Average several image stacks

[babs_18_137]

Hi,

I am trying to average several stacks, but Image Calculator only allows averaging of 2 image stacks. Is there any other function that can allow me to average a larger number of stacks?

Please and thank you!

[justin.senseney]

Hello,

Try the "Image Expression Parser" in Fiji (in the process menu).  The "+" button adds some images that you've already opened, and then you can create your own average.

-Justin Senseney
________________________________________
From: babs_18_137 [[hidden email]]
Sent: Tuesday, May 14, 2013 12:33 PM
To: List IMAGEJ
Subject: Average several image stacks

Hi,

I am trying to average several stacks, but Image Calculator only allows
averaging of 2 image stacks. Is there any other function that can allow me
to average a larger number of stacks?

Please and thank you!



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[babs_18_137]

Hi Justin,

Thanks for the advice. I am a new user to ImageJ and am struggling a bit with navigating. In my process menu, there is no Fiji or image expression parser and I can't find these functions anywhere when I search the ImageJ manual or plug-in list. Where am I going wrong.

Thanks again for your help.

-Bailey

[justin.senseney]

Bailey,

I'm sorry, let me be more clear, Fiji is a child program of ImageJ, it takes ImageJ and adds more pieces on top of it, like the Image Expression Parser.  You can download it here: http://fiji.sc/Fiji 

As you become more familiar with ImageJ, you may want to learn about the macro language, which is accessible in Plugins->Macro->Record...  The image calculator you used prints out as imageCalculator("Add create", "A","B"); so that if you would like to set up an automated function for generating averages, you could do it using successive imageCalculator operations.

-Justin Senseney
________________________________________
From: babs_18_137 [[hidden email]]
Sent: Tuesday, May 14, 2013 1:36 PM
To: List IMAGEJ
Subject: Re: Average several image stacks

Hi Justin,

Thanks for the advice. I am a new user to ImageJ and am struggling a bit
with navigating. In my process menu, there is no Fiji or image expression
parser and I can't find these functions anywhere when I search the ImageJ
manual or plug-in list. Where am I going wrong.

Thanks again for your help.

-Bailey



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[fVoisard]

Hi Justin,

I'm trying to implement Image parser in a macro, since it seems more powerful then the image calculator. However, I am not having any success.  Have you seen any example of automation that calls the image parser rather then the image calculator?


Frederic Voisard

[Jan Eglinger]

Hi Frederic,

On 09.07.2013 11:00 AM, fVoisard wrote:
> I'm trying to implement Image parser in a macro, since it seems more
> powerful then the image calculator. However, I am not having any success.
> Have you seen any example of automation that calls the image parser rather
> then the image calculator?

I would suggest using a scripting language such as Javascript, Python or
Beanshell instead of the macro language. You can easily call the Image
Expression Parser from a scripting language within Fiji: see

http://fiji.sc/Image_Expression_Parser#Calling_the_plugin_from_elsewhere

for instructions how to do this.

Hope that helps,
Jan



>
>
> Frederic Voisard
>
>

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[Krs5]

Seems that this plugin is missing in the Fiji plugin list

Kees

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Jan Eglinger [[hidden email]]
Sent: 09 July 2013 10:52
To: [hidden email]
Subject: Re: Average several image stacks

Hi Frederic,

On 09.07.2013 11:00 AM, fVoisard wrote:
> I'm trying to implement Image parser in a macro, since it seems more
> powerful then the image calculator. However, I am not having any success.
> Have you seen any example of automation that calls the image parser rather
> then the image calculator?

I would suggest using a scripting language such as Javascript, Python or
Beanshell instead of the macro language. You can easily call the Image
Expression Parser from a scripting language within Fiji: see

http://fiji.sc/Image_Expression_Parser#Calling_the_plugin_from_elsewhere

for instructions how to do this.

Hope that helps,
Jan



>
>
> Frederic Voisard
>
>

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[Jan Eglinger]

Hi Kees,

On 09.07.2013 12:12 PM, Straatman, Kees R. (Dr.) wrote:
> Seems that this plugin is missing in the Fiji plugin list

If you mean this list: http://fiji.sc/Category:Plugins

I just fixed the wiki source of http://fiji.sc/Image_Expression_Parser
in order to make it show up in this list.

Thx,
Jan

>
> Kees
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of Jan Eglinger [[hidden email]]
> Sent: 09 July 2013 10:52
> To: [hidden email]
> Subject: Re: Average several image stacks
>
> Hi Frederic,
>
> On 09.07.2013 11:00 AM, fVoisard wrote:
>> I'm trying to implement Image parser in a macro, since it seems more
>> powerful then the image calculator. However, I am not having any success.
>> Have you seen any example of automation that calls the image parser rather
>> then the image calculator?
>
> I would suggest using a scripting language such as Javascript, Python or
> Beanshell instead of the macro language. You can easily call the Image
> Expression Parser from a scripting language within Fiji: see
>
> http://fiji.sc/Image_Expression_Parser#Calling_the_plugin_from_elsewhere
>
> for instructions how to do this.
>
> Hope that helps,
> Jan
>
>
>
>>
>>
>> Frederic Voisard
>>
>>
>
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