Posted by
Patrick Dooley on
Jan 23, 2018; 4:35pm
URL: http://imagej.273.s1.nabble.com/Selecting-grid-created-ROIs-based-on-an-Initially-Defined-ROI-tp5019936.html
This is my first post here, so forgive any poor formatting issues! I also
posted this in the ImageJ forums, apologies if anyone is seeing this twice.
So the background information: I have a section of brain tissue that’s been
scanned into a .vsi file format. Using the OlympusImageJPlugin I can open
the overview of the image so I can define my initial-ROI, which currently is
the entire slice of cortex. What the Olympus plugin nicely allows me to do
is create a grid over my initial-ROI selection, then I can export each of
those set width grid-ROIs into a tiff file in a folder for analyzation
further down the line.
What I can’t quite figure out is how to only have Fiji save the grid-ROIs
that overlap with my initially defined ROI, the entire cortex slice. I read
this similar topic, which definitely gave me a few ideas, but none of them
worked…
Right now the only idea I have is to create a macro that pulls the x,y
coordinates from the grid-ROIs, checks to see if they’re within the initial
ROI, and if not delete that ROI or if they are save that ROI; not sure which
of those options would be better if I have to take this route.
Is there an easy way to do this I’m just completely missing? I am a complete
newbie with Fiji and essentially with programming, but I am ready to
learn(especially because the dataset I need to obtain is for a grant that’s
due in 6 days…!)
<
http://imagej.1557.x6.nabble.com/file/t381893/fiji_ROI_issue.png>
Alright, so there’s my sample image! My initial-ROI is the red outline, the
yellow outline is the subsequently created grid-ROIs.
What I want to try to do is only have Fiji save tiff files of the grid-ROIs
that contain any portion of the initial-ROI.
Thanks in advance!
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