Regarding Digital Image Processing In Java

[Kamal Raj]

Hi Guys

I am Kamal Raj Singh working on Digital Image Processing (planning to do
PhD). I have also worked on Java platform in Industry.
I am familiar with Java and Digital Image Processing. Can some one please
tell me how ImageJ is going to help me
in my research. I am very very much passionate to work on Java but academic
requirements bounded me to Work on MAT LAB.

Eagerly waiting for your reply. I need all information about ImageJ and
also can it will be helpful in my Research.
--
Thanks
Regards
Kamal Raj Singh
M.E. (BITS Pilani) Rajasthan (India)
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
India South Asia
Mob: [phone]

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

[pang]

Dear Kamal,

Just my quick thoughts on this, definitely it is biased and incomplete.

ImageJ is free, and it is very handy for you to do some simple image analysis tasks such as  thresholding, particle analysis, quantification of an images. You can do more complicated image analysis, but requires you a lot of knowledge in macro, Java, and algorithm itself.

Matlab  will cost your some  money  for license. If you want to develop your own segmentation method, Matlab may already have some built-in functions, so you can use them directly.

Simple comparison for doing thesholding:  matlab use graythresh(), which is based on OTSU method. ImageJ provides about 16 different methods to do it.

If you want to find the shapes or structure of an object. Matlab has Hough transformation function to help you to do it, but I did not find any function you can use from basic imageJ.

If you are advanced users for ImageJ and Matlab, the difference is probably at which one has better built-in functions for you to use (Java or Matlab).

In general, you will use matlab if you are a computer scientist, and you will  more likely to use ImageJ if you are non-computer scientist, who does not need to understand the details of how these methods are implemented, but just want them to work for their applications.

If anything described here is not accurate, please feel free to point out.

Zhengyu



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kamal Raj
Sent: Monday, February 24, 2014 2:33 PM
To: [hidden email]
Subject: Regarding Digital Image Processing In Java

Hi Guys

I am Kamal Raj Singh working on Digital Image Processing (planning to do PhD). I have also worked on Java platform in Industry.
I am familiar with Java and Digital Image Processing. Can some one please tell me how ImageJ is going to help me in my research. I am very very much passionate to work on Java but academic requirements bounded me to Work on MAT LAB.

Eagerly waiting for your reply. I need all information about ImageJ and also can it will be helpful in my Research.
--
Thanks
Regards
Kamal Raj Singh
M.E. (BITS Pilani) Rajasthan (India)
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
India South Asia
Mob: [phone]

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

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

[Safaa Al-Haj Saleh]

Hello Kamal,

ImageJ has many libraries and plugins that you can use to deal with image processing and segmentation tasks. You can use the documentation to have a look on available classes and methods. You can also use "IJ.run" to run imageJ commands directly from your java code. 

I had a challenging task during the past months that required converting matlab code for medical images segmentation and classification into Java code. Actually I found ImageJ a perfect application that helped in performing this task!

All the best,
Safaa




On Monday, February 24, 2014 10:45 PM, Kamal Raj <[hidden email]> wrote:
 
Hi Guys

I am Kamal Raj Singh working on Digital Image Processing (planning to do
PhD). I have also worked on Java platform in Industry.
I am familiar with Java and Digital Image Processing. Can some one please
tell me how ImageJ is going to help me
in my research. I am very very much passionate to work on Java but academic
requirements bounded me to Work on MAT LAB.

Eagerly waiting for your reply. I need all information about ImageJ and
also can it will be helpful in my Research.
--
Thanks
Regards
Kamal Raj Singh
M.E. (BITS Pilani) Rajasthan (India)
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
India South Asia
Mob: [phone]

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

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

[Kamal Raj]

Hi Zhengyu

I want to know that if i create some functions in Java for ImageJ. Can this
work be considered for IEEE publication or not.
I am going for research (PhD) in Digital Image Processing. If i create some
functions for ImageJ (as i have knowledge in Java and also in Digital Image
Processing).
then how my work for ImageJ will be going to help me in Research
publications.

I hope you understand.
thanks
Kamal Raj Singh



On Tue, Feb 25, 2014 at 1:36 AM, Pang, Zhengyu (GE Global Research) <
[hidden email]> wrote:

> Dear Kamal,
>
> Just my quick thoughts on this, definitely it is biased and incomplete.
>
> ImageJ is free, and it is very handy for you to do some simple image
> analysis tasks such as  thresholding, particle analysis, quantification of
> an images. You can do more complicated image analysis, but requires you a
> lot of knowledge in macro, Java, and algorithm itself.
>
> Matlab  will cost your some  money  for license. If you want to develop
> your own segmentation method, Matlab may already have some built-in
> functions, so you can use them directly.
>
> Simple comparison for doing thesholding:  matlab use graythresh(), which
> is based on OTSU method. ImageJ provides about 16 different methods to do
> it.
>
> If you want to find the shapes or structure of an object. Matlab has Hough
> transformation function to help you to do it, but I did not find any
> function you can use from basic imageJ.
>
> If you are advanced users for ImageJ and Matlab, the difference is
> probably at which one has better built-in functions for you to use (Java or
> Matlab).
>
> In general, you will use matlab if you are a computer scientist, and you
> will  more likely to use ImageJ if you are non-computer scientist, who does
> not need to understand the details of how these methods are implemented,
> but just want them to work for their applications.
>
> If anything described here is not accurate, please feel free to point out.
>
> Zhengyu
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Kamal Raj
> Sent: Monday, February 24, 2014 2:33 PM
> To: [hidden email]
> Subject: Regarding Digital Image Processing In Java
>
> Hi Guys
>
> I am Kamal Raj Singh working on Digital Image Processing (planning to do
> PhD). I have also worked on Java platform in Industry.
> I am familiar with Java and Digital Image Processing. Can some one please
> tell me how ImageJ is going to help me in my research. I am very very much
> passionate to work on Java but academic requirements bounded me to Work on
> MAT LAB.
>
> Eagerly waiting for your reply. I need all information about ImageJ and
> also can it will be helpful in my Research.
> --
> Thanks
> Regards
> Kamal Raj Singh
> M.E. (BITS Pilani) Rajasthan (India)
> Assistant Professor
> ECE Department
> IPEC Ghaziabad (U.P.)
> India South Asia
> Mob: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Thanks
Regards
Kamal Raj Singh
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
Mob: [phone]

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

[pang]

Dear Kamal,

I think if you create some functions in Java for ImageJ. You can certainly publish it at some journals. I constantly use a function called JACOP (Just another colocalization program), and authors published a paper on Journal of Microscope (S. Bolte & F. P. Cordelieres, A guided tour into subcellular colocalization analysis in light microscopy, Journal of Microscopy, Volume 224, Issue 3: 213-232.)

I have never been a reviewer for IEEE journal, but I have tried to submit some paper to IEEE journal. In general it is hard for IEEE to accept some paper talking about application.  IEEE is generally looking for a new algorithm/method, although what is considered as "new" is really at the judgments of reviewers.

The bottom line is that the use of imageJ or matlab does not affect your publication. It is the content that matters. Some contents may not be best suitable to IEEE, but can be well suited for other journals.

Zhengyu

Zhengyu Pang, Ph.D.
Biochemistry and Bioanalytics Laboratory
Life Sciences and Molecular Diagnostics Technology Organization
Diagnostics and Biomedical Technologies
GE Global Research, K1-5B37A
One Research Circle
Niskayuna, NY 12309
T: 518-387-4015
F: 518-387-7765




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kamal Raj
Sent: Monday, February 24, 2014 3:18 PM
To: [hidden email]
Subject: Re: Regarding Digital Image Processing In Java

Hi Zhengyu

I want to know that if i create some functions in Java for ImageJ. Can this work be considered for IEEE publication or not.
I am going for research (PhD) in Digital Image Processing. If i create some functions for ImageJ (as i have knowledge in Java and also in Digital Image Processing).
then how my work for ImageJ will be going to help me in Research publications.

I hope you understand.
thanks
Kamal Raj Singh



On Tue, Feb 25, 2014 at 1:36 AM, Pang, Zhengyu (GE Global Research) < [hidden email]> wrote:

> Dear Kamal,
>
> Just my quick thoughts on this, definitely it is biased and incomplete.
>
> ImageJ is free, and it is very handy for you to do some simple image
> analysis tasks such as  thresholding, particle analysis,
> quantification of an images. You can do more complicated image
> analysis, but requires you a lot of knowledge in macro, Java, and algorithm itself.
>
> Matlab  will cost your some  money  for license. If you want to
> develop your own segmentation method, Matlab may already have some
> built-in functions, so you can use them directly.
>
> Simple comparison for doing thesholding:  matlab use graythresh(),
> which is based on OTSU method. ImageJ provides about 16 different
> methods to do it.
>
> If you want to find the shapes or structure of an object. Matlab has
> Hough transformation function to help you to do it, but I did not find
> any function you can use from basic imageJ.
>
> If you are advanced users for ImageJ and Matlab, the difference is
> probably at which one has better built-in functions for you to use
> (Java or Matlab).
>
> In general, you will use matlab if you are a computer scientist, and
> you will  more likely to use ImageJ if you are non-computer scientist,
> who does not need to understand the details of how these methods are
> implemented, but just want them to work for their applications.
>
> If anything described here is not accurate, please feel free to point out.
>
> Zhengyu
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Kamal Raj
> Sent: Monday, February 24, 2014 2:33 PM
> To: [hidden email]
> Subject: Regarding Digital Image Processing In Java
>
> Hi Guys
>
> I am Kamal Raj Singh working on Digital Image Processing (planning to
> do PhD). I have also worked on Java platform in Industry.
> I am familiar with Java and Digital Image Processing. Can some one
> please tell me how ImageJ is going to help me in my research. I am
> very very much passionate to work on Java but academic requirements
> bounded me to Work on MAT LAB.
>
> Eagerly waiting for your reply. I need all information about ImageJ
> and also can it will be helpful in my Research.
> --
> Thanks
> Regards
> Kamal Raj Singh
> M.E. (BITS Pilani) Rajasthan (India)
> Assistant Professor
> ECE Department
> IPEC Ghaziabad (U.P.)
> India South Asia
> Mob: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Thanks
Regards
Kamal Raj Singh
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
Mob: [phone]

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

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

[Kamal Raj]

Thank you very much Zhengyu

I will be in touch with you.

Thanks
Kamal.


On Tue, Feb 25, 2014 at 2:16 AM, Pang, Zhengyu (GE Global Research) <
[hidden email]> wrote:

> Dear Kamal,
>
> I think if you create some functions in Java for ImageJ. You can certainly
> publish it at some journals. I constantly use a function called JACOP (Just
> another colocalization program), and authors published a paper on Journal
> of Microscope (S. Bolte & F. P. Cordelieres, A guided tour into subcellular
> colocalization analysis in light microscopy, Journal of Microscopy, Volume
> 224, Issue 3: 213-232.)
>
> I have never been a reviewer for IEEE journal, but I have tried to submit
> some paper to IEEE journal. In general it is hard for IEEE to accept some
> paper talking about application.  IEEE is generally looking for a new
> algorithm/method, although what is considered as "new" is really at the
> judgments of reviewers.
>
> The bottom line is that the use of imageJ or matlab does not affect your
> publication. It is the content that matters. Some contents may not be best
> suitable to IEEE, but can be well suited for other journals.
>
> Zhengyu
>
> Zhengyu Pang, Ph.D.
> Biochemistry and Bioanalytics Laboratory
> Life Sciences and Molecular Diagnostics Technology Organization
> Diagnostics and Biomedical Technologies
> GE Global Research, K1-5B37A
> One Research Circle
> Niskayuna, NY 12309
> T: 518-387-4015
> F: 518-387-7765
>
>
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Kamal Raj
> Sent: Monday, February 24, 2014 3:18 PM
> To: [hidden email]
> Subject: Re: Regarding Digital Image Processing In Java
>
> Hi Zhengyu
>
> I want to know that if i create some functions in Java for ImageJ. Can
> this work be considered for IEEE publication or not.
> I am going for research (PhD) in Digital Image Processing. If i create
> some functions for ImageJ (as i have knowledge in Java and also in Digital
> Image Processing).
> then how my work for ImageJ will be going to help me in Research
> publications.
>
> I hope you understand.
> thanks
> Kamal Raj Singh
>
>
>
> On Tue, Feb 25, 2014 at 1:36 AM, Pang, Zhengyu (GE Global Research) <
> [hidden email]> wrote:
>
> > Dear Kamal,
> >
> > Just my quick thoughts on this, definitely it is biased and incomplete.
> >
> > ImageJ is free, and it is very handy for you to do some simple image
> > analysis tasks such as  thresholding, particle analysis,
> > quantification of an images. You can do more complicated image
> > analysis, but requires you a lot of knowledge in macro, Java, and
> algorithm itself.
> >
> > Matlab  will cost your some  money  for license. If you want to
> > develop your own segmentation method, Matlab may already have some
> > built-in functions, so you can use them directly.
> >
> > Simple comparison for doing thesholding:  matlab use graythresh(),
> > which is based on OTSU method. ImageJ provides about 16 different
> > methods to do it.
> >
> > If you want to find the shapes or structure of an object. Matlab has
> > Hough transformation function to help you to do it, but I did not find
> > any function you can use from basic imageJ.
> >
> > If you are advanced users for ImageJ and Matlab, the difference is
> > probably at which one has better built-in functions for you to use
> > (Java or Matlab).
> >
> > In general, you will use matlab if you are a computer scientist, and
> > you will  more likely to use ImageJ if you are non-computer scientist,
> > who does not need to understand the details of how these methods are
> > implemented, but just want them to work for their applications.
> >
> > If anything described here is not accurate, please feel free to point
> out.
> >
> > Zhengyu
> >
> >
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Kamal Raj
> > Sent: Monday, February 24, 2014 2:33 PM
> > To: [hidden email]
> > Subject: Regarding Digital Image Processing In Java
> >
> > Hi Guys
> >
> > I am Kamal Raj Singh working on Digital Image Processing (planning to
> > do PhD). I have also worked on Java platform in Industry.
> > I am familiar with Java and Digital Image Processing. Can some one
> > please tell me how ImageJ is going to help me in my research. I am
> > very very much passionate to work on Java but academic requirements
> > bounded me to Work on MAT LAB.
> >
> > Eagerly waiting for your reply. I need all information about ImageJ
> > and also can it will be helpful in my Research.
> > --
> > Thanks
> > Regards
> > Kamal Raj Singh
> > M.E. (BITS Pilani) Rajasthan (India)
> > Assistant Professor
> > ECE Department
> > IPEC Ghaziabad (U.P.)
> > India South Asia
> > Mob: [phone]
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Thanks
> Regards
> Kamal Raj Singh
> Assistant Professor
> ECE Department
> IPEC Ghaziabad (U.P.)
> Mob: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Thanks
Regards
Kamal Raj Singh
Assistant Professor
ECE Department
IPEC Ghaziabad (U.P.)
Mob: [phone]

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

[Pavel Tomancak]

Dear Kamal,

Have a look at the Fiji publications page

http://fiji.sc/Publications

You can certainly publish your image analysis work done using ImageJ.

I don't know about IEEE, but I think that as long as you outperform state-of-the-art, functional implementation in ImageJ will not be seen as a disadvantage.

All the best

PAvel
-----------------------------------------------------------------------------------
Pavel Tomancak, Ph.D.

Group Leader
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden Tel.: [phone]
Germany Fax: [phone]
email: [hidden email]
homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
twitter: @PavelTomancak
-----------------------------------------------------------------------------------





On Feb 24, 2014, at 9:18 PM, Kamal Raj <[hidden email]> wrote:

> Hi Zhengyu
>
> I want to know that if i create some functions in Java for ImageJ. Can this
> work be considered for IEEE publication or not.
> I am going for research (PhD) in Digital Image Processing. If i create some
> functions for ImageJ (as i have knowledge in Java and also in Digital Image
> Processing).
> then how my work for ImageJ will be going to help me in Research
> publications.
>
> I hope you understand.
> thanks
> Kamal Raj Singh
>
>
>
> On Tue, Feb 25, 2014 at 1:36 AM, Pang, Zhengyu (GE Global Research) <
> [hidden email]> wrote:
>
>> Dear Kamal,
>>
>> Just my quick thoughts on this, definitely it is biased and incomplete.
>>
>> ImageJ is free, and it is very handy for you to do some simple image
>> analysis tasks such as  thresholding, particle analysis, quantification of
>> an images. You can do more complicated image analysis, but requires you a
>> lot of knowledge in macro, Java, and algorithm itself.
>>
>> Matlab  will cost your some  money  for license. If you want to develop
>> your own segmentation method, Matlab may already have some built-in
>> functions, so you can use them directly.
>>
>> Simple comparison for doing thesholding:  matlab use graythresh(), which
>> is based on OTSU method. ImageJ provides about 16 different methods to do
>> it.
>>
>> If you want to find the shapes or structure of an object. Matlab has Hough
>> transformation function to help you to do it, but I did not find any
>> function you can use from basic imageJ.
>>
>> If you are advanced users for ImageJ and Matlab, the difference is
>> probably at which one has better built-in functions for you to use (Java or
>> Matlab).
>>
>> In general, you will use matlab if you are a computer scientist, and you
>> will  more likely to use ImageJ if you are non-computer scientist, who does
>> not need to understand the details of how these methods are implemented,
>> but just want them to work for their applications.
>>
>> If anything described here is not accurate, please feel free to point out.
>>
>> Zhengyu
>>
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Kamal Raj
>> Sent: Monday, February 24, 2014 2:33 PM
>> To: [hidden email]
>> Subject: Regarding Digital Image Processing In Java
>>
>> Hi Guys
>>
>> I am Kamal Raj Singh working on Digital Image Processing (planning to do
>> PhD). I have also worked on Java platform in Industry.
>> I am familiar with Java and Digital Image Processing. Can some one please
>> tell me how ImageJ is going to help me in my research. I am very very much
>> passionate to work on Java but academic requirements bounded me to Work on
>> MAT LAB.
>>
>> Eagerly waiting for your reply. I need all information about ImageJ and
>> also can it will be helpful in my Research.
>> --
>> Thanks
>> Regards
>> Kamal Raj Singh
>> M.E. (BITS Pilani) Rajasthan (India)
>> Assistant Professor
>> ECE Department
>> IPEC Ghaziabad (U.P.)
>> India South Asia
>> Mob: [phone]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
> --
> Thanks
> Regards
> Kamal Raj Singh
> Assistant Professor
> ECE Department
> IPEC Ghaziabad (U.P.)
> Mob: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Gabriel Landini]

On Tuesday 25 Feb 2014 01:48:24 Kamal Raj wrote:
> I want to know that if i create some functions in Java for ImageJ. Can this
> work be considered for IEEE publication or not.

It looks like if there would not be a problem with that :-)

http://www.nature.com/news/publishers-withdraw-more-than-120-gibberish-papers-1.14763

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

[Robert Lockwood]

ImageJ also supports image formats that the Java libraries do not, such as
TIFF which I use.

(Gabriel beat me to a comment about IEEE.)


On Tue, Feb 25, 2014 at 4:09 AM, Gabriel Landini <[hidden email]>wrote:

> On Tuesday 25 Feb 2014 01:48:24 Kamal Raj wrote:
> > I want to know that if i create some functions in Java for ImageJ. Can
> this
> > work be considered for IEEE publication or not.
>
> It looks like if there would not be a problem with that :-)
>
>
> http://www.nature.com/news/publishers-withdraw-more-than-120-gibberish-papers-1.14763
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
When I was 12 I thought I would live forever.
So far, so good.

--
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