Fiji Crashes When Opening Images

fiji
imagej
mac-os

#1

Hi all. I’m new to using Fiji.

Information about my computer:
2018 Macbook running MacOS Mojave, Version 10.14.1
Processor 3.1 GHz Intel Core i5
Memory is 8Gb
Running on Java 8

I’m trying to open large TIFF files (1-4GB) and RBG JPEG files (converted from the TIFF files via Photoshop).

My first issue is that attempting to open TIFF files almost immediately crashes the program without any error messages.

My second issue is that my JPEG files won’t open either. I keep getting the error message: “Error loading image (Note: IJ cannot open CMYK JPEGs)” even though my JPEGs are RGB. For this issue, the console gives me the message below:

Exception in thread "Image Fetcher 0" java.lang.OutOfMemoryError: Java heap space
	at java.awt.image.DataBufferInt.<init>(DataBufferInt.java:75)
	at java.awt.image.Raster.createPackedRaster(Raster.java:467)
	at java.awt.image.DirectColorModel.createCompatibleWritableRaster(DirectColorModel.java:1032)
	at sun.awt.image.ImageRepresentation.createBufferedImage(ImageRepresentation.java:253)
	at sun.awt.image.ImageRepresentation.setPixels(ImageRepresentation.java:559)
	at sun.awt.image.ImageDecoder.setPixels(ImageDecoder.java:138)
	at sun.awt.image.JPEGImageDecoder.sendPixels(JPEGImageDecoder.java:119)
	at sun.awt.image.JPEGImageDecoder.readImage(Native Method)
	at sun.awt.image.JPEGImageDecoder.produceImage(JPEGImageDecoder.java:141)
	at sun.awt.image.InputStreamImageSource.doFetch(InputStreamImageSource.java:269)
	at sun.awt.image.ImageFetcher.fetchloop(ImageFetcher.java:205)
	at sun.awt.image.ImageFetcher.run(ImageFetcher.java:169)

I have tried deleting and reinstalling Fiji multiple times. The same issues occur.


#2

Hi @isabelag,

Welcome to the forum.

Your first issue may be tricky to figure out. Where did the TIFF files that you’re having trouble come from? How were they generated? and how big are they? If you’re able to upload one to the forum, it could help us figure it out.

For your second issue:
You can allow imagej to use more memory with:
Edit > Options > Memory & Threads ...
It may be set to a value that is too low, so increasing it may help.
6000MB or so will be a good value (going too high can also cause issues)

There’s a bit more information here, but not sure it’ll be relevant for you.

Good luck, and please post back if you’re still having issues (or if this worked for you!)

John


#3

Hi there. Thanks for the response.

The files I’m trying to open are too big to upload here. Hopefully this dropbox link works: https://www.dropbox.com/sh/em9q9c85fjw0r39/AADnLXP4E-0d7ldqUUAXC8hJa?dl=0

In this folder is the JPEG I’m having trouble opening, as well as the TIFF files. The latter were converted from KTL files (also in the folder) using software that comes with a fluorescence microscope (BZ-X series).

I’ve also recently tried using a Windows computer that allows for 15000+ memory use. Even then, the TIFF files won’t open.

EDIT: Just tried the suggestion for expanding my laptop’s memory. I no longer get the error message about my file being CMYK. However, the image still doesn’t open. Below is the pop-up that shows up:

(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51n; Java 1.8.0_66 [64-bit]; Mac OS X 10.14.1; 4091MB of 5966MB (68%)
 
java.lang.OutOfMemoryError: Java heap space
	at ij.process.ColorProcessor.<init>(ColorProcessor.java:33)
	at ij.ImagePlus.setupProcessor(ImagePlus.java:766)
	at ij.ImagePlus.isInvertedLut(ImagePlus.java:1283)
	at ij.measure.Calibration.<init>(Calibration.java:86)
	at ij.ImagePlus.getLocalCalibration(ImagePlus.java:2153)
	at ij.ImagePlus.setType(ImagePlus.java:1136)
	at ij.ImagePlus.setImage(ImagePlus.java:538)
	at ij.ImagePlus.<init>(ImagePlus.java:112)
	at ij.io.Opener.openJpegOrGif(Opener.java:640)
	at ij.io.Opener.openImage(Opener.java:343)
	at ij.io.Opener.openImage(Opener.java:243)
	at ij.io.Opener.open(Opener.java:110)
	at ij.io.Opener.openAndAddToRecent(Opener.java:292)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
	at java.lang.Thread.run(Thread.java:745)


#4

Hi @isabelag,

I have problems opening one of those files as well (CD3-58NoTAE-20xMontage-062618.tif)
but I’m on a linux workstation with a ton of memory.

While we’re figuring this out, another thing you could try is to go back to an older version of Fiji / imageJ:

Maybe start with the version from 2017 May 30.

Thanks for reporting the issue,
John