Re: Specifying a predetermined ROI

Posted by Herbie on
URL: http://imagej.273.s1.nabble.com/Specifying-a-predetermined-ROI-tp5023001p5023009.html

Will shall see Abdul!

"The image was scanned and originally saved in a ''.ndpi'' format, after
which I scaled it [...]"

Scaling is not a good idea!
As you may have seen from the older thread, what is needed, is a 90deg
turned image excerpt. Something like the attached image but with the
best spatial resolution possible (no scaling). Please make sure what
bit-depth the original image has. Is it an 24bit RGB-image (8bit per
color)? If yes, you may convert it to 16bit gray-scale. Perhaps even
8bit gray-scale may suffice.

I don't have time tonight to dig deeper in the older investigations but
I shall do so tomorrow and I shall try with your sample image(s).

re: attached older result
In any case the cyan line must be drawn first. The macro then draws the
yellow line. Please read the whole thread on the Forum.
(Actually I've automatically drawn the cyan line but I'm not sure this
will work with your sample image [we shall know tomorrow]. The plugin
that finds the cyan contour isn't available for free and I'm reluctant
to give it away because it isn't easy to operate.)

Please stay tuned

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::
Am 03.03.20 um 18:56 schrieb Abdulhameed Bakreen:

> Hi Herbie,
>
> Please find attached a ''.png'' format of the sample image. The image was scanned and originally saved in a ''.ndpi'' format, after which I scaled it and saved it as ''.tif'' (too big to send) and then finally as ''.png''. Hope this is OK!
>
> P.S. I went through the thread you provided and I tried your macro. I believe that's what I've been looking for. Could you please clarify few things for me, e.g. should the macro for the perilesional area be run before or after highlighting the lesion; should the highlighted lesion be enclosed or is just a straight line across the lesion border enough; how do I make sure that only the perilesional area is being analyzed; and what happens if I have more than 1 perilesional areas for 1 sample image?
>
> Please forgive my ignorance here, I'm pretty new to ImageJ. I really appreciate your immense assistance.
>
> Best regards,
> Abdul
>
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