time series from Image stacks

[jep]

I'm sure these will be naive questions. I've written a code that I want to turn into an ImageJ plug in. I'm not a java programmer nor am I an ImageJ user. ImageJ was suggested by my colleagues who asked me to write the code in the first place. I have working versions that I've written in C, R, and now java. The code operates on time series. So far what I have reads an ASCI input file containing raw data (the file is just a column of numbers) and then runs my algorithm on it. The code produces an output time series so I guess you might consider it to be "filtered". In any event I need to visually compare the input time series to some of the output time series to make sure that my algorithm produced something reasonable. There are something like 8 command line arguments including the name of the file containing the raw data and about a half dozen parameters. Ultimately I'd like to turn the parameter initialization into some sort of gui thing and also to be able to select a bunch of files in a window to input into my algorithm.  I'm going at this from two different directions. One is reading the example plugins to see the code. The other is by playing with an image stack in ImageJ. The image stack is consists of 10,000 16 bit gray scale images. For starters I'd like to select a pixel and then view the timeseries for that pixel . I've spent an hour or two  failing to do that. Ideally I'd like to select a region of interest, store the time series for each pixel in the ROI in a separate file and then run my algorithm on each of the files. I'm flailing a bit. Comments/suggestions appreciated!

[Cammer, Michael]

Hi.
What you're describing sounds precisely what ImageJ does well.  However, the description of what you need to do is difficult to understand.  Would you be able to give an example such as a series of images or a sample data file on a server?
Regards,
Michael
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of jep [[hidden email]]
Sent: Saturday, January 26, 2013 2:11 PM
To: [hidden email]
Subject: time series from Image stacks

I'm sure these will be naive questions. I've written a code that I want to
turn into an ImageJ plug in. I'm not a java programmer nor am I an ImageJ
user. ImageJ was suggested by my colleagues who asked me to write the code
in the first place. I have working versions that I've written in C, R, and
now java. The code operates on time series. So far what I have reads an ASCI
input file containing raw data (the file is just a column of numbers) and
then runs my algorithm on it. The code produces an output time series so I
guess you might consider it to be "filtered". In any event I need to
visually compare the input time series to some of the output time series to
make sure that my algorithm produced something reasonable. There are
something like 8 command line arguments including the name of the file
containing the raw data and about a half dozen parameters. Ultimately I'd
like to turn the parameter initialization into some sort of gui thing and
also to be able to select a bunch of files in a window to input into my
algorithm.  I'm going at this from two different directions. One is reading
the example plugins to see the code. The other is by playing with an image
stack in ImageJ. The image stack is consists of 10,000 16 bit gray scale
images. For starters I'd like to select a pixel and then view the timeseries
for that pixel . I've spent an hour or two  failing to do that. Ideally I'd
like to select a region of interest, store the time series for each pixel in
the ROI in a separate file and then run my algorithm on each of the files.
I'm flailing a bit. Comments/suggestions appreciated!



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[jep]

" However, the description of what you need to do is difficult to understand.  Would you be able to give an example such as a series of images or a sample data file on a server? "

I don't have a server but this is pretty generic stuff for ImageJ I think. The main thing is that I need to turn a  java program into an ImageJ plug in. A "Hello world" example would get me started.

In the mean time I've found out how to save a time-series as a text file but it saves the time index too. Is there a way to tell it not to save the time index?

[Barry DeZonia]

Hello,

One can see example plugin skeletons by running the Plugins > New > ...
commands from within ImageJ. There are also numerous plugin examples here:
http://rsbweb.nih.gov/ij/plugins/index.html#examples  You can also read a
plugin writing tutorial here: http://www.imagingbook.com/index.php?id=102



On Mon, Jan 28, 2013 at 6:24 AM, jep <[hidden email]> wrote:

> " However, the description of what you need to do is difficult to
> understand.
> Would you be able to give an example such as a series of images or a sample
> data file on a server? "
>
> I don't have a server but this is pretty generic stuff for ImageJ I think.
> The main thing is that I need to turn a  java program into an ImageJ plug
> in. A "Hello world" example would get me started.
>
> In the mean time I've found out how to save a time-series as a text file
> but
> it saves the time index too. Is there a way to tell it not to save the time
> index?
>
>
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/time-series-from-Image-stacks-tp5001556p5001567.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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