Out of memory but only using 50% of total memory? BIOP plugin

fiji

#1

I’m using the BIOP plugin to try and extract a .tiff from a .vsi file. It works for my images at 10x, however, when I try with my 20x images, I receive the java out of memory error (but Fiji is only using 50% of my total allocated memory)… I am new to Fiji, so I might just be doing something wrong?

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_172 [64-bit]; Mac OS X 10.14.2; 3123MB of 6222MB (50%)

java.lang.OutOfMemoryError: Java heap space
at ij.CompositeImage.updateImage(CompositeImage.java:263)
at ij.CompositeImage.updateAndDraw(CompositeImage.java:186)
at ij.IJ.setMinAndMax(IJ.java:1216)
at ij.IJ.setMinAndMax(IJ.java:1205)
at ij.macro.Functions.setMinAndMax(Functions.java:5526)
at ij.macro.Functions.doFunction(Functions.java:105)
at ij.macro.Interpreter.doStatement(Interpreter.java:250)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.doStatement(Interpreter.java:295)
at ij.macro.Interpreter.doFor(Interpreter.java:557)
at ij.macro.Interpreter.doStatement(Interpreter.java:277)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.doStatement(Interpreter.java:295)
at ij.macro.Interpreter.doIf(Interpreter.java:1012)
at ij.macro.Interpreter.doStatement(Interpreter.java:271)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.doStatement(Interpreter.java:295)
at ij.macro.Interpreter.doIf(Interpreter.java:1012)
at ij.macro.Interpreter.doStatement(Interpreter.java:271)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.runUserFunction(Interpreter.java:334)
at ij.macro.Interpreter.doStatement(Interpreter.java:256)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.doStatement(Interpreter.java:295)
at ij.macro.Interpreter.doIf(Interpreter.java:1012)
at ij.macro.Interpreter.doStatement(Interpreter.java:271)
at ij.macro.Interpreter.doIf(Interpreter.java:1025)
at ij.macro.Interpreter.doStatement(Interpreter.java:271)
at ij.macro.Interpreter.doBlock(Interpreter.java:635)
at ij.macro.Interpreter.runUserFunction(Interpreter.java:334)
at ij.macro.Interpreter.doStatement(Interpreter.java:256)
at ij.macro.Interpreter.doStatements(Interpreter.java:236)

Thanks for your help!


#2

Hi @belliveau13,

How much total ram does your machine have? If you have 6GB in total, it is possible that several other open applications are eating away at your RAM and that you do not really have 6 GB available for Fiji/

However it is unusual, Could you let us know the final size of the image you will be getting (number of pixels in X and Y)? How many channels you have or if it’s an RGB image?

On a separate note, we are super glad you are using the VSI Reader we wrote a while back :slight_smile:!

For completion, though. We have been increasingly moving away from the VSI Reader in favor of QuPath, as it can open VSI files (With the right extension) and can do image processing through ImageJ/Fiji without the intermediate Export/Resave as Tif step.


#3

Hi @oburri,

Thank you so much for your quick response, my machine has 8GB of RAM total.

The image is RGB. The size of the original image is (39553, 51264). The ROI I would (ideally) like to extract is (3200,26300).

I will definitely be looking into QuPath.

Thank you so much.


#4

@oburri unfortunately QuPath cannot open the .vsi of .jp2 files I have !


#5

As an aside as maybe this isn’t all that much help to your immediate problem but there is a Google Group for QuPath users where you could search to see if people had a similar problem to you regarding this type of .vsi file.

Alternatively, maybe we can try calling @petebankhead to this thread to see if he has any insight. You may need to provide an example of one of your images.


#6

Ah, been summoned…

@belliveau13 did you install the Bio-Formats extension for QuPath, which @oburri linked to above? This should be using the same Bio-Formats as BIOP (I presume), and so if it works in one it should work in the other*.

  • It might not if there is a bug in the QuPath extension, but I think all the ones related to .vsi that I know about have been addressed. @oburri will know more about this than me, since he is typically the source of the information about .vsi-related bugs (but not the source of the bugs).

#7

@oburri @Pete @lmurphy

I completely missed the part about downloading the Bio-Formats extension. It works!

Thank you so much, I think QuPath will be just what I need to complete my image analysis.

Claudia