Issue with ROI importation using the Bio-format plugin

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Issue with ROI importation using the Bio-format plugin

Philippe CARL
Dear all,

I apologize in the case this is not the good place for reporting a
bio-format issue and please indicate me where I should then alternatively
post such a bio-format bug report.

So if I open the following file (178MB - sorry I don’t have a smaller
version of it!):

http://punias.free.fr/ImageJ/Bio/FRAP_15.06.2018_10_50_31.tif

with the bio-format plugin by activating the "Display ROIs" option, I get
the following result for the ROI:

http://punias.free.fr/ImageJ/Bio/BioFormat.jpg

As if I alternatively open the same picture using the vanilla ImageJ loader
and launch the following macro:

http://punias.free.fr/ImageJ/Bio/read_iMIC_meta_data.ijm

I get this result:

http://punias.free.fr/ImageJ/Bio/Macro.jpg

From this comparison it comes out that there is a float to int conversion
somewhere within the code when getting the coordinates of the points
building up the ROI.

My best regards,

Philippe

 

Philippe CARL

Laboratoire de Bioimagerie et Pathologies

UMR 7021 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin

67401 ILLKIRCH

Tel : +33(0)3 68 85 41 84


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Re: Issue with ROI importation using the Bio-format plugin

David Gault (Staff)
Hi Philippe,

using the sample file you listed I have been able to reproduce the problem. As you have suggested this appears to have been caused due to the Bio-Formats plugin casting the point values to int.
I have created a Trello card to track the issue on the Bio-Formats inbox - https://trello.com/c/4hqyLC8s/257-plugins-roi-points-cast-to-int

With Thanks,
David Gault

On 28 Jun 2018, at 11:08, Philippe CARL <[hidden email]<mailto:[hidden email]>> wrote:

Dear all,

I apologize in the case this is not the good place for reporting a
bio-format issue and please indicate me where I should then alternatively
post such a bio-format bug report.

So if I open the following file (178MB - sorry I don't have a smaller
version of it!):

http://punias.free.fr/ImageJ/Bio/FRAP_15.06.2018_10_50_31.tif

with the bio-format plugin by activating the "Display ROIs" option, I get
the following result for the ROI:

http://punias.free.fr/ImageJ/Bio/BioFormat.jpg

As if I alternatively open the same picture using the vanilla ImageJ loader
and launch the following macro:

http://punias.free.fr/ImageJ/Bio/read_iMIC_meta_data.ijm

I get this result:

http://punias.free.fr/ImageJ/Bio/Macro.jpg

From this comparison it comes out that there is a float to int conversion
somewhere within the code when getting the coordinates of the points
building up the ROI.

My best regards,

Philippe



Philippe CARL

Laboratoire de Bioimagerie et Pathologies

UMR 7021 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin

67401 ILLKIRCH

Tel : +33(0)3 68 85 41 84


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


The University of Dundee is a registered Scottish Charity, No: SC015096

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