multichannel kymographs

[Jeff Spector-2]

Greetings,
I have a stack that is 1800 frames and composed of 2 channels. I would like
to draw a line and get the kymographs for each channel individually. Is
there a way to do this without having to split the channels and generate
the kymograph for each channel by hand?  If I try to make a kymograph of
the original 1800 frame, 2 channel stack, I end up getting a 3600 line long
kymograph where the channels are intersperesed, i.e. it goes ch1 ch2 ch1
ch2 etc..
I would like them to be separated ( and overlayed on each other if
possible). Does this tool exist ?
thanks..
Jeff

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[Krs5]

Dear Jeff,

I have made some changes to one of the macros I have written for kymographs so that it might work for your files. It is written for a Hyperstack with 2 channels.

Install the macro and you will get an icon in the tool bar. Open your image, draw a line, select the icon and click in your image and hopefully your kymograph will be created. The line width can be changed by double clicking on the icon. Default = 5 but can easily be changed in the code below by changing the value of x.

The output is a merged image with kymograph for channel 1 in  red and for channel 2 in green.


// This macro will take a line selection (Straight line, Segmented line or Freehand line) and
// create a kymograph. It is written for a Hyperstack composed of 2 channels.
// The user can change the width of the line by double clicking the icon. The default is 5. Once changed
// this keeps the new value till the macro is restarted. This value can be changed in the code
// below by changing the value of x.
// Kees Straatman, University of Leicester, 23 May 2014

var x = 5;

macro "kymograph Tool - C000C333C222Dd3C222C333D5bC333Db5C333D78C333dC4C444D2cD69C444D4bC444D97C444Da6C444C555D1cC555De1C555C666D87C666D0dC666D3bC666De2C666C777Df0C777Dd2C777Dd4C777C888Dc5C888C999Db6C999D4aC999D3cC999D88C999CaaaD6aCaaaD68CaaaD0cD96CaaaD59CbbbD5bCbbbDe0CbbbDc3CbbbD1dCbbbD2bCbbbD79CbbbCcccDf1CcccDa5CcccDa7CcccD77CcccCdddDb4CdddDe3CdddCeeeD4cCeeeD98CeeeDd1CeeeD2dDd5CeeeCfffD1bCfffD86CfffDc6CfffDc2CfffD3aCfffD0eCfffD89Df2CfffDe4CfffD0fD58D5cD6bCfffD3dD67D95Db7CfffD0aD0bD1eD1fD49D7aDa4Db3CfffD00D01D02D03D04D05D06D07D08D09D10D11D12D13D14D15D16D17D18D19D1aD20D21D22D23D24D25D26D27D28D29D2aD2eD2fD30D31D32D33D34D35D36D37D38D39D3eD3fD40D41D42D43D44D45D46D47D48D4dD4eD4fD50D51D52D53D54D55D56D57D5dD5eD5fD60D61D62D63D64D65D66D6cD6dD6eD6fD70D71D72D73D74D75D76D7bD7cD7dD7eD7fD80D81D82D83D84D85D8aD8bD8cD8dD8eD8fD90D91D92D93D94D99D9aD9bD9cD9dD9eD9fDa0Da1Da2Da3Da8Da9DaaDabDacDadDaeDafDb0Db1Db2Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc7Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe5De6De7De8De9DeaDebDecDedDeeDefDf3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDff"{
        //setBatchMode(true);
        title = getTitle();
        getDimensions(width, height, channels, slices, frames);
        frames = channels*slices*frames;
        frames2 = frames/2;
        run("Straighten...", "line="+x+" process");
        title2=getTitle();
        run("Rotate 90 Degrees Left");
        //run("16 Colors");
        title = getTitle();
        Stack.setChannel(1);
        run("Make Montage...", "columns="+frames2+" rows=1 scale=1 first=1 last="+frames+" increment=1 border=0 font=12");
        rename("Montage-"+title+" channel 1");
        resetMinAndMax();
        selectWindow(title);
        Stack.setChannel(2);
        run("Make Montage...", "columns="+frames2+" rows=1 scale=1 first=2 last="+frames+" increment=2 border=0 font=12");
        rename("Montage-"+title+" channel 2");
        resetMinAndMax();
        run("Merge Channels...", "c1=[Montage-"+title+" channel 1] c2=[Montage-"+title+" channel 2]");
        rename("kymograph-"+title);
        selectWindow(title);
        close();
        setBatchMode("exit and display");

}

macro "MicroTubBleach Tool Options"{
        x = getNumber("line width = ", x);
}


As always not extensively tested.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jeff Spector
Sent: 23 May 2014 16:00
To: [hidden email]
Subject: multichannel kymographs

Greetings,
I have a stack that is 1800 frames and composed of 2 channels. I would like to draw a line and get the kymographs for each channel individually. Is there a way to do this without having to split the channels and generate the kymograph for each channel by hand?  If I try to make a kymograph of the original 1800 frame, 2 channel stack, I end up getting a 3600 line long kymograph where the channels are intersperesed, i.e. it goes ch1 ch2 ch1
ch2 etc..
I would like them to be separated ( and overlayed on each other if possible). Does this tool exist ?
thanks..
Jeff

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[Rasband, Wayne (NIH/NIMH) [E]]

On May 23, 2014, at 11:00 AM, Jeff Spector wrote:

> Greetings,
> I have a stack that is 1800 frames and composed of 2 channels. I would like
> to draw a line and get the kymographs for each channel individually. Is
> there a way to do this without having to split the channels and generate
> the kymograph for each channel by hand?  If I try to make a kymograph of
> the original 1800 frame, 2 channel stack, I end up getting a 3600 line long
> kymograph where the channels are intersperesed, i.e. it goes ch1 ch2 ch1
> ch2 etc..
> I would like them to be separated ( and overlayed on each other if
> possible). Does this tool exist ?

The Image>Stacks>Reslice command in the latest ImageJ daily build (1.49b8) can create
multichannel kymographs from time-lapse 4D hyperstacks (c>1,z=1,t>1). To make a kymograph,  create a line selection, press "/" (shortcut for Reslice) and click "OK" in the dialog (defaults are fine). There is a kymograph tutorial at

   http://fiji.sc/Generate_and_exploit_Kymographs

-wayne

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[Jeff Spector-2]

On Fri, May 23, 2014 at 2:31 PM, Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]> wrote:

> On May 23, 2014, at 11:00 AM, Jeff Spector wrote:
>
> > Greetings,
> > I have a stack that is 1800 frames and composed of 2 channels. I would
> like
> > to draw a line and get the kymographs for each channel individually. Is
> > there a way to do this without having to split the channels and generate
> > the kymograph for each channel by hand?  If I try to make a kymograph of
> > the original 1800 frame, 2 channel stack, I end up getting a 3600 line
> long
> > kymograph where the channels are intersperesed, i.e. it goes ch1 ch2 ch1
> > ch2 etc..
> > I would like them to be separated ( and overlayed on each other if
> > possible). Does this tool exist ?
>
> The Image>Stacks>Reslice command in the latest ImageJ daily build (1.49b8)
> can create
> multichannel kymographs from time-lapse 4D hyperstacks (c>1,z=1,t>1). To
> make a kymograph,  create a line selection, press "/" (shortcut for
> Reslice) and click "OK" in the dialog (defaults are fine). There is a
> kymograph tutorial at
>
>    http://fiji.sc/Generate_and_exploit_Kymographs
>
> -wayne
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

This works great! Thanks!. Is the thickness of the line of the kymograph
defined by the thickness of the line tool used for drawing the roi, or is
it doing only doing a 1 pixel wide line? (is this adjustable?) thanks!

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