8-bit image strange thresholding.

[ArturMezh]

Hello.

I am using Fiji, latest edition on Mac OS X.

When I did the thresholding of 8-bit grey image before (and also now on other machines) by default the threshold, for example, like (0;100, B§W) detect everything which is darker then "100", and makes invisible (white) everything which is above that threshold.
After working with other Java-based program (GemIdent), the threshold in Fiji works strange. If using the settings: (Default, 0;100, B§W), then everything which is darker then "100" is turned to white, and above 100 to black.
This is nor Fiji bag, because it works fine on other machines. And I reinstalled Fiji and Java 6 with no result.

Does anyone knows how to fix it?

Artur

[Jacqueline Ross]

Hi Artur,

You could select Dark background.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of ArturMezh
Sent: Tuesday, 6 May 2014 5:29 a.m.
To: [hidden email]
Subject: 8-bit image strange thresholding.

Hello.

I am using Fiji, latest edition on Mac OS X.

When I did the thresholding of 8-bit grey image before (and also now on other machines) by default the threshold, for example, like (0;100, B§W) detect everything which is darker then "100", and makes invisible (white) everything which is above that threshold.
After working with other Java-based program (GemIdent), the threshold in Fiji works strange. If using the settings: (Default, 0;100, B§W), then everything which is darker then "100" is turned to white, and above 100 to black.
This is nor Fiji bag, because it works fine on other machines. And I reinstalled Fiji and Java 6 with no result.

Does anyone knows how to fix it?

Artur







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[ArturMezh]

Hi Jacqui and thank you for response.

Well, I can select dark background but it still does not work like it should. I mean, I can solve the problem, but I can not fix it! I want to understand what is wrong.

I have attached example images to illustrate my question.

Artur

[Michael Schmid]

Hi Artur,

sorry, your screenshot is too small for me to see what happens (downscaled a lot, the resolution is too low).

A few things to try:
- Does it work correctly in Threshold mode 'Red'?
- Did you make sure that Process>Binary>Options has the same setting for 'Black background'?
- Is there a problem with the display of other colors as well?

Michael
________________________________________________________________
On May 13, 2014, at 11:02, ArturMezh wrote:

> Hi Jacqui and thank you for response.
>
> Well, I can select dark background but it still does not work like it
> should. I mean, I can solve the problem, but I can not fix it! I want to
> understand what is wrong.
>
> I have attached example images to illustrate my question.
>
> Artur
> <http://imagej.1557.x6.nabble.com/file/n5007711/question.png>

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