[ome-users] Viewing and annotating large z-stacked tifs

[Brendan Ffrench]

Dear ome-users,

I am new to this mailing list and hope that someone may be able to advise
me.
I am combining digitized slide images taken on a NanoZoomer (.ndpi files)
with matched fluorescence images scanned on an epiflouresent
microscope (.tif files).

Using ImageJ, Bio-Formats and GIMP, I have managed to extract, align and
stack the images (both .ndpi and .tif files) into a 4 level z-stacked .tif
file. The full .tif files are approx. 9500x9500 pixels (1GB; I am happy to
share a sample if it helps). I was hoping to use Bio-Formats (ImageJ) to
export these stacked .tif files back into a format that could be viewed and
annotated by whole slide viewing software such as ImageScope or NDPview.
Any software that allows me to make annotations and track the areas viewed
on a thumbnail would suit my needs.

ImageScope can open these files but it is not is not representing the
z-stacks correctly. I imagine this can be fixed by editing fields in the
files' metadata. However, I do not know how to start going about this. I
have also tried exporting as .ome and .ome.tiff but none of the viewing
software I have can open these files.

Any insights into this would be greatly appreciated. Alternatively,
another strategy for viewing, tracking and annotating large z-stacked tifs
would be very helpful.

Regards,

Brendan.
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