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.

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