This page lists known recurring issues. If you have a problem with the app, check also the repository issue tracker and eventually file a new issue there.
- Installation Problems
- High-throughput microscopy
rJava is an R package that allows R to use libraries written in Java. It requires a Java Development Kit (JDK) installed and findable by R. If you experience issues installing rJava, first make sure that Java is installed. Open a terminal and enter:
> java -version
The output should be similar to:
openjdk version "1.8.0_265" OpenJDK Runtime Environment (build 1.8.0_265-8u265-b01-0ubuntu2~16.04-b01) OpenJDK 64-Bit Server VM (build 25.265-b01, mixed mode)
If the output is different, Java is probably not installed. Install it using the procedure appropriate for your system. For example, on Ubuntu and related Linux distributions:
> sudo apt install openjdk-11-jdk
After installing Java, the JDK needs to be registered with R. In a terminal, run:
> R CMD javareconf
This command may also need to be run after an update of R or Java.
Then install rJava from the R console:
Alternatively, issues may be resolved by installing rJava using your system package manager, e.g. on Ubuntu-like systems:
> sudo apt install r-cran-rjava
To allocate more memory to Java, find the following line towards the top of image_data_explorer.R:
option(java-parameters= c("-Xmx4g", "-Xss4m" ))
Replace the value of the -Xmx parameter by the number of GB you want to allocate.
On some system with Java 11 and higher, the default stack size of the JVM is too small resulting in java.lang.StackOverflowError. If you get this error, you may want to increase the value of the -Xss parameter.
This package is the R interface to the Bioformats Java library and therefore depends on rJava. However, it also uses other packages such as fftwtools and tiff that depend on system libraries. Inspect any error message for clues as to which library might be missing. For example, if missing, libfftw and libtiff can be installed on Ubuntu-like systems with:
> sudo apt install libfftw3-dev libtiff5-dev
Problem with plate viewer/wrong plate format
This is likely caused by missing wells. The IDE expects all wells of a given plate to be present in the data. This means that there must be one row per well with the corresponding well identifier column not empty.
Can't connect to S3 bucket
This can be caused by a DNS issue. If this is the case, set DNS servers when starting the container using the --dns flag, e.g. using Cloudflare's public DNS at 126.96.36.199:
> sudo docker run --dns 188.8.131.52 --rm -p 5476:5476 -v /user/home/dir:/data image-data-explorer
The container inherits the DNS configuration from the host machine /etc/resolv.conf file. New DNS servers can be added to the file /etc/resolvconf/resolv.conf.d/base (create the file if it doesn't exist) by adding e.g. nameserver 184.108.40.206