Re: AW: Fiji Intensity plot - Multi Measure in the ROI manager.

[Daniel James White]

Hi Hugo,


On Jan 11, 2011, at 1:21 PM, Hugo.Ostermann wrote:

> Hi Dan,
> thanks for your detailed answer.
> This was exactly was I was able to do (see attached imge)

Ah! Good!

> but what I was
> looking for was a Plot rather than a list of values.

I see.

> Of course I could copy this to EXCEL and get my plot but I was hoping to get
> this also done in Fiji or ImageJ.

As it stands, thats the best way.
ImageJ isn't really a plotting program,
and the basic plot tool doesn't know how to do the things you want by itself.

In this case one would need to write a macro or python or beanshell script
that does the following

Loop through the ROIs
        loop through the color channels
                loop through the time frames
                        measure the desired property from that ROI in that channel, in that time frame
                        put the result in an array for that ROI and channel
use the plot function to plot the multiple arrays you just made.

see

http://rsb.info.nih.gov/ij/developer/macro/macros.html

http://rsb.info.nih.gov/ij/macros/examples/ThreeColorPlot.txt

http://rsb.info.nih.gov/ij/macros/ExamplePlots.txt

http://rsb.info.nih.gov/ij/macros/PlotStack.txt

http://rsb.info.nih.gov/ij/macros/RGB_Profile_Plot.txt

cheers

Dan

>
> Best regards
>
> Hugo
>
> Hugo Ostermann
>
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>
> -----Ursprüngliche Nachricht-----
> Von: Daniel James White [mailto:[hidden email]]
> Gesendet: Dienstag, 11. Januar 2011 09:54
> An: [hidden email]
> Cc: Image Processing Facility; fiji-users; ImageJ Interest Group
> Betreff: Re: Fiji Intensity plot - Multi Measure in the ROI manager.
>
> Hi Hugo and All,
>
> the functionality you need is all there already, in the fantastic ROI
> manager built into imageJ (no extra plugins needed)
>
> Open the hyperstack image you have saved on your hard disk.
> It should be displayed as a hyper stack, with a slider for time, and channel
> (and also z if there is z stack)
>
> open the ROI manager,
> or simply make an ROI however you like, then press the "T" key This will
> open the ROI manager and add that ROI to the list.
>
> Add moreROIs to the list as you please, then select them all in the list
> (click the first, then shift click the last)
>
> Next, in the ROI manager, click the More button (the last one) then choose
> "Muti Measure"
>
> this will ask you what dimensions of the htper stack you want to measure in,
> you probably want all of them.
>
> this will give you a number of columns = number of ROIs and the measurement
> for each "slice" will be listed in the rows...
> sadly they are interleaved in the order
> slice 1 ,channel 1
> slice 1,  channel 2
> slice 2, channel 1
> slice2, channel 2
>
> etc.
>
> so you might have to do some spread sheet magic to get them how you like.
>
> Try turning off the "One Row per Slice" button, and maybe that is better
> formatted output.
>
>
> Or you can write a python or beanshell script, or macro that makes imageJ/
> Fiji do exactly what you want.
>
> see attached screenshots:
>
> hope that helps , let me know if you still struggle...
>
> the ROI manager is possibly "THE" most useful gadget in ImageJ!
>
> cheers
>
> Dan
>
> <LA1.6_Fiji_Multi_ROI_Analysis_of ratio_image.jpg>

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
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01307 DRESDEN
Germany

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