Installation.md

+Note: These instructions assume a Linux operating system. They've been shown to also work for macOS Sierra but haven't been tested on Windows.
+
+## Requirements
+
+The IDE needs a computer with an [R environment version >=3.5.0](https://www.r-project.org/). The IDE requires some R packages and will try to install them if it can't detect them on the system. In case of problems, it may be better to install the required packages manually.  
+The IDE requires the following packages from CRAN: DT, shiny, shinyFiles, shinycssloaders, shinydashboard, shinyjs, shinyWidgets, shinybusy, assertthat, ggplot2, plotly, RANN, MASS, uwot.
+
+From within an R console, install with:
+
+```
+> > install.packages("DT", "shiny", "shinyFiles", "shinycssloaders", "shinydashboard", "shinyjs", "shinyWidgets", "shinybusy", "assertthat", "ggplot2", "plotly", "RANN", "MASS", "uwot")
+```
+
+and from Bioconductor: EBImage and RBioFormats  
+From within an R console, install with:
+
+```
+> install.packages("BiocManager")
+> BiocManager::install("EBImage")
+> BiocManager::install("aoles/RBioFormats")
+```
+
+* * *
+## Launching the app
+
+Open a terminal, download the code from the project's repository and run it from within the project directory:
+
+```
+> git clone https://git.embl.de/meechan/image-data-explorer.git
+> cd image-data-explorer
+> R -e 'shiny::runApp("image_data_explorer.R", host = "0.0.0.0", port = 5476)'
+```
+
+The app is then accessible from a web browser (on the same machine the app was started on) at http://127.0.0.1:5476  
+
+Alternatively, open the file image_data_explorer.R with RStudio then click the 'Run App' button.
+
+
+Before using the app, check that the data conforms to the structure laid out in [Preparing the data for use with the IDE](./Preparing the data for use with the IDE) page.
+
+If you're experiencing problems, please check the [known issues and troubleshooting](./Known issues and troubleshooting) page before [submitting a new issue](https://git.embl.de/meechan/image-data-explorer/-/issues)
+
+
+## Building and running the app in a container
+
+Download and install Docker then clone this repository.
+From a terminal:
+- Navigate to the directory containing the Dockerfile
+- Build the container (be patient, this may take a while) with
+> sudo docker build --rm -t image-data-explorer .
+- Run the app in the container with:
+> sudo docker run --rm -p 5476:5476 -v /user/home/dir:/data image-data-explorer
+Replace /user/home/dir with the path to your user's home directory or any other directory under which the image root directory resides. This is necessary to make the image root directory accessible to the app.
+The app can then be accessed from a web browser on the same machine at http://127.0.0.1:5476
+
+## Accessing the app remotely
+
+To access the app over the network, simply replace 127.0.0.1 by the IP address of the machine on which the app is running, i.e. point your browser to http:<IP address>:5476
+