Re: Segmentation issue

[Peter Haub]

Dear Alan,

attached you find a simple macro which creates a background images,
performs a 'flat field' correction, applies a threshold and count the
particles with the Particle Analyzer.

The results I got with this macro are (size=300-Infinity):

Slice                     Count         Total Area        Average Size  
    %Area       IntDen
control                    180        498631.000       2770.172        
15.607    706393.917
10 micromolar        147        259839.000       1767.612 8.133      
450741.122
50 micromolar        121        82643.000          683.000     2.587    
     174165

Hope this will help you to find a way into your work.

Regards,
Peter

On 02.10.2013 23:42, Alan Thames wrote:

>   Hi Peter,
>                 Sorry that i had to write a direct mail to you as i cannot
> attach many images to imageJ mailing list. As you have suggested, i tried
> to use filter as Process > filter>minimum - Radius 2.0 pixels for each 8
> bit image - control and 10 micromolar concentration . Then i followed my
> previous step - choosing IMAGE>adjust > threshold. I do not change anything
> under threshold setting. After that i go to Analyze> analyze particles >
> size 0 - infinity, circularity 0.01-1.0/ 0.5 - 1.0 , then chose -exclude on
> edges. the summary of the result
>
> circularity 0.01-1.0
>                               count   total area           average size
>   percent area
> control                    681 448209.000000 658.162996 14.028978
> 10 uM                    1089 293413.000000 269.433425 9.183850
>
> circularity 0.5 - 1.0
>
> control                     614 230438.000000 375.306189 7.212728
>     10 uM                   978 174331.000000 178.252556 5.456574
>
>
> I have attached three pictures , control, 10 uM and 50 uM drug
> concentrations.
>
> I would also like to learn how to do flat field correction.
> Will you please take a look at what i have done above? i have been having a
> hard time figuring out how to do this as i want to see decrease in both
>   count and size with increasing drug concentrations. This is part of my
> masters thesis project. I cannot one any one near me.
>
> Sincerely,
> Alan
>

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