Calcium imaging

[Santoro, Francesca]

Hi,
is there anyone who knows how to process Calcium Imaging videos? I would like to create different ROIs (like dividing every frame in a grid and every square of the grid is a ROI). For every ROI I would have a pixel intensity profile as a function of time, and finally I would like to calculate the phase shift between all the profiles (assuming that one profile is like a wave).
I hope that someone can help me!!

Bests,
Francesca


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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Bernhard Reber]

Hi Francesca,

I wrote a lot of Calcium imaging analysis macros for NIH image many years ago. I include two macros still written in Pascal like language as it was used with NIH-Image when there was no imagej. It would ahbve to be rewritten to the new java like language. Maybe I'll do it some times.

To help you more precisely, let me know how your calcium videos are alike. On video tape or already digitized in any video format so that it max be imported as a stack into imagej ?

Maybe you'll find the solution to your problem already in the macros provided with the ImageJ download.


Sincerely yours

Bernhard Reber


The following MACROS do not work on ImageJ !

Macro 'Stack of ROI';
var
MaxSlice, I, WinCount, n: integer;
RoiLeft,RoiTop,Roiwidth,Roiheight,WinWidth: integer;

BEGIN;
    MaxSlice:=nSlices;
    SelectPIc(1);
    selectSlice(1);
    GetRoi (RoiLeft,RoiTop,Roiwidth, Roiheight);
    WinWidth:=RoiWidth-1;
    SetNewSize(WinWidth,RoiHeight);
    For n:= 1 to MaxSlice Do begin;
    ChoosePic(1);
    SelectSlice(n);
    MakeRoi(RoiLeft,RoiTop,Roiwidth, Roiheight);
    copy;
                                MakeNewWindow('*');
    paste;
                                end;
end;

Macro 'Int with threshold vs Slice';
var
Height, Width,Piccount,BckColor,MaxPic,MaxOff,Xpos,Ypos,PixCount,YRoi,XRoi: integer;
RoiLeft, RoiTop, RoiWidth, RoiHeight,RoiBottom,OutWidth,OutHeight,Sum:integer;
MaxSlice:integer;
LutFile: string;
nPixels,mean,mode,min,max:real;
Begin;
        ResetCounter;
        ChoosePic(1);
SetThreshold(5);
SelectSlice(1);
        GetRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);;
  if RoiWidth=0 then begin;
                PutMessage('The Setup macro expects a determined ROI on the first picture of the serie to be displayed.');
    exit;
        end;
SelectPic(1);
        MaxSlice:=nSlices;
        Maxoff:= MaxSlice;
MaxPic:=nPics;
  SelectPic(MaxPic);
        SetBackGroundColor(0);
        ChoosePic(1);
SelectSlice(1);
        MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);

        Measure;
 GetResults(nPixels,mean,mode,min,max);
        Xpos:=50  ;
        Ypos:=290-Mean;
        ChoosePic(MaxPic);
        Moveto(Xpos,Ypos);
        For Piccount:= 2 to MaxOff do begin;
  ChoosePic(1);
SelectSlice(Piccount);
  MakeRoi(RoiLeft,RoiTop,RoiWidth,RoiHeight);

                Measure;
  GetResults(nPixels,mean,mode,min,max) ;
  Xpos:=Xpos+1;
  Ypos:=290-Mean;
                ChoosePic(MaxPic);
                Lineto (Xpos,Ypos);
        end;
Xpos:=100;
Ypos:=290;

Moveto(Xpos,Ypos);

Lineto (Xpos+20,Ypos);



ChoosePic(1);
SetThreshold(-1);
end;

Am 29.01.2013 um 16:09 schrieb Santoro, Francesca:

> Hi,
> is there anyone who knows how to process Calcium Imaging videos? I would like to create different ROIs (like dividing every frame in a grid and every square of the grid is a ROI). For every ROI I would have a pixel intensity profile as a function of time, and finally I would like to calculate the phase shift between all the profiles (assuming that one profile is like a wave).
> I hope that someone can help me!!
>
> Bests,
> Francesca
>
>
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> ------------------------------------------------------------------------------------------------
> ------------------------------------------------------------------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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