Segmentation troubleshooting

Posted by Allison Hall on Jan 19, 2007; 12:10am
URL: http://imagej.273.s1.nabble.com/Segmentation-troubleshooting-tp3700540.html

Hi,

 

I am at present using Image J to quantify functional fluorescently

> stained blood vessels present in mouse tissues from treated animals.

> We have previously utilized the OTSU plug-in followed by the despeckle


> filter for the analysis of these mouse tissues, but found that we were


> unable to utilize this plug-in for the analysis of mouse tumours. I

> believed that is was due to the lack of "information" within the

> tumour section (due to its disorganized structure, and the lack to

> fluorescence due to vasculature shutdown). The trial that I am

> analyzing at present is now seeing the tumour section issue, where due


> to vasculature shutdown OTSU is dramatically under thresholding the

> images. Please find attached an example of a control original

> composite image and an image which has almost complete vasculature

> shutdown, and the respective OTSU outputs. Note: these are both kidney


> sections

>  

> We have had a play around with other filters and found that on a small


> subset of affected and nonaffected sections and found that Dynamic

> Threshold 1b appears to threshold to mirror the information seen on

> the original composite image. What is the mask size?? Note: I used

> mask size of 1 in generating the images attached.

 

Control kidney.bmp

https://www7.sendthisfile.com/d.jsp?t=ZuSm75qT6H6vnVUWsNDeF7wF

Mean dynamic control kidney.bmp

https://www5.sendthisfile.com/d.jsp?t=X6TT76sbTpfc0z2yEDIkIIUX

Median dynamic control kidney.bmp

https://www7.sendthisfile.com/d.jsp?t=YP2jPKUH1tDwRNDRWPPIzQvX

OTSU control kidney no threshold.bmp

https://www2.sendthisfile.com/d.jsp?t=T9mrfT6EQbj1rtXADCociIl0

OTSU control kidney with threshold.bmp

https://www6.sendthisfile.com/d.jsp?t=slNIa1XOU13OQBMwAfWI3iCO

treated kidney.bmp

https://www3.sendthisfile.com/d.jsp?t=MpLepGjfSWtt6CIAihVR8MQz

Mean dynamic treated kidney.bmp

https://www7.sendthisfile.com/d.jsp?t=0opyINN6ajmITjGWqutDSM4d

Median dynamic treated kidney.bmp

https://www7.sendthisfile.com/d.jsp?t=JX0PebhsC9meeD48Ix5ttFvg

OTSU treated kidney no threshold.bmp

https://www3.sendthisfile.com/d.jsp?t=OlwBibxYmKaPTyYYuksLg9sp

OTSU treated kidney with threshold.bmp

https://www4.sendthisfile.com/d.jsp?t=lUbn47BQ7pWSYckHmfTD8CqH

 

Note: These images are only available for 6 days after being uploaded

 

Also is it more accurate to OTSU threshold with a selection around the
section of interest or just the entire composite image, from playing
around the threshold is set higher when the selection is applied prior
to thresholding than not.

>  

> If you could please have a look at the images and hopefully you will

> have some suggestions, like is there a more suitable filter or plugin

> we could use, etc

>  

 

 

Allison Hall

Research Assistant

Cancer Drug Discovery Group

 

Bionomics Limited

31 Dalgleish Street

Thebarton SA 5031

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