<1% of memory is used - plot Z axis really slow

fiji
memory
memoryandspeed
#1

Hi all,

I am trying to plot Z axis (or intensity v time monitor) of one ROI on an .avi file using the following function:

> stacks > Z Axis profile plot

  • Running version FIJI 2.0.0-rc-69/1.52n; Java 1.8.0_172 [64-bit]
  • It runs <1% of allocated memory (8 threads) 106 MB of 49000 MB making all my analysis impossible to do
  • I have selected virtual stack and grayscale options
  • I have not been able to find a JAVA environment variable limiting memory usage
  • running 64 bit windows, 64 GB RAM
  • the files I am analyzing are 480 by 512 but around a million slices. However I am analyzing only 118 by 180 of that.

Is there a way I can make FIJI use more memory so that it is done more quickly?

Thank you!

ps I am new here so my apologies if I don’t follow the exact format<a class=“attachment”

UPDATE: I did a stackdump, maybe someone can figure something out from this?

stackDump.txt (10.7 KB)

#2

Hello vide,
How are you trying to do that? Are you using Image > Stacks > Z Axis Profile plot?
Bob

#3

Hi Robert, yes this is what I am doing. Do you think there might be a better way?

vide

#4

Well Hello vide,
At 118 X 180 X 1000000 that comes to 21.24 Gigapixels, at 8bit format that would be 5.4 Terabits so you will definitely have to use smaller slice stacks and do each separately then link all the data.
Bob