Reading and displaying images with .SCN file extension at full resolution

Hello,

I am trying to load and display images that have a .SCN file extension (from Aperio ImageScope). I am using the imread() and imshow() functions to do this. However, when I try to zoom in on the images, I am not getting the same high resolution that I get when zooming in on Aperio ImageScope. When I use the cpselect tool, I am able to see the full resolution image. How can I get the same resolution and image that I see in Aperio ImageScope in MATLAB? Are there other loading and displaying functions for these file types?

Thank you!

Answer 1

[Suryaansh Mata]

I'm given to understand the '.scn' is a BIOFORMATS file. The association that created the format, "The Open Microscopy Environment", has posted a function called "bfopen" that has this capability.

Check out this link for more info - https://docs.openmicroscopy.org/bio-formats/5.9.2/developers/matlab-dev.html

DISCLAIMER: These are my own views and in no way depict those of MathWorks.

[Elizabeth Khoury]

Hi Suryaansh,

Thank you for your answer. I have tried the bfopen function and the following exception is raised:

Java exception occurred:
java.lang.IllegalArgumentException: Array size too large: 49433 x 70910 x 1

	at loci.common.DataTools.safeMultiply32(DataTools.java:1286)

	at loci.common.DataTools.allocate(DataTools.java:1259)

	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:160)
    

Do you have any suggestions for getting around this? I am dealing with quite large images, so that may be the issue. Thanks again.

[Walter Roberson]

Preferences and adjust Java heap memory as large as it will go

However my calculations are that your image is too large to fit in the Java heap memory if it is double precision, as it is over 16 gigabytes I figure.

[Elizabeth Khoury]

Hi Walter,

Thank you for your response. I will try adjusting the Java heap memory. I am working with multiple images that range from around 2-4 GB.

[Elizabeth Khoury]

Hi again,

Your calculations were right, because increasing the Java heap memory to its max didn't change anything. Thank you for the advice. If you have any suggestions, they would be much appreciated.