Annotation Image Viewer
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README.md

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 .

OpenIAV


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
 $ 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
 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)
 $ 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 .