Analyze particles bug?

[Lachlan Whitehead]

Hi All,

After running my morning update of FIJI I seem to be experiencing a bug in the Analyze Particles function which seems to provide a list of many more particles than it should.
What it appears to be doing is detecting objects correctly, but then assigning every pixel within each object as a separate object (with an area of 0 interestingly).
Needless to say this is causing all sorts of havoc in my analysis routines.

To replicate the bug you can do the following:
- Set Measurements to include "Limit to Threshold"*
- Open blobs test image (or any other image)
- Threshold and analyze particles (display results and/or add to ROI manager to see what I'm talking about).

I've tried this on three PCs running win7, and have had a colleague check it out too.

Any insights would be greatly appreciated.

Thanks,
-Lachie

* Unsetting "limit to threshold" was found to be a workaround, but will be particularly annoying if I have to alter all my previous macros to unset this setting only to re-set it when performing other measurement steps



--


Lachlan Whitehead PhD
BioImage Analyst
Centre for Dynamic Imaging
The Walter & Eliza Hall Institute
1G Royal Parade, Parkville
Victoria 3052, Australia



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[Rasband, Wayne (NIH/NIMH) [E]]

> On Apr 27, 2015, at 12:05 AM, Lachlan Whitehead <[hidden email]> wrote:
>
> Hi All,
>
> After running my morning update of FIJI I seem to be experiencing a bug in the Analyze Particles function which seems to provide a list of many more particles than it should.
> What it appears to be doing is detecting objects correctly, but then assigning every pixel within each object as a separate object (with an area of 0 interestingly).
> Needless to say this is causing all sorts of havoc in my analysis routines.
>
> To replicate the bug you can do the following:
> - Set Measurements to include "Limit to Threshold"*
> - Open blobs test image (or any other image)
> - Threshold and analyze particles (display results and/or add to ROI manager to see what I'm talking about).
>
> I've tried this on three PCs running win7, and have had a colleague check it out too.
>
> Any insights would be greatly appreciated.

... [show rest of quote]

This regression is in ImageJ 1.49r. You can work around it by downgrading to ImageJ 1.49q, which you can do by using the the Help>Update ImageJ command and selecting “previous” from the drop down menu.

-wayne




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[Rasband, Wayne (NIH/NIMH) [E]]

On Apr 27, 2015, at 12:05 AM, Lachlan Whitehead <[hidden email]> wrote:

>
> Hi All,
>
> After running my morning update of FIJI I seem to be experiencing a bug in the Analyze Particles function which seems to provide a list of many more particles than it should.
> What it appears to be doing is detecting objects correctly, but then assigning every pixel within each object as a separate object (with an area of 0 interestingly).
> Needless to say this is causing all sorts of havoc in my analysis routines.
>
> To replicate the bug you can do the following:
> - Set Measurements to include "Limit to Threshold"*
> - Open blobs test image (or any other image)
> - Threshold and analyze particles (display results and/or add to ROI manager to see what I'm talking about).

This ImageJ 1.49r regression is fixed in the latest daily build (1.49s9). You can upgrade by using the Help>Update ImageJ command and selecting “daily build” from the drop down menu.

-wayne


>
> I've tried this on three PCs running win7, and have had a colleague check it out too.
>
> Any insights would be greatly appreciated.
>
> Thanks,
> -Lachie
>
> * Unsetting "limit to threshold" was found to be a workaround, but will be particularly annoying if I have to alter all my previous macros to unset this setting only to re-set it when performing other measurement steps



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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Lachlan Whitehead]

Hi Wayne,

Many thanks!



----- Original Message -----
From: "Wayne Rasband (NIH/NIMH) [E]" <[hidden email]>
To: [hidden email]
Sent: Tuesday, 28 April, 2015 5:56:27 AM
Subject: Re: Analyze particles bug?

On Apr 27, 2015, at 12:05 AM, Lachlan Whitehead <[hidden email]> wrote:

>
> Hi All,
>
> After running my morning update of FIJI I seem to be experiencing a bug in the Analyze Particles function which seems to provide a list of many more particles than it should.
> What it appears to be doing is detecting objects correctly, but then assigning every pixel within each object as a separate object (with an area of 0 interestingly).
> Needless to say this is causing all sorts of havoc in my analysis routines.
>
> To replicate the bug you can do the following:
> - Set Measurements to include "Limit to Threshold"*
> - Open blobs test image (or any other image)
> - Threshold and analyze particles (display results and/or add to ROI manager to see what I'm talking about).

This ImageJ 1.49r regression is fixed in the latest daily build (1.49s9). You can upgrade by using the Help>Update ImageJ command and selecting “daily build” from the drop down menu.

-wayne


>
> I've tried this on three PCs running win7, and have had a colleague check it out too.
>
> Any insights would be greatly appreciated.
>
> Thanks,
> -Lachie
>
> * Unsetting "limit to threshold" was found to be a workaround, but will be particularly annoying if I have to alter all my previous macros to unset this setting only to re-set it when performing other measurement steps



--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

______________________________________________________________________
The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.
______________________________________________________________________

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html