clojure and fiji

[rabih assaf-2]

Is there anyone familiar with using clojure language in imagej?
     
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[Jan Eglinger]

Hi Rabih,

On 28.01.15 14:03, rabih assaf wrote:
> Is there anyone familiar with using clojure language in imagej?
>    

You can find some clojure scripting examples here:
http://fiji.sc/Clojure_Scripting

For more specific questions, this list is the best place to ask.

Cheers,
Jan

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[rabih assaf-2]

Hello, does anyone know how to calculate variance of a selected area using clojure?

> Date: Wed, 28 Jan 2015 14:24:31 +0100
> From: [hidden email]
> Subject: Re: clojure and fiji
> To: [hidden email]
>
> Hi Rabih,
>
> On 28.01.15 14:03, rabih assaf wrote:
> > Is there anyone familiar with using clojure language in imagej?
> >    
>
> You can find some clojure scripting examples here:
> http://fiji.sc/Clojure_Scripting
>
> For more specific questions, this list is the best place to ask.
>
> Cheers,
> Jan
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

     
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[Albert Cardona-2]

Rabih: all the pieces you need are listed in http://fiji.sc/Clojure_
Scripting

I know because I wrote them myself.

Albert

2015-01-28 10:17 GMT-05:00 rabih assaf <[hidden email]>:

> Hello, does anyone know how to calculate variance of a selected area using
> clojure?
>
> > Date: Wed, 28 Jan 2015 14:24:31 +0100
> > From: [hidden email]
> > Subject: Re: clojure and fiji
> > To: [hidden email]
> >
> > Hi Rabih,
> >
> > On 28.01.15 14:03, rabih assaf wrote:
> > > Is there anyone familiar with using clojure language in imagej?
> > >
> >
> > You can find some clojure scripting examples here:
> > http://fiji.sc/Clojure_Scripting
> >
> > For more specific questions, this list is the best place to ask.
> >
> > Cheers,
> > Jan
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
http://albert.rierol.net
http://www.janelia.org/lab/cardona-lab
http://www.ini.uzh.ch/~acardona/

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[Herbie-4]

Rabih,

didn't you ask for variance computation a week or so ago?

Michael Schmid gave you valuable hints.

However, I really should like to know whether the Standard Deviation
(STD) would do for your purposes? If yes, you don't need any programming
language because ImageJ does provide the STD of a selected region.

 From "Analyze > Set Measurements" check "Standard deviation", then
select the desired area and use "Analyze > Measure". The STD of this
area will appear in the Results window. If you need the command in a
script you may record the command from "Plugins > Macros > Record"
(select the desired script language).

If you really need the variance instead, you may (later) square the STD.

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
On 28.01.15 16:17, rabih assaf wrote:

> Hello, does anyone know how to calculate variance of a selected area
> using clojure?
>
>> Date: Wed, 28 Jan 2015 14:24:31 +0100 From: [hidden email]
>> Subject: Re: clojure and fiji To: [hidden email]
>>
>> Hi Rabih,
>>
>> On 28.01.15 14:03, rabih assaf wrote:
>>> Is there anyone familiar with using clojure language in imagej?
>>
>> You can find some clojure scripting examples here:
>> http://fiji.sc/Clojure_Scripting
>>
>> For more specific questions, this list is the best place to ask.
>>
>> Cheers, Jan
>>
>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>  -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Jan Eglinger]

Hi,

using the functions built into ImageJ, you can do something like this in
Clojure:

(def ^:dynamic *imp* (ij.WindowManager/getCurrentImage))
(.setRoi *imp* 10 10 40 40)
(ij.IJ/run "Set Measurements..." "standard redirect=None decimal=3")
(ij.IJ/run *imp* "Measure" "")

Hope that helps
Jan


On 28.01.15 16:29, Albert Cardona wrote:

> Rabih: all the pieces you need are listed in http://fiji.sc/Clojure_
> Scripting
>
> I know because I wrote them myself.
>
> Albert
>
> 2015-01-28 10:17 GMT-05:00 rabih assaf <[hidden email]>:
>
>> Hello, does anyone know how to calculate variance of a selected area using
>> clojure?
>>
>>> Date: Wed, 28 Jan 2015 14:24:31 +0100
>>> From: [hidden email]
>>> Subject: Re: clojure and fiji
>>> To: [hidden email]
>>>
>>> Hi Rabih,
>>>
>>> On 28.01.15 14:03, rabih assaf wrote:
>>>> Is there anyone familiar with using clojure language in imagej?
>>>>
>>>
>>> You can find some clojure scripting examples here:
>>> http://fiji.sc/Clojure_Scripting
>>>
>>> For more specific questions, this list is the best place to ask.
>>>
>>> Cheers,
>>> Jan
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>

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[rabih assaf-2]

thank you,
do you have an idea how to find the dimensions of an image using clojure?

> Date: Wed, 28 Jan 2015 17:34:09 +0100
> From: [hidden email]
> Subject: Re: clojure and fiji
> To: [hidden email]
>
> Hi,
>
> using the functions built into ImageJ, you can do something like this in
> Clojure:
>
> (def ^:dynamic *imp* (ij.WindowManager/getCurrentImage))
> (.setRoi *imp* 10 10 40 40)
> (ij.IJ/run "Set Measurements..." "standard redirect=None decimal=3")
> (ij.IJ/run *imp* "Measure" "")
>
> Hope that helps
> Jan
>
>
> On 28.01.15 16:29, Albert Cardona wrote:
> > Rabih: all the pieces you need are listed in http://fiji.sc/Clojure_
> > Scripting
> >
> > I know because I wrote them myself.
> >
> > Albert
> >
> > 2015-01-28 10:17 GMT-05:00 rabih assaf <[hidden email]>:
> >
> >> Hello, does anyone know how to calculate variance of a selected area using
> >> clojure?
> >>
> >>> Date: Wed, 28 Jan 2015 14:24:31 +0100
> >>> From: [hidden email]
> >>> Subject: Re: clojure and fiji
> >>> To: [hidden email]
> >>>
> >>> Hi Rabih,
> >>>
> >>> On 28.01.15 14:03, rabih assaf wrote:
> >>>> Is there anyone familiar with using clojure language in imagej?
> >>>>
> >>>
> >>> You can find some clojure scripting examples here:
> >>> http://fiji.sc/Clojure_Scripting
> >>>
> >>> For more specific questions, this list is the best place to ask.
> >>>
> >>> Cheers,
> >>> Jan
> >>>
> >>> --
> >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >
> >
>
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