Measurement Outlines

davek604

Hello

I have a mask image that is basically a doughnut, I perform a count to get the outline of the doughnut, When I apply the doughnut outline to another image it gives 2 measurements 1 from the outer ring and another from the inner ring, Is there a way I can get Premier to only measure the area between the outer and inner ring I need this to complete my script. I can simply take 1 away from the other for area but intensity measurements will be wrong.

All help appreciated

David

YuriG

I assume that you create a mask of DAPI nucleus and then create a distance map of it. Using histogram of the distance map you can find threshold levels that would split it into 5 equal areas (1 internal polygon and 4 rings outside of it). Then you can simply apply these thresholds by pairs in a loop (min/max for the given ring) executing Count - it will produce a ring object (with one hole), which you can then put to the Features Manager. You can collect all 5 rings to the Features Manager one by one and then place them (all 5) to another image - that will give you doughnut-shape objects with proper measurements - all 5 in one data table.

You can also create threshold segmentation on distance map with 5 classes, each with different threshold range. Then a single Count will give you 5 ring objects that can be transferred at once to another image using Features Manager.

Yuri

YuriG

Hello David,

How do you create the doughnut outline? 

If you create it by image segmentation in Count/Size, then you shouldn't have a problem. Just use Features Manager to transfer outline from one image to another and you will get the right doughnut-shape object on the new image.

If you draw 2 doughnut outlines manually, then you have to use ROI to measure it correctly. In Region Of Interest ribbon bar (on Select tab) open Options button dropdown and select XOR ROIs option, then segment everything inside these ROIs - it will give you all measurements inside the doughnut.

Yuri

davek604

Hello Yuri

I threshold 1 dapi nucleus, convert it to a mask and then split it into 5 rings (~equal based on area) which make up the doughnuts. The script then takes a measurement of the doughnuts which produces an outline. However when I look at the measurement table there are 2 measurements consisting of the inner and outer parts of the doughnut ring. Save measurements will apply the outline to the other image but its the same problem of measuring the inner and outer ring it doesn't give just 1 measurement corresponding to the area between the inner and outer ring. I remember when I did this on Image Pro Plus I had to use a special script that basically turned the ring into a sort of tube its presumably going to be the same again.

Dave 

davek604

Hello Yuri

Thinking about it, I could apply the smallest region which is actually solid, make my measurements and then delete the area to leave a black hole which can be thresholded out when I apply the next doughnut region. To do this I would need to convert my measurement region to an AOI, how can you do that in Premier.

Regards

David  

davek604

Hello Juri

That works

Thanks 

David