Public Repository

Last pushed: 2 years ago
Short Description
OpenIAV: an open-source Web application platform for image annotation viewer by RegMed project.
Full Description

OpenIAV (image annotation viewer)


SIGNIFICANCE

OpenIAV (image annotation viewer) is an open source Web-based image annotation platform for data share and archive in a biomedical laboratory.


INTRODUCTION

OpenIAV (image annotation viewer) is a Web-based image annotation tool. It can store a high-resolution figure, and view scale-free slide smooth. This tool includes a rich user interface for graphical annotation such as shape of a line, circle, rectangle, and color pallet. Additionally, you can describe a annotated information for an image as metadata. Detail information of this tools was provided at RegMed project .


NOTICE


INSTALL

Preparation of Docker for Mac OSX
  • M-1. Install "Command Line Tools for Xcode".
    $ xcode-select --install
    
  • M-2. Install a package management system of "Homebrew".
    $ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    
  • M-3. Update the package of Homebrew.
    $ brew update
    $ brew upgrade
    
  • M-4. Install application of "VirtualBox."
  • M-5. Install Boot2Docker and Docker.
    $ brew install boot2docker docker
    
  • M-6. Upgrade Boot2Docker.
    $ boot2docker upgrade
    
  • M-7. Check the IP address assigned using the command of Boot2Docker.
    $ boot2docker ip
    

Preparation of Docker for Windows

Preparation of Docker for Linux
  • LC-0. Install Docker from EPEL of Fedora in CentOS 6. (you do not need this process at after version 6.5)
    $ sudo rpm -ivh http://ftp.riken.jp/Linux/fedora/epel/6/x86_64/epel-release-6-8.noarch.rpm
    
  • LC-1. Update package of yum.
    $ sudo yum update
    
  • LC-2. Install Docker.
    $ sudo yum install docker-io (in case CentOS 6)
    $ sudo yum install docker (in case CentOS 7)
    
  • LC-3. Set up to start Docker at the time of boot of CentOS.
    $ sudo chkconfig docker on
    
  • LC-4. Start Docker service.
    $ sudo /etc/rc.d/init.d/docker start
    
  • LC-5. Inspect a host name, to access from a browser to a Web server.
    Please search an IP address with ifconfig

Install Image Annotation Viewer as common process
  • C-0. Register your account into Docker Hub.
    https://registry.hub.docker.com/ (Link to other Website)
  • C-1. If you encounter the message of "Cannot connect to the Docker daemon. Is 'docker -d' running on this host?" then you execute next command.
    $ export $(boot2docker shellinit)
    
  • C-2. login to Docker Hub.
    $ docker login
    
  • C-3. Pull container image of Image Annotation Viewer from Docker Hub.
    $ docker pull komiyama/binder
    
  • C-4. Check an information of container image.
    $ docker images
    
  • C-5. Start a container as a daemon and assign HTTP port to the container.
* $ docker run -t -i -d -p 80:80 --name binder komiyama/binder
  • C-6. Check a started container.
    $ docker ps -a
    
  • C-7. Access http://HOSTNAME:PORT/binder/login/ via a browser.
  • C-8. Default user accounts were registered as each user roles.
    Administrator: (ID:admin, Password:adminadmin)
    User: (ID:user1, Password:useruser)
    Supervisor: (ID:demo1, Password:demodemo)
    
  • C-9. Set up the CONTAINER ID into a stop option of Docker at the termination of a container.
$ docker stop CONTAINER_ID

Common process of local installation for Image Annotation Viewer from Docker Images of TAR file
  • C'-1. If you encounter the message of "Cannot connect to the Docker daemon. Is 'docker -d' running on this host?" then you execute next command.
    $ export $(boot2docker shellinit)
    
  • C'-2. Download the TAR file of container image of annotation image viewer from our Web site.https://regmed.hgc.jp/docker/ImageAnnotationViewer_latest.tar.gz
  • C'-3. Load the TAR file in to your docker.
    $ docker load -i /YOUR/FILE/PATH/AnnotationImageViewer_latest.tar.gz
    
  • C'-4. Check an information of container image.
    $ docker images
    
  • C'-5. Set a human readable tag to the loaded IAV image.
    $ docker tag IMAGE_ID komiyama/binder:latest
    
  • C'-6. Start a container as a daemon and assign HTTP port to the container.
    $ docker run -t -i -d -p 10080:80 --name binder komiyama/binder
    
  • C'-7. Check a sturted container.
    $ docker ps -a
    
  • C'-8. Access http://DOCKER_HOST:PORT/binder/login/ via a browser.
    Example: http://192.168.59.103:10080/binder/login/
  • C'-9. Default user accounts were registered as each user roles.
    Administrator: (ID:admin, Password:adminadmin)
    User: (ID:user1, Password:useruser)
    Supervisor: (ID:demo1, Password:demodemo)
  • C'-10. Set up the CONTAINER ID into an option parameter of docker stop command at the termination of a container.
    $ docker stop CONTAINER_ID
    

USAGE

Usage and detail information

Please visit the RegMed project Web site.

Docker Pull Command
Owner
komiyama

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