Blank window / no image data when opening big files


#1

Hi,

I have large tiff files (e.g. 58000x35000 px). When I open them in fiji (BioFormats import as hyperstack) I get a new window that is plain grey - however I would expect to see my image there. Here is a screenshot of this window:

The window is of the size of my image. I can zoom in this “image” and see an indicator of where I am in the full image. I see that fiji uses an appropriate amount of memory. However I don’t see the image data (that I can see e.g. in GIMP).

Everything seems to work just fine if images are smaller.

Metadata of the image, in case in might help:

BitsPerPixel 8
DimensionOrder XYCZT
IsInterleaved false
IsRGB false
LittleEndian true
PixelType uint8
Series 0 Name NF2_secco_ORG_gimp.tiff
SizeC 1
SizeT 1
SizeX 57861
SizeY 34756
SizeZ 1
BitsPerSample 8
Compression Uncompressed
Document Name /home/b/phd2_daten/3184/stitched/NF2_secco/NF2_secco_ORG_gimp.tiff
ImageLength 34756
ImageWidth 57861
Location /home/b/phd2_daten/3184/stitched/NF2_secco/NF2_secco_ORG_gimp.tiff
MetaDataPhotometricInterpretation Monochrome
MetaMorph no
NewSubfileType 0
NumberOfChannels 1
Orientation 1st row - top; 1st column - left
PhotometricInterpretation BlackIsZero
PlanarConfiguration Chunky
ResolutionUnit Inch
SamplesPerPixel 1
XResolution 72.00900354121013
YResolution 72.00900354121013

What am I doing wrong? Why is the image not displayed?


Blank window when attempting to open an image
#2

Dear @oeb,

Nothing!

Most definitely, because it’s a huge plane. Does, by chance, resizing the window help? This should trigger a re-drawing of the window’s content.

Do you see any errors/exceptions in the log and/or console window? if not, could you follow the instructions in http://imagej.net/Debugging#Command_line_debugging and report back, if you see any errors in the terminal?

Best,
Stefan


#3

Dear @stelfrich , thanks for your answer!

Resizing the window does not result in a drawn image in the window.

The console window stays empty after opening and resizing one of the files in question.
I guess the log window is the one that will pop up by itself, when it’s filled? Anyway, I

Using the command line debugging, I’m afraid, there is nothing useful or unusual as well:
When I open the software, a lot of [DEBUG] information is displayed. When I open and rescale the file, nothing new happens.
Closing the file results in an output:

[DEBUG] unregister legacy image: img[“NFst2_secco_ORG.tiff” (-5), 8-bit, 57860x34756x1x1x1]
[DEBUG] unregister legacy image: img[“NFst2_secco_ORG.tiff” (-5), 0-bit, 57860x34756x1x1x1]

After I have opened the image, I can use the shortcuts and the mousewheel to zoom in on the image.
A pictogram is drawn to show me what fraction of the full image I have zoomed into. However no actual image information is displayed … :confused:

For some reason, I can display the files in TrackEM2:
If I import the file in TrackEM2, I get:

TrakEM: empty cache – please free up some memory
TrakEM: empty cache – please free up some memory
WARNING: Can’t fit 20109829792 bytes in memory.
WARNING: Can’t fit 20109829792 bytes in memory.
WARNING: Can’t fit 20109829792 bytes in memory.
WARNING: Can’t fit 20109829792 bytes in memory.
WARNING: Can’t fit 20109829792 bytes in memory.
WARNING: Can’t fit 16087865344 bytes in memory.
Opener: File is not in a supported format, a reader
plugin is not available, or it was not found.
Can’t fit 20109829792 bytes in memory.

the debug consoloe shows after some time:

Red phone at port 29391
MipMaps with area downsampling: creation took 1287ms, saving took 12896ms, total: 14183ms

Free memory, after opening the file, is 6GB (of 16GB in total) The image size is about 2GB.

I can’t be the only one trying to open somewhat larger images…?
Anything more I can do or try?

Cheers


Blank window with big files
#4

Well, the default ImageJ1 image viewer, wasn’t really intended to lift that kind of load. While you should still be below the 2G pixels limit per plane according to your image size, you are pretty close to it.

There is detailed reply by @ctrueden to a similar request on the mailing list that might be of interest to you:

http://imagej.1557.x6.nabble.com/Large-image-tp5015380p5015389.html

Best,
Stefan