Merge pull request #20 from BIOP/biop-desktop-011

Biop desktop 011

Author: romainGuiet

docker/Dockerfile-ms

@@ -7,7 +7,7 @@ ARG ALIAS=biop/
 # 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=v0.5.1-01
 ARG ILASTIK_VERSION=1.4.0-gpu
-ARG FIJI_VERSION=20240429
+ARG FIJI_VERSION=20240816
 ARG CELLPOSE_VERSION=2.2.2
 ARG DEVBIO_VERSION=0.10.1
 ARG SAMAPI_VERSION=0.4.0

docker/fiji/Dockerfile-fiji

@@ -37,6 +37,7 @@ RUN ${fiji} ${updateCommand} \
                                 "3D ImageJ Suite" "https://sites.imagej.net/Tboudier/" \
                                 "IJPB-plugins" "https://sites.imagej.net/IJPB-plugins/" \
                                 "ilastik" "https://sites.imagej.net/Ilastik/" \
+                               # "ImageScience" "https://sites.imagej.net/ImageScience/" \
                                 "CSBDeep" "https://sites.imagej.net/CSBDeep/" \
                                 "StarDist" "https://sites.imagej.net/StarDist/" \
                                 "OMERO 5.5-5.6" "https://sites.imagej.net/OMERO-5.5-5.6/" \
@@ -57,6 +58,22 @@ RUN wget -q -q https://www.dropbox.com/sh/dxofkiyseuxn4l4/AADrPjPBbJK_77Ai2WCfaO
         && unzip -o Linux-2.2.0.16.zip -d /opt/Fiji.app/ -x / \
         && rm Linux-2.2.0.16.zip \ 
         && rm /opt/Fiji.app/plugins/clij2-fft_-2.2.0.15.jar
+
+# Install some extratool for PhD Course
+# ThunderSTORM
+RUN wget -q https://github.com/zitmen/thunderstorm/releases/download/v1.3/Thunder_STORM.jar -O /opt/Fiji.app/plugins/Thunder_STORM.jar \
+    && chmod -R a+rwX /opt/Fiji.app/plugins
+
+#ij2-LocalizeJ (depends from)
+RUN wget -q https://maven.scijava.org/service/local/repositories/central/content/colt/colt/1.2.0/colt-1.2.0.jar -O /opt/Fiji.app/jars/colt-1.2.0.jar \
+    && chmod -R a+rwX /opt/Fiji.app/jars
+
+RUN wget -q "https://maven.scijava.org/service/local/artifact/maven/redirect?r=releases&g=sc.fiji&a=imagescience&v=3.0.0&e=jar" -O /opt/Fiji.app/jars/imagescience-3.0.0.jar \
+    && chmod -R a+rwX /opt/Fiji.app/jars
+
+RUN wget -q  https://github.com/ArneS70/ij2-LocalizeJ/raw/main/target/LocalizeJ-0.1.0-SNAPSHOT.jar -O /opt/Fiji.app/jars/LocalizeJ-0.1.0-SNAPSHOT.jar \
+    && chmod -R a+rwX /opt/Fiji.app/jars
+
 ## NOT WORKING
 # /opt/Fiji.app/ImageJ-linux64 --update update
 # [WARNING] Skipping plugins/clij2-fft_-2.2.0.15.jar

docker/openpiv/Dockerfile-openpiv

@@ -0,0 +1,43 @@
+ARG BASE_IMAGE=0.1.0
+ARG ALIAS="biop/"
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
+
+USER root
+
+##############################################################################
+# install devbio-napari
+COPY openpiv/env_openpiv.yml /tmp/env_openpiv.yml
+RUN conda env update -n openpiv -f /tmp/env_openpiv.yml \
+    && conda clean --all -f -y \
+    && conda env export -n "biop" \
+     && rm /tmp/env_openpiv.yml
+
+#create shortcut to start devbio-napari 
+COPY napari/napari-icon.ico /opt/devbio/napari-icon.ico
+COPY openpiv/start_devbio.sh /opt/devbio/start_devbio.sh
+RUN chmod +x /opt/devbio/start_devbio.sh \
+    && chmod -R a+rwX /opt/devbio/ 
+
+RUN mkdir -p /home/biop/Desktop && chown -R biop:biop /home/biop/Desktop \
+    && printf '[Desktop Entry]\nVersion=0.10.1\nName=devbio-napari+OpenPIV\nGenericName=devbio-napari\nX-GNOME-FullName=devbio-napari\nComment=Scientific Image Analysis\nType=Application\nCategories=Education;Science;ImageProcessing;\nExec=/opt/devbio/start_devbio.sh\nTryExec=/opt/devbio/start_devbio.sh\nTerminal=true\nStartupNotify=true\nIcon=/opt/devbio/napari-icon.ico\nStartupWMClass=devbio-napari\n' > /home/biop/Desktop/devbio-napari.desktop \
+    && chown -R biop:biop /home/biop \
+    && chmod +x /home/biop/Desktop/devbio-napari.desktop 
+
+USER biop
+
+# adds openpiv kernel
+RUN source activate openpiv \
+&& python -m ipykernel install --user --name openpiv --display-name "Python (openpiv)" \
+&& conda deactivate
+    
+User root 
+
+#################################################################
+# 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/openpiv/env_openpiv.yml

@@ -0,0 +1,13 @@
+name: "openpiv"
+channels:
+  - conda-forge
+  - pytorch
+  - alexlib 
+  - defaults
+dependencies:
+  - python=3.9 
+  - devbio-napari=0.10.1
+  - pyqt
+  - pip
+  - openpiv
+prefix: "/opt/conda/envs/openpiv"

docker/openpiv/readme.md

@@ -0,0 +1,7 @@
+docker build -f openpiv/Dockerfile-openpiv -t biop/biop-openpiv:0.25.3 .
+
+docker run -it --rm -p 8888:8888 --gpus device=0 --mount src=D:/,target=/home/biop/local,type=bind biop/biop-openpiv:0.25.3
+
+docker tag biop-openpiv:0.25.3 biop/biop-openpiv:0.25.3 
+
+docker push biop/biop-openpiv:0.25.3 

docker/openpiv/start_devbio.sh

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