Doubts about the Particle Analyzer

[Sidnei Paciornik]

Dear colleagues,

I would like to start with a very basic doubt:
Given that ImageJ allows us to select particles to be formed by white
pixels on a black background, why is it that the "Show Masks" option in
"Analyze Particles" shows the particles black against a white background?

It seems very confusing to have a set of white particles, filter them by
size/shape, create a mask to see the result, and have black particles as a
result.

Am I missing something obvious?

Now for a second doubt:
When particles have holes "Show Masks" and "Overlay Masks" have different
behavior. "Overlay Masks" fills the holes with its default blue color,
regardless of the "Include Holes" option being clicked or not. "Show Masks"
correctly responds to the "Include Holes" option.

It there any reason for this difference?

Thank you for your patience.

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia de Materiais
PUC-Rio <http://www.puc-rio.br/>
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: [phone]

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[Cammer, Michael]

I find the best thing to do when having doubts such as these is to test the software with datasets of known properties.  These are created by programming, imaging, Photoshop, or a combination.  Test datasets should have extreme examples as well as standard examples.  These would answer the questions you have.   They are also good for probing the analysis software to understand what the measurements mean.


_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Sidnei Paciornik [[hidden email]]
Sent: Saturday, June 15, 2013 11:33 PM
To: [hidden email]
Subject: Doubts about the Particle Analyzer

Dear colleagues,

I would like to start with a very basic doubt:
Given that ImageJ allows us to select particles to be formed by white
pixels on a black background, why is it that the "Show Masks" option in
"Analyze Particles" shows the particles black against a white background?

It seems very confusing to have a set of white particles, filter them by
size/shape, create a mask to see the result, and have black particles as a
result.

Am I missing something obvious?

Now for a second doubt:
When particles have holes "Show Masks" and "Overlay Masks" have different
behavior. "Overlay Masks" fills the holes with its default blue color,
regardless of the "Include Holes" option being clicked or not. "Show Masks"
correctly responds to the "Include Holes" option.

It there any reason for this difference?

Thank you for your patience.

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia de Materiais
PUC-Rio <http://www.puc-rio.br/>
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: [phone]

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[Gabriel Landini]

On Sunday 16 Jun 2013 04:33:24 you wrote:
> I would like to start with a very basic doubt:
> Given that ImageJ allows us to select particles to be formed by white
> pixels on a black background, why is it that the "Show Masks" option in
> "Analyze Particles" shows the particles black against a white background?
>
> It seems very confusing to have a set of white particles, filter them by
> size/shape, create a mask to see the result, and have black particles as a
> result.

Most likely historical reasons. It is an inverted LUT, so black is 255.
Yes it is extremely confusing, but changing its behaviour might break lots of
old scripts. Apply the normal greyscale LUT to it.
Or instead use Convert to Mask that respects the settings in the
Process>Binary>Options.

Cheers
Gabriel

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