues/2155)
 # we can still do a list of all sub-blocks here to be able to use them in the COPY --from=... below
 # base needs to be last, Don't Ask Wky !  (I don't know) ! and it seems it need to be named 'base' , D.A:W.2 ! but it works !
-ARG QUPATH_VERSION=v0.5.1
+ARG QUPATH_VERSION=v0.5.1-01
 ARG ILASTIK_VERSION=1.4.0-gpu
-ARG FIJI_VERSION=20240325
+ARG FIJI_VERSION=20240429
 ARG CELLPOSE_VERSION=2.2.2
 ARG DEVBIO_VERSION=0.10.1
 ARG SAMAPI_VERSION=0.4.0
-ARG EM_VERSION=0.2.3
+ARG EM_VERSION=1.1.0
 ARG STARDIST_VERSION=0.8.5
-ARG ABBA_VERSION=0.8.0
+ARG ABBA_VERSION=0.8.0-01
 ARG CELLPROFILER_VERSION=4.2.6
 ARG INKSCAPE_VERSION=0.0.1
-ARG OMNI_VERSION=1.0.7-dev
+ARG OMNI_VERSION=1.0.7-dev2
+ARG BRAINRENDER_VERSION=0.0.3
 
 FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} as qupath-image
 FROM ${ALIAS}biop-ilastik:${ILASTIK_VERSION} as ilastik-image
@@ -29,7 +30,8 @@ FROM ${ALIAS}biop-stardist:${STARDIST_VERSION} as stardist-image
 FROM ${ALIAS}biop-abba:${ABBA_VERSION} as abba-image
 FROM ${ALIAS}biop-cellprofiler:${CELLPROFILER_VERSION} as cellprofiler-image
 FROM ${ALIAS}biop-inkscape:${INKSCAPE_VERSION} as inkscape-image
-FROm ${ALIAS}biop-omnipose:${OMNI_VERSION} as omnipose-image
+FROM ${ALIAS}biop-omni:${OMNI_VERSION} as omnipose-image
+FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} as brainrender-image
 
 FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} as base
 
@@ -163,8 +165,17 @@ COPY fiji/Fiji_setWrappersPaths.groovy /home/biop/tmp/Fiji_setWrappersPaths.groo
 RUN chown -R biop:biop /home/biop/tmp \
     && chmod -R a+rwX /home/biop/tmp
 
+# add brainrender-napari env 
+COPY --from=brainrender-image /opt/conda/envs/brainrender /opt/conda/envs/brainrender
+
 USER biop
 RUN /opt/Fiji.app/ImageJ-linux64 --headless --run /home/biop/tmp/Fiji_setWrappersPaths.groovy
+
+# download allen_mouse_25um atlas from brainrender-napari
+RUN source activate brainrender \
+    && brainglobe install -a allen_mouse_25um \
+    && conda deactivate
+
 USER root
 RUN rm -rf /home/biop/tmp
 
@@ -195,21 +206,6 @@ COPY --from=omnipose-image /opt/conda/envs/omnipose/ /opt/conda/envs/omnipose/
 # To make the different conda env available in jupyter
 COPY jupyter/kernels/ /home/biop/.local/share/jupyter/kernels/
 
-
-#################################################################
-# # Install OpenCL ( for clij ... )
-# Doesn't work (anymore) on local WSL2 but works on runai !!!
-# see https://github.com/NVIDIA/nvidia-container-toolkit/issues/371
-# We move at the end so that we can build a normal version and WSL one without it, as it is not supported anyway.
-RUN apt-get update \
-    && apt-get install -y nvidia-opencl-dev \
-    && apt remove -y libnvidia-compute-545 \
-    && apt-get autoremove --purge \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && rm -rf /tmp/* \
-    && find /var/log -type f -exec cp /dev/null \{\} \;
-
 #################################################################
 # final chown and chmod
 RUN chown -R biop:biop /home/biop/ \

docker/QuPath/Dockerfile-qupath

@@ -42,11 +42,11 @@ RUN chown -R biop:biop /opt/QuPath/QuPath_Common_Data_0.5 \
     && chmod -R a+rwx /opt/QuPath/QuPath_Common_Data_0.5     
 
 # # TODO : discuss if we prepare unzip from zenodo, or if we update when container start via a git pull ... (less good for reproducibility but better to keep scripts up-to-date)
-RUN wget -q https://zenodo.org/records/10869324/files/QuPath_Common_Data_0.5.zip?download=1 -O ${TEMP_DIR}/QuPath_Common_Data_0.5.zip
+RUN wget -q https://zenodo.org/records/11091309/files/QuPath_Common_Data_0.5.zip?download=1 -O ${TEMP_DIR}/QuPath_Common_Data_0.5.zip
 RUN unzip ${TEMP_DIR}/QuPath_Common_Data_0.5.zip -d /opt/QuPath/QuPath_Common_Data_0.5 \
     && rm ${TEMP_DIR}/QuPath_Common_Data_0.5.zip 
 
-
+    
 
 # #  Prepare to set QP_prefs 
 COPY QuPath/QuPath_setPaths.groovy /home/biop/tmp/QuPath_setPaths.groovy

docker/abba/Dockerfile-abba

@@ -1,13 +1,15 @@
 # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes/rel-23-07.html 
 #FROM superelastix/elastix:5.0.1 as elastix-image
-ARG QUPATH_VERSION=v0.5.1
-ARG FIJI_VERSION=20240325
+ARG QUPATH_VERSION=v0.5.1-01
+ARG FIJI_VERSION=20240429
 ARG DEEPSLICE_VERSION=1.1.5
+ARG BRAINRENDER_VERSION=0.0.3
 ARG ALIAS=biop/
 
 FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} as qupath-image
 FROM ${ALIAS}biop-fiji:${FIJI_VERSION} as fiji-image
 FROM ${ALIAS}biop-deepslice:${DEEPSLICE_VERSION} as deepslice-image
+FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} as brainrender-image
 
 FROM ${ALIAS}biop-vnc-base:0.0.3 as base
 
@@ -137,6 +139,27 @@ RUN  printf '[Desktop Entry]\nVersion=0.8.0\nName=ABBA\nGenericName=ABBA\nX-GNOM
 RUN  chown -R biop:biop /opt/Fiji.app/ \
     && chmod -R a+rwX /opt/Fiji.app/
 
+# install brainrender
+COPY --from=brainrender-image /opt/conda/envs/brainrender /opt/conda/envs/brainrender
+
+
+USER biop
+
+# adds brainrender kernel
+RUN source activate brainrender \
+    && python -m ipykernel install --user --name brainrender --display-name "Python (brainrender)" \
+    && conda deactivate
+
+# download allen_mouse_25um atlas
+RUN source activate brainrender \
+    && brainglobe install -a allen_mouse_25um \
+    && conda deactivate
+
+USER root 
+
+RUN chmod -R a+rwX /home/biop/ \
+    && chown -R biop:biop /home/biop/
+
 #################################################################
 # Container start
 USER biop

docker/brainrender/Dockerfile-brainrender

@@ -1,4 +1,4 @@
-ARG BASE_IMAGE=0.0.3
+ARG BASE_IMAGE=0.1.0
 ARG ALIAS=biop/
 FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
 
@@ -13,10 +13,12 @@ RUN conda env update -n brainrender -f /tmp/env_brainrender.yml \
 
 USER biop
 
+# adds brainrender kernel
 RUN source activate brainrender \
     && python -m ipykernel install --user --name brainrender --display-name "Python (brainrender)" \
     && conda deactivate
 
+# download allen_mouse_25um atlas
 RUN source activate brainrender \
     && brainglobe install -a allen_mouse_25um \
     && conda deactivate

docker/brainrender/env_brainrender.yml

@@ -1,4 +1,4 @@
-name: "devbio"
+name: "brainrender-napari"
 channels:
   - conda-forge
 dependencies:
@@ -7,5 +7,6 @@ dependencies:
   - pyqt
   - pip
   - pip :
-    - brainrender-napari
-prefix: "/opt/conda/envs/devbio"
+    - brainrender-napari==0.0.3
+    - bg-atlasapi
+prefix: "/opt/conda/envs/brainrender-napari"

docker/celldetection/Dockerfile-celldetection

@@ -0,0 +1,42 @@
+ARG BASE_IMAGE=0.0.3
+ARG ALIAS=biop/
+
+
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
+
+
+USER root
+
+# install celldetection and download models ( https://celldetection.readthedocs.io/en/latest/models.html )
+COPY celldetection/env_celldetection.yml /tmp/env_celldetection.yml
+RUN conda env update -n celldetection -f /tmp/env_celldetection.yml \
+    && conda clean --all -f -y \
+    && conda env export -n "biop" \ 
+    && rm /tmp/env_celldetection.yml 
+
+# get model
+RUN mkdir -p /home/biop/.cache/torch/hub/checkpoints/
+RUN wget https://celldetection.org/torch/models/ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c.pt -O /home/biop/.cache/torch/hub/checkpoints/ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c.pt
+RUN wget https://celldetection.org/torch/models/.pt -O /home/biop/.cache/torch/hub/checkpoints/.pt
+
+RUN mkdir -p /home/biop/celldetection/ \
+    && chown -R biop:biop /home/biop/ \
+    && chmod -R a+rwX /home/biop/
+
+COPY celldetection/start_celldetection.sh /opt/celldetection/start_celldetection.sh
+COPY napari/napari-icon.ico /opt/celldetection/napari-icon.ico
+
+RUN  printf '[Desktop Entry]\nVersion=0.0.1\nName=celldetection\nGenericName=celldetection\nX-GNOME-FullName=celldetection\nComment=Scientific Image Analysis\nType=Application\nCategories=Education;Science;ImageProcessing;\nExec=/opt/celldetection/start_celldetection.sh\nTryExec==/opt/celldetection/start_celldetection.sh\nTerminal=true\nStartupNotify=true\nMimeType=image/*;\nIcon=/opt/celldetection/napari-icon.ico\nStartupWMClass=celldetection\n' > /home/biop/Desktop/celldetection.desktop \
+    && chown -R biop:biop /home/biop \
+    && chmod +x /home/biop/Desktop/celldetection.desktop 
+
+
+RUN chmod -R a+rwX /home/biop/ \
+    && chown -R biop:biop /home/biop/
+
+#################################################################
+# Container start
+USER biop
+WORKDIR /home/biop
+ENTRYPOINT ["/usr/local/bin/jupyter"]
+CMD ["lab", "--allow-root", "--ip=*", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--notebook-dir=/home/biop"]

docker/celldetection/env_celldetection.yml

@@ -0,0 +1,19 @@
+name: "celldetection"
+channels:
+  - pytorch
+  - nvidia
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - pytorch
+  - pyqt
+  - napari
+  - torchvision
+  - pytorch-cuda=11.8
+  - pip
+  - pip :
+    - celldetection
+    - git+https://github.com/FZJ-INM1-BDA/celldetection-napari.git
+    - ipykernel
+prefix: "/opt/conda/envs/celldetection"

docker/celldetection/start_celldetection.sh

@@ -0,0 +1,4 @@
+source activate celldetection
+napari
+$ read -rsp $'Press enter to continue...\n'
+Press enter to continue...

docker/empanada/Dockerfile-empanada

@@ -1,5 +1,6 @@
-ARG BASE_IMAGE=0.0.1
-FROM biop-vnc-base:${BASE_IMAGE}
+ARG BASE_IMAGE=0.0.3
+ARG ALIAS=biop/
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} as base
 #ARG DEBIO_VERSION=0.10.1
 #FROM biop-devbio:${DEBIO_VERSION} as base
 

docker/empanada/env_empanada-gpu.yml

@@ -1,14 +1,21 @@
 name: "empanada"
 channels:
+  - ome
   - conda-forge
   - defaults
 dependencies:
   - python=3.9
+  - ome::zeroc-ice36-python
+  - ipykernel
+  - napari
+  - conda-forge::omero-py
   - pyqt
   - pip
   - pip:
-      - napari[all]
-      - empanada-napari==0.2.3
+      - empanada-napari==1.1.0
       - scikit-image
+      - napari-ome-zarr 
+      - ome-zarr
+      - napari-omero
 prefix: "/opt/conda/envs/empanada"
 #TODO napari-ome-zarr

docker/fiji/Dockerfile-fiji

@@ -1,11 +1,11 @@
 # https://docs.nvidia.com/deeplearning/frameworks/pytorch-release-notes/rel-23-07.html 
 # FROM nvcr.io/nvidia/pytorch:23.07-py3
-ARG BASE_IMAGE=0.0.3
+ARG BASE_IMAGE=0.1.0
 ARG ALIAS=biop/
 FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
 
 ENV OMEROIJ_VERSION 5.8.3
-ENV SOC_VERSION 5.16.0
+ENV SOC_VERSION 5.18.0
 
 USER root
 
@@ -49,7 +49,6 @@ RUN wget -q https://github.com/ome/omero-insight/releases/download/v${OMEROIJ_VE
     && chmod -R a+rwX /opt/Fiji.app/plugins
 
 # Install simple-omero-client
-
 RUN wget -q https://github.com/GReD-Clermont/simple-omero-client/releases/download/${SOC_VERSION}/simple-omero-client-${SOC_VERSION}.jar -O /opt/Fiji.app/plugins/simple-omero-client-${SOC_VERSION}.jar \
     && chmod -R a+rwX /opt/Fiji.app/plugins
 
@@ -65,23 +64,6 @@ RUN wget -q -q https://www.dropbox.com/sh/dxofkiyseuxn4l4/AADrPjPBbJK_77Ai2WCfaO
 # [WARNING] Skipping lib/linux64/libjniclij2fftWrapper.so
 
 
-# OpenCL installation for clij
-# specificy version of "nvidia-opencl-dev" , because of the error : ... usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1: file exists: unknown.  
-# TODOs : find out which version make it crash !!! https://packages.ubuntu.com/search?suite=default&section=all&arch=any&keywords=+nvidia-opencl-dev&searchon=names
-# list  :
-# - jammy (22.04LTS) : 11.5.1-1ubuntu1 , WORKS ! (https://packages.ubuntu.com/jammy/nvidia-opencl-dev)
-# - lunar (23.04) : 11.8.89 , try but can't find it (https://packages.ubuntu.com/lunar/nvidia-opencl-dev)
-# - mantic (23.10) : 12.0.140, try but can't find it (https://packages.ubuntu.com/mantic/nvidia-opencl-dev)
-# >sudo apt-get update returns, jammy-security ...   might be why it can't find others (lunar and mantic)
-RUN apt-get update \
-    && apt-get install -y nvidia-opencl-dev \
-    && apt remove -y libnvidia-compute-545 \
-    && apt-get autoremove --purge \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && rm -rf /tmp/* \
-    && find /var/log -type f -exec cp /dev/null \{\} \;
-
 # create icon
 RUN mkdir -p /home/biop/Desktop && chown -R biop:biop /home/biop/Desktop \
     && printf '[Desktop Entry]\nVersion=1.0\nName=ImageJ\nGenericName=ImageJ\nX-GNOME-FullName=ImageJ\nComment=Scientific Image Analysis\nType=Application\nCategories=Education;Science;ImageProcessing;\nExec=/opt/Fiji.app/ImageJ-linux64 %F\nTryExec=/opt/Fiji.app/ImageJ-linux64\nTerminal=false\nStartupNotify=true\nMimeType=image/*;\nIcon=/opt/Fiji.app/images/icon.png\nStartupWMClass=net-imagej-launcher-ClassLauncher\n' > /home/biop/Desktop/Fiji.desktop

docker/jupyter/kernels/brainrender/kernel.json

@@ -0,0 +1,14 @@
+{
+ "argv": [
+  "/opt/conda/envs/brainrender/bin/python",
+  "-m",
+  "ipykernel_launcher",
+  "-f",
+  "{connection_file}"
+ ],
+ "display_name": "brainrender",
+ "language": "python",
+ "metadata": {
+  "debugger": true
+ }
+}