Merge branch 'master' into 'heriche-master-patch-94259'

# Conflicts:
#   rstudio/Singularity.rstudio

avivator/Dockerfile

+# Stage 1: Compile and Build Avivator
+FROM ubuntu:20.04 as builder
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+ENV LANG en_US.UTF-8 \
+    LC_ALL en_US.UTF-8 \
+    LANGUAGE en_US:en \
+    TZ=Europe/Berlin 
+
+WORKDIR /usr/local/app
+
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
+    echo $TZ > /etc/timezone
+
+RUN apt update -qq && \
+    apt-get -y install curl \
+	 gnupg \
+         libx11-6 \
+         libxtst6 \
+         git
+
+RUN git clone https://github.com/hms-dbmi/viv.git
+
+RUN curl -sL https://raw.githubusercontent.com/nodesource/distributions/master/deb/setup_14.x -o setup_14.sh
+
+RUN bash setup_14.sh
+
+RUN apt update -y && \
+    apt install nodejs -y
+
+WORKDIR /usr/local/app/viv
+
+RUN npm install --unsafe-perm
+
+RUN npm run build:avivator
+
+# Stage 2: Serve Avivator in nginx server
+FROM nginx:latest
+
+LABEL base_image="ubuntu:20.04, nginx:latest"
+LABEL version="1"
+LABEL software="Viv/avivator"
+LABEL software.version="0.12.3"
+LABEL about.summary="Avivator is a lightweight batteries-included WebGL viewer for remote imaging data, built around Viv. "
+LABEL about.home="https://github.com/hms-dbmi/viv/tree/master/avivator"
+LABEL about.license="MIT License"
+LABEL about.license_file="https://raw.githubusercontent.com/hms-dbmi/viv/master/LICENSE"
+LABEL about.documentation="http://viv.gehlenborglab.org/"
+LABEL extra.identifiers.biotools=avivator
+LABEL maintainer ="sunyi000@gmail.com"
+
+COPY --from=builder /usr/local/app/viv/avivator/dist /usr/share/nginx/html
+ 
+EXPOSE 80
+
+#docker run -d -p 8080:80 avivator:latest

cellpose/Dockerfile

 FROM continuumio/miniconda3
 
+LABEL base_image="miniconda3"
+LABEL version="0"
+LABEL software="cellpose"
+LABEL software.version="0.6.5"
+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.documentation="https://cellpose.readthedocs.io/en/latest/"
+
+LABEL maintainer ="sunyi000@gmail.com"
+
 ARG DEBIAN_FRONTEND="noninteractive"
 
-ENV LANG="en_US.UTF-8" \
-    LC_ALL="en_US.UTF-8" \
+ENV LANG en_US.UTF-8 \
+    LC_ALL en_US.UTF-8 \
+    LANGUAGE en_US:en  \
     PATH=/opt/conda/envs/env/bin:$PATH
 
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           apt-utils \
-           bzip2 \
-           ca-certificates \
-           curl \
-           locales \
-           unzip \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
-    && dpkg-reconfigure --frontend=noninteractive locales #\
-    && update-locale LANG="en_US.UTF-8" \
-    && chmod 777 /opt && chmod a+s /opt 
+RUN apt-get update -qq && \
+    apt-get install -y -q --no-install-recommends \
+            apt-utils \
+            bzip2 \
+            ca-certificates \
+            curl \
+            locales \
+            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 chmod 777 /opt && \
+    chmod a+s /opt 
 
 COPY environment.yml /opt/environment.yml
-RUN  conda env create --name cellpose --file /opt/environment.yml
-RUN conda run -n cellpose python -m pip install cellpose
-SHELL ["conda", "run", "-n", "cellpose", "python", "-m","cellpose"]
 
+RUN conda env create --name cellpose --file /opt/environment.yml && \
+    conda run -n cellpose python -m pip install cellpose
+
+SHELL ["conda", "run", "-n", "cellpose", "python", "-m","cellpose"]
 
+WORKDIR /cellpose
 ENTRYPOINT ["conda", "run", "-n", "cellpose", "python", "-m", "cellpose"]
+
+CMD ["","--help"]

cellpose/readme

+docker built -t cellpose .
+
+docker run -v ~/test:/cellpose cellpose --dir /cellpose --pretrained_model cyto --save_png
+
+"test" folder contains the 3 test images.

cellprofiler4/Singularity

@@ -34,5 +34,5 @@ IncludeCmd: yes
 
     wget https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-16.04/wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
     python3.8 -m pip3 install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
-    python3.8 -m pip3 install cellprofiler
+    python3.8 -m pip3 install cellprofiler==4.1.3
 

cellprofiler4/Singularity.u20

@@ -26,12 +26,14 @@ IncludeCmd: yes
     apt-get install -y python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev git
 
     
-    #python3 -m easy_install pip
-    #python3 -m pip install numpy
-
     wget https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04/wxPython-4.1.0-cp38-cp38-linux_x86_64.whl 
     pip3 install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
     
     
 #    pip3 install cellprofiler
+    cd /opt
+    git clone --branch v4.1.3 https://github.com/CellProfiler/CellProfiler.git 
+    cd /opt/CellProfiler
+    pip3 install .
+   
 

chimerax/Singularity

+BootStrap: docker
+From: ubuntu:20.04
+
+
+%startscript
+%runscript
+
+%post
+  apt update -y
+
+  apt install -y wget 
+      libglu1-mesa-dev \
+      qt5-default \
+      libgl1-mesa-glx \
+      cmake \
+      pkg-config \
+      mesa-utils libglu1-mesa-dev \
+      freeglut3-dev mesa-common-dev \
+      libglew-dev libglfw3-dev libglm-dev \
+      libao-dev libmpg123-dev \
+      openssh-client \
+      git \
+      libxinerama-dev \
+      libxcursor-dev \
+      libxi-dev \
+      unzip \
+      libegl1-mesa \
+
+
+  cd /tmp
+  wget https://git.embl.de/ysun/band-artifacts/-/raw/main/ucsf-chimerax_1.3ubuntu20.04_amd64.deb  
+
+  DEBIAN_FRONTEND=noninteractive apt install -y /tmp/ucsf-chimerax_1.3ubuntu20.04_amd64.deb
+
+  rm /tmp/ucsf-chimerax_1.3ubuntu20.04_amd64.deb
+
+    wget https://sourceforge.net/projects/virtualgl/files/3.0/virtualgl_3.0_amd64.deb/download -O virtualgl_3.0_amd64.deb
+    dpkg -i virtualgl*_amd64.deb
+    vglserver_config -config +s +f -t
+    apt update
+    apt -y upgrade  

chimerax/Singularity.0.8

+Bootstrap: shub
+From: Characterisation-Virtual-Laboratory/CharacterisationVL-Software:1804-cuda9
+
+%labels
+    MAINTAINER_NAME  Jay van Schyndel
+    MAINTAINER_EMAIL jay.vanschyndel@monash.edu
+
+    APPLICATION_NAME ubuntu
+    APPLICATION_VERSION 18.04
+
+    HARDWARE GPU
+
+    LAST_UPDATED 06-MAY-2019
+
+%files
+    chimerax-0.8.tar.gz /tmp
+
+%environment
+    CHIMERAXPATH=/opt/chimerax/bin
+    export PATH=$CHIMERAXPATH:$PATH
+
+%post
+    echo "*********************************************************"
+    echo "Setup and display environment"
+    echo "*********************************************************"
+    export LC_ALL=en_AU.UTF-8
+    export LANGUAGE=en_AU.UTF-8
+    export DEBIAN_FRONTEND=noninteractive
+    echo $LC_ALL
+    echo $LANGUAGE
+    echo $DEBIAN_FRONTEND
+    echo "*********************************************************"
+    echo "Install repositories"
+    echo "*********************************************************"
+    apt-get install -y software-properties-common
+    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic main restricted'
+    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates main restricted'
+    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic universe'
+    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates universe'
+    echo "*********************************************************"
+    echo "Update repositories and install desktop"
+    echo "*********************************************************"
+    apt update
+    apt upgrade -y
+    apt install -y locales
+    locale-gen en_AU.UTF-8
+
+    apt -y install mesa-utils
+    mkdir -p /opt/
+    #cd /tmp/
+    #tar xvf chimerax-0.8.tar.gz -C /opt/
+
+%runscript
+    $*
+

dlc/Singularity.dlcgui

+BootStrap: docker
+From: deeplabcut:deeplabcut:base
+
+%runscript 
+ python3 -m deeplabcut
+ 
+%startscript
+
+%environment
+ export DLClight=False
+
+%post
+
+  # Get dependencies
+  apt-get -y update
+
+  DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    libgtk-3-dev \
+    python3-wxgtk4.0 \
+    locales
+
+  apt-get clean
+
+  rm -rf /var/lib/apt/lists/*
+  
+  pip install --no-cache-dir --upgrade pip
+  pip install --no-cache-dir --upgrade "deeplabcut[gui]>=2.2.0.2" numpy==1.19.5 decorator==4.4.2 tensorflow==2.5.0

dlc/Singularity.dlcjupyter

+BootStrap: docker
+From: ubuntu:20.04
+
+
+%startscript
+  /opt/jupyter/startjupyter.sh
+
+%runscript
+  /opt/jupyter/startjupyter.sh
+
+%files
+ startjupyter.sh /tmp 
+
+%environment
+ export DLClight=False
+
+%post
+  apt update -y
+  apt install -y wget python3-pip python3-dev
+
+  DEBIAN_FRONTEND=noninteractive apt install -y curl \
+		 				libcurl4-openssl-dev \
+						libssl-dev \
+						firefox \
+						ffmpeg \
+						libsm6 \
+						libxext6 \
+						libgtk-3-dev \
+						python3-wxgtk4.0
+		
+  pip3 install ipykernel
+  pip3 install ipython 
+  python3 -m ipykernel install --user
+
+
+  cd /tmp
+  curl -sL https://deb.nodesource.com/setup_14.x | bash -
+
+  DEBIAN_FRONTEND=noninteractive apt install -y nodejs
+ 
+  pip3 install jupyter jupyterlab==2.3.1
+
+
+  rm -rf /var/lib/apt/lists/*     
+  pip3 install --no-cache-dir --upgrade "deeplabcut>=2.2.0.2" numpy==1.19.5 decorator==4.4.2 tensorflow==2.5.0
+  chmod a+rwx -R /usr/local/lib/python3.8/dist-packages/deeplabcut/pose_estimation_tensorflow/models/pretrained
+
+  #mkdir /opt/jupyter-dlc
+  #mv /tmp/startjupyter.sh /opt/jupyter-dlc
+  #chmod +x /opt/jupyter-dlc/startjupyter.sh

dlc/startjupyter.sh

+#!/bin/bash
+
+jupyter lab --allow-root --NotebookApp.token='' &
+
+sleep 2s
+/usr/bin/firefox -new-window http://localhost:8888
+

fiji/Singularity.fiji

@@ -7,7 +7,24 @@ From: ubuntu:16.04
 
 
 %runscript
-  ImageJ-linux64 "$@"
+  # ImageJ-linux64 --update add-update-site BAR http://sites.imagej.net/Tiago/
+  # ImageJ-linux64 --update add-update-site BASIC http://sites.imagej.net/BaSiC/
+  # ImageJ-linux64 --update add-update-site BIG-EPFL http://sites.imagej.net/BIG-EPFL/
+  # ImageJ-linux64 --update add-update-site BioVoxxel http://sites.imagej.net/BioVoxxel/
+  # ImageJ-linux64 --update add-update-site CMP-BIAtools http://sites.imagej.net/CMP-BIA/
+  # ImageJ-linux64 --update add-update-site TrackMate-MorphoLibJ https://sites.imagej.net/TrackMate-MorphoLibJ
+  # ImageJ-linux64 --update add-update-site BigStitcher https://sites.imagej.net/BigStitcher/
+  # ImageJ-linux64 --update add-update-site IBMP-CNRS http://sites.imagej.net/Mutterer/
+  # ImageJ-linux64 --update add-update-site IJPB-plugins http://sites.imagej.net/IJPB-plugins/
+  # ImageJ-linux64 --update add-update-site ImageScience http://sites.imagej.net/ImageScience/
+  # ImageJ-linux64 --update add-update-site IMCFUniBasel http://sites.imagej.net/UniBas-IMCF/
+  # ImageJ-linux64 --update add-update-site MOSAICToolSuite http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite
+  # ImageJ-linux64 --update add-update-site PTBIOP http://biop.epfl.ch/Fiji-Update
+  #ImageJ-linux64 --ij2 --headless --update update
+
+  # ImageJ-linux64 "$@"
+  ImageJ-linux64 -Dij1.plugin.dirs=/opt/fiji/Fiji.app/jars:/opt/fiji/Fiji.app/plugins:$HOME/.plugins
+
 
 %post
    apt -y update
@@ -17,4 +34,4 @@ From: ubuntu:16.04
    cd /tmp
     wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
 
-  unzip -d /opt/fiji/ fiji-linux64.zip
+   unzip -d /opt/fiji/ fiji-linux64.zip

ilastik/Singularity.ilastik-gpu

+Bootstrap: docker
+From: continuumio/miniconda3
+
+%files
+    
+
+%runscript
+ exec  /opt/conda/envs/ilastik/bin/"$@"
+
+%environment
+    export NUMBA_CACHE_DIR=/tmp/numba_cache
+    CONDA_BIN_PATH="/opt/conda/bin"
+    export PATH="$CONDA_BIN_PATH:$PATH"
+
+%post
+   apt-get update -y
+
+   apt install -y build-essential \
+         libglu1-mesa-dev \
+         qtcreator \
+         libgl1-mesa-glx
+
+   export PATH="/opt/conda/bin:$PATH"
+   conda install mamba -n base -c conda-forge
+   mamba create -n ilastik --override-channels -c pytorch -c ilastik-forge -c conda-forge ilastik
+
+  #/opt/conda/bin/conda create -n ilastik --override-channels -c pytorch -c ilastik-forge -c conda-forge ilastik
+  
+
+
+   
+

ilastik/environment.yml

+name: ilastik
+channels:
+  - ilastik-forge
+  - pytorch
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_kmp_llvm
+  - absl-py=1.0.0=pyhd8ed1ab_0
+  - affogato=0.3.3=py37hb3b4854_0
+  - alsa-lib=1.2.3.2=h166bdaf_0
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - astor=0.8.1=pyh9f0ad1d_0
+  - attrs=21.4.0=pyhd8ed1ab_0
+  - bioimageio.core=0.5.3.post2=pyhd8ed1ab_0
+  - bioimageio.spec=0.4.5.post6=pyhd8ed1ab_0
+  - blas=2.114=mkl
+  - blas-devel=3.9.0=14_linux64_mkl
+  - blosc=1.21.1=h83bc5f7_2
+  - boost=1.74.0=py37h796e4cb_5
+  - boost-cpp=1.74.0=h6cacc03_7
+  - brotli=1.0.9=h166bdaf_7
+  - brotli-bin=1.0.9=h166bdaf_7
+  - brotlipy=0.7.0=py37h540881e_1004
+  - brunsli=0.1=h9c3ff4c_0
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.18.1=h7f98852_0
+  - c-blosc2=2.1.1=h7a311fb_0
+  - ca-certificates=2021.10.8=ha878542_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cachetools=5.0.0=pyhd8ed1ab_0
+  - certifi=2021.10.8=py37h89c1867_2
+  - cffi=1.15.0=py37h036bc23_0
+  - cfitsio=4.0.0=h9a35b8e_0
+  - charls=2.3.4=h9c3ff4c_0
+  - charset-normalizer=2.0.12=pyhd8ed1ab_0
+  - click=8.1.3=py37h89c1867_0
+  - cloudpickle=2.0.0=pyhd8ed1ab_0
+  - coin-or-cbc=2.10.8=h3786ebc_0
+  - coin-or-cgl=0.60.6=he2f9439_0
+  - coin-or-clp=1.17.6=h256e9bb_3
+  - coin-or-osi=0.108.7=h3b589db_0
+  - coin-or-utils=2.11.6=h573740c_0
+  - coincbc=2.10.8=0_metapackage
+  - colorama=0.4.4=pyh9f0ad1d_0
+  - cpuonly=2.0=0
+  - cryptography=36.0.2=py37h38fbfac_1
+  - cudatoolkit=11.0.3=h15472ef_10
+  - cycler=0.11.0=pyhd8ed1ab_0
+  - cytoolz=0.11.2=py37h540881e_2
+  - dask-core=2022.2.0=pyhd8ed1ab_0
+  - dbus=1.13.6=h5008d03_3
+  - decorator=4.4.2=py_0
+  - dill=0.3.4=pyhd8ed1ab_0
+  - dpct=1.2.post39=py37_0_hc75b0f0_gb6c703d
+  - et_xmlfile=1.0.1=py_1001
+  - expat=2.4.8=h27087fc_0
+  - fastfilters=0.2.4.post83=py37_0_g4c7b2d9
+  - fftw=3.3.10=nompi_h77c792f_102
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.14.0=h8e229c2_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.33.3=py37h540881e_0
+  - freetype=2.10.4=h0708190_1
+  - fs=2.4.15=pyhd8ed1ab_0
+  - fsspec=2022.3.0=pyhd8ed1ab_0
+  - future=0.18.2=py37h89c1867_5
+  - gast=0.5.3=pyhd8ed1ab_0
+  - gettext=0.19.8.1=h73d1719_1008
+  - giflib=5.2.1=h36c2ea0_2
+  - glpk=4.65=h9202a9a_1004
+  - gmp=6.2.1=h58526e2_0
+  - google-pasta=0.2.0=pyh8c360ce_0
+  - greenlet=1.1.2=py37hd23a5d3_2
+  - grpcio=1.41.1=py37hb27c1af_1
+  - grpcio-tools=1.41.1=py37hcd2ae1e_1
+  - gst-plugins-base=1.20.2=hcf0ee16_0
+  - gstreamer=1.20.2=hd4edc92_0
+  - h5py=3.6.0=nompi_py37hd308b1e_100
+  - hdf5=1.12.1=nompi_h2386368_104
+  - hytra=1.1.4.post77=py_0_g3a9ebe9
+  - icu=69.1=h9c3ff4c_0
+  - idna=3.3=pyhd8ed1ab_0
+  - ilastik=1.4.0b28=0
+  - ilastik-core=1.4.0b28=py_0
+  - ilastik-feature-selection=0.123.post32=py_0_gffb1748
+  - ilastikrag=0.1.3.post40=py_1001_ha6e9690_g3390b38
+  - ilastiktools=0.2.post37=py37_0_h8e2faf5_gb056a5f
+  - imagecodecs=2021.11.20=py37h119f88a_2
+  - imageio=2.19.1=pyhcf75d05_0
+  - imath=3.1.5=h6239696_0
+  - importlib-metadata=4.11.3=py37h89c1867_1
+  - importlib_resources=5.7.1=pyhd8ed1ab_0
+  - inferno=v0.4.2=pyhd8ed1ab_1
+  - jbig=2.1=h7f98852_2003
+  - joblib=1.1.0=pyhd8ed1ab_0
+  - jpeg=9e=h166bdaf_1
+  - jsonschema=4.5.1=pyhd8ed1ab_0
+  - jxrlib=1.1=h7f98852_2
+  - keras-applications=1.0.8=py_1
+  - keras-preprocessing=1.1.2=pyhd8ed1ab_0
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.2=py37h7cecad7_1
+  - krb5=1.19.3=h3790be6_0
+  - lcms2=2.12=hddcbb42_0
+  - ld_impl_linux-64=2.36.1=hea4e1c9_2
+  - lemon=1.3.1=hf0e68b2_5
+  - lerc=3.0=h9c3ff4c_0
+  - libaec=1.0.6=h9c3ff4c_0
+  - libblas=3.9.0=14_linux64_mkl
+  - libbrotlicommon=1.0.9=h166bdaf_7
+  - libbrotlidec=1.0.9=h166bdaf_7
+  - libbrotlienc=1.0.9=h166bdaf_7
+  - libcblas=3.9.0=14_linux64_mkl
+  - libclang=13.0.1=default_hc23dcda_0
+  - libcurl=7.83.1=h7bff187_0
+  - libdeflate=1.10=h7f98852_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libevent=2.1.10=h9b69904_4
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=12.1.0=h8d9b700_16
+  - libgfortran-ng=12.1.0=h69a702a_16
+  - libgfortran5=12.1.0=hdcd56e2_16
+  - libglib=2.70.2=h174f98d_4
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.9.0=14_linux64_mkl
+  - liblapacke=3.9.0=14_linux64_mkl
+  - libllvm11=11.1.0=hf817b99_3
+  - libllvm13=13.0.1=hf817b99_2
+  - libnghttp2=1.47.0=h727a467_0
+  - libnsl=2.0.0=h7f98852_0
+  - libogg=1.3.4=h7f98852_1
+  - libopus=1.3.1=h7f98852_1
+  - libpng=1.6.37=h21135ba_2
+  - libpq=14.3=hd77ab85_0
+  - libprotobuf=3.20.1=h6239696_0
+  - libssh2=1.10.0=ha56f1ee_2
+  - libstdcxx-ng=12.1.0=ha89aaad_16
+  - libtiff=4.3.0=h542a066_3
+  - libuuid=2.32.1=h7f98852_1000
+  - libuv=1.43.0=h7f98852_0
+  - libvorbis=1.3.7=h9c3ff4c_0
+  - libwebp=1.2.2=h3452ae3_0
+  - libwebp-base=1.2.2=h7f98852_1
+  - libxcb=1.13=h7f98852_1004
+  - libxkbcommon=1.0.3=he3ba5ed_0
+  - libxml2=2.9.12=h885dcf4_1
+  - libzlib=1.2.11=h166bdaf_1014
+  - libzopfli=1.0.3=h9c3ff4c_0
+  - llvm-openmp=14.0.3=he0ac6c6_0
+  - llvmlite=0.38.0=py37h0761922_1
+  - locket=1.0.0=pyhd8ed1ab_0
+  - lz4-c=1.9.3=h9c3ff4c_1
+  - mamutexport=0.2.1.post6=py39_0_g9ab21f6
+  - marching_cubes=0.3.post9=py37_0_hb110ab7_g1a4aa17
+  - markdown=3.3.7=pyhd8ed1ab_0
+  - marshmallow=3.15.0=pyhd8ed1ab_1
+  - marshmallow-jsonschema=0.13.0=pyhd8ed1ab_0
+  - marshmallow-union=0.1.15.post1=pyhd8ed1ab_0
+  - matplotlib-base=3.5.2=py37hc347a89_0
+  - mkl=2022.0.1=h8d4b97c_803
+  - mkl-devel=2022.0.1=ha770c72_804
+  - mkl-include=2022.0.1=h8d4b97c_803
+  - mrcfile=1.3.0=pyh44b312d_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mysql-common=8.0.29=haf5c9bc_0
+  - mysql-libs=8.0.29=h28c427c_0
+  - ncurses=6.3=h27087fc_1
+  - ndstructs=0.0.5dev0=py_0
+  - networkx=2.5.1=pyhd8ed1ab_0
+  - nifty=1.2.1=py37h023b2db_3
+  - ninja=1.10.2=h4bd325d_1
+  - nose=1.3.7=py_1006
+  - nspr=4.32=h9c3ff4c_1
+  - nss=3.77=h2350873_0
+  - numba=0.55.1=py37h43839f2_1
+  - numpy=1.21.6=py37h976b520_0
+  - openexr=3.1.5=he0ac6c6_0
+  - openjpeg=2.4.0=hb52868f_1
+  - openpyxl=3.0.9=pyhd8ed1ab_0
+  - openssl=1.1.1o=h166bdaf_0
+  - packaging=21.3=pyhd8ed1ab_0
+  - pandas=0.24.2=py37hb3f55d8_1
+  - partd=1.2.0=pyhd8ed1ab_0
+  - pcre=8.45=h9c3ff4c_0
+  - pillow=9.1.0=py37h44f0d7a_2
+  - pip=22.1=pyhd8ed1ab_0
+  - protobuf=3.20.1=py37hd23a5d3_0
+  - psutil=5.9.0=py37h540881e_1
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pyopengl=3.1.6=pyhd8ed1ab_1
+  - pyopenssl=22.0.0=pyhd8ed1ab_0
+  - pyparsing=3.0.9=pyhd8ed1ab_0
+  - pyqt=5.12.3=py37h89c1867_8
+  - pyqt-impl=5.12.3=py37hac37412_8
+  - pyqt5-sip=4.19.18=py37hcd2ae1e_8
+  - pyqtchart=5.12=py37he336c9b_8
+  - pyqtgraph=0.12.4=pyhd8ed1ab_0
+  - pyqtwebengine=5.12.1=py37he336c9b_8
+  - pyrsistent=0.18.1=py37h540881e_1
+  - pysocks=1.7.1=py37h89c1867_5
+  - python=3.7.12=hb7a2778_100_cpython
+  - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-elf=0.4.3=pyhd8ed1ab_0
+  - python-stdnum=1.17=pyhd8ed1ab_0
+  - python_abi=3.7=2_cp37m
+  - pytiff=0.8.1=py37h5e73a3c_4
+  - pytorch=1.7.0=py3.7_cuda11.0.221_cudnn8.0.3_0
+  - pytorch-mutex=1.0=cpu
+  - pytz=2022.1=pyhd8ed1ab_0
+  - pywavelets=1.3.0=py37hda87dfa_1
+  - pyyaml=6.0=py37h540881e_4
+  - qimage2ndarray=1.8.3=pyhd8ed1ab_0
+  - qt=5.12.9=h1304e3e_6