Convert to Mask command does slightly different things on FIJI and ImageJ ¿bug?

[Soriano.Joaquim]

Hi everyone!

The command "Convert to Mask"  {Convert to Mask (in Process > Binary) [ij.plugin.Thresholder("mask")]

} does slightly different things on FIJI and ImageJ.

Open an image and run:

setAutoThreshold("RenyiEntropy dark");

run("Convert to Mask");

You'll see that you don't get the same result on image j and FIJI.

The Binary image is the same, but the look up table is inverted.

I can invert the look up table, but still is causing me problems.

Can anyone help me?

Thank you very much in advance.

 

 

Joaquim Soriano Felipe.

Confocal Microscopy Unit

Spanish National Cancer Research Centre (CNIO)

Melchor Fernández Almagro,3, E-28029 Madrid, Spain

Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email] <mailto:[hidden email]>

 



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[Rocco D'Antuono]

Hi Joaquim I also noted that if you try to do "Process\Binary\Erode" or "Process\Binary\Dilate" the actions were inverted until I checked also in Fiji the box "Process\Binary\Options\Black Background". Try to do it and retry to see if you have again the same kind "problems" (that you didn't specify: "...I can invert the look up table, but still is causing me problems." ).
Hasta luego,
Rocco

[Thomas Boudier]

Hi,

Check the options in Edit/options/aapearance, the "use inverted lut" may
be selected.

Thomas


Le 25/06/2012 12:50, Soriano.Joaquim a écrit :

> Hi everyone!
>
> The command "Convert to Mask"  {Convert to Mask (in Process>  Binary) [ij.plugin.Thresholder("mask")]
>
> } does slightly different things on FIJI and ImageJ.
>
> Open an image and run:
>
> setAutoThreshold("RenyiEntropy dark");
>
> run("Convert to Mask");
>
> You'll see that you don't get the same result on image j and FIJI.
>
> The Binary image is the same, but the look up table is inverted.
>
> I can invert the look up table, but still is causing me problems.
>
> Can anyone help me?
>
> Thank you very much in advance.
>
>
>
>
>
> Joaquim Soriano Felipe.
>
> Confocal Microscopy Unit
>
> Spanish National Cancer Research Centre (CNIO)
>
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain
>
> Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email]<mailto:[hidden email]>
>
>
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, y en su caso los ficheros adjuntos, pueden contener informaciÿn protegida para el uso exclusivo de su destinatario. Se prohÿbe la distribuciÿn, reproducciÿn o cualquier otro tipo de transmisiÿn por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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[Soriano.Joaquim]

Yesssssssssss!
That did really worked out!!!
Thank you very much!!!
Un saludo!!!

Joaquim Soriano Felipe.
Confocal Microscopy Unit
Spanish National Cancer Research Centre (CNIO)
Melchor Fernández Almagro,3, E-28029 Madrid, Spain
Phone  + 34 917 328 000, exts.: 3161, 3162. [hidden email]


-----Mensaje original-----
De: ImageJ Interest Group [mailto:[hidden email]] En nombre de Rocco D'Antuono
Enviado el: lunes, 25 de junio de 2012 13:31
Para: [hidden email]
Asunto: Re: Convert to Mask command does slightly different things on FIJI and ImageJ ¿bug?

Hi Joaquim I also noted that if you try to do "Process\Binary\Erode" or "Process\Binary\Dilate" the actions were inverted until I checked also in Fiji the box "Process\Binary\Options\Black Background". Try to do it and retry to see if you have again the same kind "problems" (that you didn't
specify: "...I can invert the look up table, but still is causing me problems." ).
Hasta luego,
Rocco

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