Issues Scripting in AWS Windows

Hello All,
I am trying to use Fiji on a Windows Amazon Web Services (AWS) instance. I need to use AWS because the analysis I am trying to do goes beyond what my computer can handle, and I am using a Windows instance because it automatically has a GUI so I can see what Fiji is doing.

I set up the instance using the instructions provided here ( and was able to download and run Fiji without an issue. However, when I try to run a Python script in Fiji is see the error:
console: Failed to install ‘’: java.nio.charset.UnsupportedCharsetException: cp0.
I see this problem has been reported before (Script editor error when working with python scripts), but when I attempt to implement the proposed solution (adding -Dpython.console.encoding=UTF-8 to the command line when launching) Fiji simply fails to launch (the icon pops up very briefly and then nothing happens).

Further when I attempt to run:
from ij import IJ

imp = IJ.getImage()
print imp
from the tutorial here (, I get the previous error and a new one:
Traceback (most recent call last):
File “”, line 3, in
at ij.IJ.abort(
at ij.IJ.getImage(
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(
at sun.reflect.DelegatingMethodAccessorImpl.invoke(
at java.lang.reflect.Method.invoke(
java.lang.RuntimeException: java.lang.RuntimeException: Macro canceled

I am not sure what is causing either of these errors or if they are related, but if anyone can offer me advice on addressing them, or tell me how they got Fiji working in an AWS Windows instance, I would greatly appreciate it. If I can provide anymore information to be helpful please let me know. I am new to both Fiji and AWS so sorry if I missed something.

I use fiji on an aws workspace windows instance.

Don’t worry about that error:
‘’: java.nio.charset.UnsupportedCharsetException: cp0."

It happens whenever I open a new script. Ignore it.

To run the script you show you need to have an image open. The “imp” is printed out: img[“20190417_EG16_GFP_PV_restain_slide_34_Scan1_sec_rgb.tif” (-2), 24-bit, 7504x6592x1x1x1]

Should look like this if it’s working:

Thank you so much. Sorry for having missed that. I should have remembered, just shows how new to Fiji I am. BTW, do you mind mentioning what AWS instance type you use. I am trying to do 3D object analysis from large (several Gigs) starting files. So it seems very computationally demanding.

Sorry for the delay responding, but I recently have started to work with images greater then 1 Gb and I’m finding that the aws workspace instance I was using (8 core, 32 Gb ram) has been really struggling and often failing with memory errors when using CellProfiler, Ilastik and ImageJ. I tested an EC2 instance on aws (not the simple manage Workspace) with 128 Gb of ram and got past the memory errors, but big ram instances are very expensive to rent and so I’m giving up on cloud processing and buying a workstation.

No problem. I think I am in a similar situation in terms of image sizes and and RAM requirements, but it is good to hear that you were able to make good use of AWS at least somewhat. Good luck with your workstation!