Which journal to publish an ImageJ based application

[Eddie Iannuccelli]

Hello,

I am developping a standalone java application based on Thomas Boudier
SmartFish3D (new user interface, database storage for results, ...). I
would like to publish an application note like manuscript (2 technical
pages like in BioInformatics) somewhere but I don't know the kind of
journal to submit. I had a look on Cytometry A but it seems that
articles usually presents a study with a software, not only a sofware.

Any suggestions ?

--
******************************************
Eddie Iannuccelli
Laboratoire de génétique cellulaire
INRA - Castanet Tolosan
Tel: [phone] / Fax: [phone]

[John Oreopoulos]

I am aware of three papers published in different journals about in-
house developed ImageJ applications:

http://www3.interscience.wiley.com/journal/122508089/abstract

http://www3.interscience.wiley.com/journal/112099888/abstract?
CRETRY=1&SRETRY=0

http://www.biomedcentral.com/1471-2105/9/346

Maybe you could try one of those journals. Perhaps Microscopy  
Research and Technique or Journal of Microscopy would be appropriate.  
Most reviewers will want to see some kind of application though or  
proof of concept about the utility of the application. There is also  
magazines like Microscopy Today, Biophotonics, and BioTechniques that  
might allow a short communication about an application.

John Oreopoulos


On 5-Aug-09, at 4:00 AM, Eddie Iannuccelli wrote:

> Hello,
>
> I am developping a standalone java application based on Thomas  
> Boudier SmartFish3D (new user interface, database storage for  
> results, ...). I would like to publish an application note like  
> manuscript (2 technical pages like in BioInformatics) somewhere but  
> I don't know the kind of journal to submit. I had a look on  
> Cytometry A but it seems that articles usually presents a study  
> with a software, not only a sofware.
>
> Any suggestions ?
>
> --
> ******************************************
> Eddie Iannuccelli
> Laboratoire de génétique cellulaire
> INRA - Castanet Tolosan
> Tel: [phone] / Fax: [phone]

[Aryeh Weiss]

I cannot seem to print anything from getMetadata.

The following produces a blank output followed by the
===== string.

selectWindow("testimage")
mdat=getMetadata("Info");
print(mdat);
print("====");

On the other hand:

selectWindow("testimage")
mdat=getMetadata("Label");
print(mdat);
print("====");

produces the expected output. I saw some discussion of getMetadata in
the archives, but I did not find the solution. I assume that I do not
understand how to use this function.

Also, I think that the getMetadata("Info") only returns the text in the
image info window (is that correct?). If so, is there a way to read
arbitrary TIFF labels in a macro (other than calling bio-formats,
getting the matadata in a text window, and then reading the text from
that window?

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Gabriel Landini]

On Tuesday 08 September 2009 20:50:40 Aryeh Weiss wrote:
> I cannot seem to print anything from getMetadata.

I can, but maybe this is not what you want?:
setMetadata("test 123");
print(getMetadata());
print("====");

Sorry to ask the obvious, does the image you are using contain any metadata?
What do you see when you run the gui Image>Show Info... ?

I can see the "test 123" set with the above.

Cheers

Gabriel

[Aryeh Weiss]

Thank you for your reply. The image has metadata, but the metadata were
not created originally by ImageJ. I received the following from Wayne
that explains the issue.

> The getMetadata() function can only retrieve metadata saved by ImageJ
> in the TIFF header. It returns an empty string if no ImageJ metadata
> is found. You have to use the Bio-formats plugin to retrieve metadata
> saved in TIFF headers by other applications.

A plugin or macro-command that reads any TIFF tag would beuseful, so we
will try to write something based on TiffDecoder.

--aryeh

Gabriel Landini wrote:

> On Tuesday 08 September 2009 20:50:40 Aryeh Weiss wrote:
>> I cannot seem to print anything from getMetadata.
>
> I can, but maybe this is not what you want?: setMetadata("test 123");
>  print(getMetadata()); print("====");
>
> Sorry to ask the obvious, does the image you are using contain any
> metadata? What do you see when you run the gui Image>Show Info... ?
>
> I can see the "test 123" set with the above.
>
> Cheers
>
> Gabriel
>

--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

[Joachim Wesner]

Hi Aryeh,

I once wrote a Java class that can read general TIFF tags and even use it
in one of my plugins, but it´s in the moment not directly callable from a
macro.

Getting to work this would require some tweeking, I´m in the moment a bit
busy with other things.......

If you don´t get the Bioformat reader to work, please contact me again by
PM!

Cheers!

Joachim Wesner



                                                                           
             Aryeh Weiss                                                  
             <[hidden email]                                            
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             Gesendet von:              [hidden email]                
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             <[hidden email].                                       Thema
             GOV>                       Re: getMetada problem              
                                                                           
                                                                           
             09.09.2009 05:39                                              
                                                                           
                                                                           
              Bitte antworten                                              
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             [hidden email].                                            
                    il                                                    
                                                                           
                                                                           




Thank you for your reply. The image has metadata, but the metadata were
not created originally by ImageJ. I received the following from Wayne
that explains the issue.

> The getMetadata() function can only retrieve metadata saved by ImageJ
> in the TIFF header. It returns an empty string if no ImageJ metadata
> is found. You have to use the Bio-formats plugin to retrieve metadata
> saved in TIFF headers by other applications.

A plugin or macro-command that reads any TIFF tag would beuseful, so we
will try to write something based on TiffDecoder.

--aryeh

Gabriel Landini wrote:

> On Tuesday 08 September 2009 20:50:40 Aryeh Weiss wrote:
>> I cannot seem to print anything from getMetadata.
>
> I can, but maybe this is not what you want?: setMetadata("test 123");
>  print(getMetadata()); print("====");
>
> Sorry to ask the obvious, does the image you are using contain any
> metadata? What do you see when you run the gui Image>Show Info... ?
>
> I can see the "test 123" set with the above.
>
> Cheers
>
> Gabriel
>

--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]




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[Wayne Rasband]

 > Thank you for your reply. The image has metadata, but the
 > metadata werenot created originally by ImageJ. I received
 > the following from Wayne that explains the issue.

 >> The getMetadata() function can only retrieve metadata saved by
 >> ImageJ in the TIFF header. It returns an empty string if no ImageJ
 >> metadata is found. You have to use the Bio-formats plugin to
 >> retrieve ImageJ saved in TIFF headers by other applications.

 > A plugin or macro-command that reads any TIFF tag would beautiful,
 > so we will try to write something based on TiffDecoder.

In the ImageJ 1.43g daily build, the getMetadata() macro function and
the Image>Show Info command will retrieve the DateTime and Software
TIFF tags.

-wayne

[Aryeh Weiss]

Wayne Rasband wrote:

>  > Thank you for your reply. The image has metadata, but the
>  > metadata werenot created originally by ImageJ. I received
>  > the following from Wayne that explains the issue.
>
>  >> The getMetadata() function can only retrieve metadata saved by
>  >> ImageJ in the TIFF header. It returns an empty string if no ImageJ
>  >> metadata is found. You have to use the Bio-formats plugin to
>  >> retrieve ImageJ saved in TIFF headers by other applications.
>
>  > A plugin or macro-command that reads any TIFF tag would beautiful,
>  > so we will try to write something based on TiffDecoder.
>
> In the ImageJ 1.43g daily build, the getMetadata() macro function and
> the Image>Show Info command will retrieve the DateTime and Software TIFF
> tags.
>
> -wayne
>

Thank you Wayne -- that is great.
Thanks also to Joachim Wesner who sent me a plugin that reads the
various TIFF tags, and provides a good base for a plugin that that reads
  what we want.

For the convenience of anyone interested in TIFF tags, the following
site is useful

http://www.awaresystems.be/imaging/tiff/tifftags.html

--aryeh
--
Aryeh Weiss
School of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]