... | ... | @@ -38,22 +38,32 @@ Alternatively, issues may be resolved by installing rJava using your system pack |
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> sudo apt install r-cran-rjava
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```
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To allocate more memory to Java, find the following line towards the top of image_data_explorer.R:
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##### **RBioFormats**
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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:
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```
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> sudo apt install libfftw3-dev libtiff5-dev
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```
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### **Java memory issues**
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##### **java.lang.OutOfMemoryError: Java heap space**
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If you see this in the image viewer space, it means Bioformats has run out of memory when reading the image. To allocate more memory to Java (and Bioformats), find the following line towards the top of image_data_explorer.R:
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```
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option(java-parameters= c("-Xmx4g", "-Xss4m" ))
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```
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Replace the value of the -Xmx parameter by the number of GB you want to allocate.
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Alternatively, reduce the size of the images for use with the IDE. We recommend to use images with less than 2000 x 2000 pixels.
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##### **java.lang.StackOverflowError**
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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.
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##### **RBioFormats**
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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:
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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 java parameter. For this, find the following line towards the top of image_data_explorer.R:
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```
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> sudo apt install libfftw3-dev libtiff5-dev
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option(java-parameters= c("-Xmx4g", "-Xss4m" ))
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```
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Replace the value of the -Xss parameter by the number of MB you want to allocate.
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### **Data table**
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... | ... | @@ -75,5 +85,5 @@ nameserver 1.1.1.1 |
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### **Performance**
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The main bottleneck is reading the images.
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The main bottleneck is reading the images. Large images (e.g. from electron microscopy) can exceed the available resources and fail to display. You can increase the amount of memory available to Bioformats for reading large images by increasing the value of the java -Xmx parameter [as explained above](https://git.embl.de/heriche/image-data-explorer/-/wikis/Known%20issues%20and%20troubleshooting#javalangOutOfMemoryError-Java-heap-space). We do however recommend to resize large images to under 2000 x 2000 pixels for use with the IDE.
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Data table interactions also get slower as the number of columns increases. |