Re: Find Maxima - Segmented Particles

[Adam Waite]

Hi Michael,

I'm afraid I've been experiencing the same problem as Dani.

I have been processing my grayscale images to make the background as uniform
as possible. Then I would run "Find Maxima" with segmented particles as the
output.  Finally, by running "Analyze Particles", I could make accurate
selections around my regions of interest (cells, to be specific).  This
would allow me to obtain size, shape, and intensity information about the
selection.

With the current implementation, I get what looks like a voroni diagram,
which obviously gets rid of anything approaching accurate size information.

I would like to restore the old behavior and tried to follow your advice
(quoted below), but when I go to "Find Maxima", I do not see a checkbox for
"Above Lower Threshold".  Is this check box located somewhere else?
Additionally, I do not see a place where I can enter the lower or upper
threshold.  

I am currently running the most recent version of ImageJ (1.43o).

Thanks in advance for your time and help,
Adam

 
On Sun, 15 Nov 2009 17:52:21 +0100, Michael Schmid <[hidden email]>
wrote:


>You can restore the old behavior by setting the lower threshold to the
>background value plus one (don't care about the upper threshold, it can
>be, e.g. the maximum pixel value or the same as the lower threshold) and
>checking "Above Lower Threshold". In case your particles are minima of the
>pixel value, not maxima, you have to invert the image before "Find
>Maxima".

[Michael Schmid]

Hi Adam,

the checkbox 'above lower threshold' appears only if your image has a
threshold.
Use Image>Adjust>Threshold to set the threshold; in your case the easiest
would probably be the 'set' button (if you background is zero, set the
lower threshold to 1). Don't care about the upper threshold, it is ignored
by 'Find Maxima'.
If the tolerance of 'Find maxima' is always the same, you can have a macro
for combining the two steps. Use Plugins>Macros>Record to create one.

Michael
_______________________________________________________________________

On Fri, January 29, 2010 06:07, Adam Waite wrote:

> Hi Michael,
>
> I'm afraid I've been experiencing the same problem as Dani.
>
> I have been processing my grayscale images to make the background as
> uniform
> as possible. Then I would run "Find Maxima" with segmented particles as
> the
> output.  Finally, by running "Analyze Particles", I could make accurate
> selections around my regions of interest (cells, to be specific).  This
> would allow me to obtain size, shape, and intensity information about the
> selection.
>
> With the current implementation, I get what looks like a voroni diagram,
> which obviously gets rid of anything approaching accurate size
> information.
>
> I would like to restore the old behavior and tried to follow your advice
> (quoted below), but when I go to "Find Maxima", I do not see a checkbox
> for
> "Above Lower Threshold".  Is this check box located somewhere else?
> Additionally, I do not see a place where I can enter the lower or upper
> threshold.
>
> I am currently running the most recent version of ImageJ (1.43o).
>
> Thanks in advance for your time and help,
> Adam
>
>
> On Sun, 15 Nov 2009 17:52:21 +0100, Michael Schmid wrote:
>
>
>>You can restore the old behavior by setting the lower threshold to the
>>background value plus one (don't care about the upper threshold, it can
>>be, e.g. the maximum pixel value or the same as the lower threshold) and
>>checking "Above Lower Threshold". In case your particles are minima of
>> the
>>pixel value, not maxima, you have to invert the image before "Find
>>Maxima".
>