A quick exploration tool for multivariate bioimages. A reference if you use QUIMBI in your own work will be available soon.
To create appropriate data files navigate into the quimbi/pyscripts directory and call:
docker build -t quimbi/dataparser .
docker run -v path-to-data:/data --rm quimbi/dataparser
For information about the required command line parameter use -h
.
The script needs the MSI data to be in HDF5 format. In case of raw data we refer to our preprocessing pipeline ProViM. In case of processed data we refer to our parser imzML-to-HDF5-Parser.
It's important to place your data files in a folder called data
in quimbis root directory: quimbi/data
To create a docker version of quimbi several prerequirements have to be fulfilled.
Docker is not compatible with Windows 7, 8 and 10 Home. For details about a workaround see instructions below.
To build the docker image you simply run docker build -t $IMAGE_NAME .
in the root folder of the quimbi project.
If you want to change anything inside quimbi you have to rerun the build and run process.
To run the docker image enter
docker run -v $(pwd)/data:/usr/share/nginx/html/data -p $PORT:80 --rm --name $CONTAINER_NAME $IMAGE_NAME
.
Afterwards quimbi is available at: http://localhost:$PORT
.
The following lines will create a docker image of quimbi named quimbi_image and creates and runs a container of said image called quimbi_container
docker build -t quimbi_image .
Powershell
docker run -p 8080:80 -v ${PWD}/data:/usr/share/nginx/html/data --rm --name quimbi_container quimbi_image
CMD
docker run -p 8080:80 -v %cd%/data::/usr/share/nginx/html/data --rm --name quimbi_container quimbi_image
Linux
docker run -p 8080:80 -v $(pwd)/data:/usr/share/nginx/html/data --rm --name quimbi_container quimbi_image
Quimbi is now available at: localhost:8080
To stop docker:
Press CTRL+C and call docker stop quimbi_container
To run the project you need node
and npm
. To get access to both download node.js from https://nodejs.org/en/download/ and install the correct version for your OS. Afterwards, clone this repository, use your command shell to navigate into the repository and run npm install
and then npm run build
to build the project.
The bundled project is saved into the dist
folder.
To start developing enter npm run start:dev
. This starts a node based webpack development server at localhost:8080
with live reload. Note: if you make
changes to static files like the index.html or you edit the webpack config file, you need to
restart the server to see changes.
To start the tool for production, go to the dist/index.html
. In this folder you have to start a webserver for example
the build-in from php with php -S localhost:8000
. You can then access the app in your browser
with the url http://localhost:8000
A Github Pages live demo can be used at https://biodatamininggroup.github.io/quimbi/.
docker-machine create default --virtualbox-no-vtx-check
. A restart may be required.