A bug from the new "Auto_Threshold"?

[Rogerio Hein-2]

Dear friends,

I really enjoy the new Auto_Threshold plugin from Gabriel Landini, as a drop
down menu for 16 different thresholding methods since 1.42p, a great tool!
But I have noticed that its use combined to watershed tool
(Process>Binary>Watershed) results in empty measurements tables in most
cases. If the watershed tool is not applied, some of displayed objects from
binary images are not considered for particle analysis. It occurs, as I
tested, in versions 1.41o (as a plugin), 1.42o (as a plugin), 1,42p and even
for the daily build 1.42q, running under MS Windows XP, XP-64 and Vista.
Can somebody check it, please?

Thanks in advance,

Rogerio Hein

[Gabriel Landini]

On Sunday 31 May 2009, Rogerio Hein wrote:

> Dear friends,
>
> I really enjoy the new Auto_Threshold plugin from Gabriel Landini, as a
> drop down menu for 16 different thresholding methods since 1.42p, a great
> tool! But I have noticed that its use combined to watershed tool
> (Process>Binary>Watershed) results in empty measurements tables in most
> cases. If the watershed tool is not applied, some of displayed objects from
> binary images are not considered for particle analysis. It occurs, as I
> tested, in versions 1.41o (as a plugin), 1.42o (as a plugin), 1,42p and
> even for the daily build 1.42q, running under MS Windows XP, XP-64 and
> Vista. Can somebody check it, please?
>
> Thanks in advance,
>
> Rogerio Hein

This seems to work OK in my setup

run("AuPbSn 40 (56K)");
setAutoThreshold("Huang");
run("Convert to Mask");
run("Watershed");

Please post a macro that shows the problem (and upload an image somewhere so
we can test it).

Cheeers

G.

[Rogerio Hein-2]

OK, it works! But it is necessary to manually include the line:

run("Convert to Mask");

I was using, for instance:

run("Auto Threshold", "method=Moments stack");
run("Watershed", "stack");
run("Set Measurements...", "area perimeter bounding fit shape feret's
redirect=None decimal=2");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Outlines display exclude clear include summarize record stack");

As displayed by macro recorder tool. Now, with:

run("Auto Threshold", "method=Moments stack");
run("Convert to Mask");
run("Watershed", "stack");
run("Set Measurements...", "area perimeter bounding fit shape feret's
redirect=None decimal=2");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
show=Outlines display exclude clear include summarize record stack");

It works fine for stacks (8-bit, 2080x1540, large "n" images). Many thanks,
Gabriel!

Best regards,

Rogerio


----- Original Message -----
From: "Gabriel Landini" <[hidden email]>
To: <[hidden email]>
Sent: Sunday, May 31, 2009 11:45 AM
Subject: Re: A bug from the new "Auto_Threshold"?

> On Sunday 31 May 2009, Rogerio Hein wrote:
>> Dear friends,
>>
>> I really enjoy the new Auto_Threshold plugin from Gabriel Landini, as a
>> drop down menu for 16 different thresholding methods since 1.42p, a great
>> tool! But I have noticed that its use combined to watershed tool
>> (Process>Binary>Watershed) results in empty measurements tables in most
>> cases. If the watershed tool is not applied, some of displayed objects
>> from
>> binary images are not considered for particle analysis. It occurs, as I
>> tested, in versions 1.41o (as a plugin), 1.42o (as a plugin), 1,42p and
>> even for the daily build 1.42q, running under MS Windows XP, XP-64 and
>> Vista. Can somebody check it, please?
>>
>> Thanks in advance,
>>
>> Rogerio Hein
>
> This seems to work OK in my setup
>
> run("AuPbSn 40 (56K)");
> setAutoThreshold("Huang");
> run("Convert to Mask");
> run("Watershed");
>
> Please post a macro that shows the problem (and upload an image somewhere
> so
> we can test it).
>
> Cheeers
>
> G.

[Gabriel Landini]

On Sunday 31 May 2009, Rogerio Hein wrote:
> OK, it works! But it is necessary to manually include the line:
> run("Convert to Mask");

No, sorry this was my confusion. I thought that you were using the new "Adjust
Threshold" command rather than my "Auto Threshold" plugin.

So to answer your question:
After converting the image to binary with the Auto Threshold plugin and runing
the Watershed separation, you still need to set the threshold in the binary
image in red, so the particle analyser knows what is the particle phase to be
analysed.
Either:
setThreshold(255, 255);
or
setThreshold(0, 0);

Depending on whether your objects are white or black in the binary image.

I hope that this answers the question.

Cheers

Gabriel