Sequence of difference images generated from a time-lapse image sequence

[John Oreopoulos]

Hello ImageJ users:

I'd like to create a macro or plugin that generates a sequence of difference images from a time-lapse image sequence. For example, suppose I have a time-lapse sequence of 1000 images. I'd like the macro/plugin to create a new sequence of 999 images where each frame is the resultant subtraction of the next frame minus the previous frame (Frame[N+1] minus Frame[N]). I think this operation is simple enough that I could code it myself, but I just wanted to check and see if anyone else knew of an existing ImageJ plugin or macro that already does this. No sense in re-creating the wheel.

Thanks!


John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca

[Rainer M. Engel]

Am 08.12.2011 18:24, schrieb John Oreopoulos:
> Hello ImageJ users:
>
> I'd like to create a macro or plugin that generates a sequence of difference images from a time-lapse image sequence. For example, suppose I have a time-lapse sequence of 1000 images. I'd like the macro/plugin to create a new sequence of 999 images where each frame is the resultant subtraction of the next frame minus the previous frame (Frame[N+1] minus Frame[N]). I think this operation is simple enough that I could code it myself, but I just wanted to check and see if anyone else knew of an existing ImageJ plugin or macro that already does this. No sense in re-creating the wheel.
>

Hey.. I don't know if this has exactly been done before but you find
useful fragments to create your own macro here.

Simply hit Strg+Shift+N to paste the macro into editor..


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

imageCalculator
http://rsb.info.nih.gov/ij/macros/ImageCalculatorDemo.txt


Maybe someone else has even more hints or you find better starting
points in the docs.

Regards,
Rainer

--
Rainer M. Engel
www.scientific-media.de

[Jerome Mutterer-3]

John,

You might try :

http://rsb.info.nih.gov/ij/macros/Slice-to-Slice%20Difference.txt

Jerome

On 8 December 2011 18:24, John Oreopoulos <[hidden email]>wrote:

> Hello ImageJ users:
>
> I'd like to create a macro or plugin that generates a sequence of
> difference images from a time-lapse image sequence. For example, suppose I
> have a time-lapse sequence of 1000 images. I'd like the macro/plugin to
> create a new sequence of 999 images where each frame is the resultant
> subtraction of the next frame minus the previous frame (Frame[N+1] minus
> Frame[N]). I think this operation is simple enough that I could code it
> myself, but I just wanted to check and see if anyone else knew of an
> existing ImageJ plugin or macro that already does this. No sense in
> re-creating the wheel.
>
> Thanks!
>
>
> John Oreopoulos
> Research Assistant
> Spectral Applied Research
> Richmond Hill, Ontario
> Canada
> www.spectral.ca
>

[John Oreopoulos]

Thank you all for your replies so far the Slice-to-Slice difference macro looks perfect. Michael, I wouldn't mind checking out what you have as well.

Thanks again.

John Oreopoulos


On 2011-12-08, at 1:02 PM, Jerome Mutterer wrote:

> John,
>
> You might try :
>
> http://rsb.info.nih.gov/ij/macros/Slice-to-Slice%20Difference.txt
>
> Jerome
>
> On 8 December 2011 18:24, John Oreopoulos <[hidden email]>wrote:
>
>> Hello ImageJ users:
>>
>> I'd like to create a macro or plugin that generates a sequence of
>> difference images from a time-lapse image sequence. For example, suppose I
>> have a time-lapse sequence of 1000 images. I'd like the macro/plugin to
>> create a new sequence of 999 images where each frame is the resultant
>> subtraction of the next frame minus the previous frame (Frame[N+1] minus
>> Frame[N]). I think this operation is simple enough that I could code it
>> myself, but I just wanted to check and see if anyone else knew of an
>> existing ImageJ plugin or macro that already does this. No sense in
>> re-creating the wheel.
>>
>> Thanks!
>>
>>
>> John Oreopoulos
>> Research Assistant
>> Spectral Applied Research
>> Richmond Hill, Ontario
>> Canada
>> www.spectral.ca
>>

[Michael Schell]

Isn't this just plugins-stacks-deltaFdown (or deltaF up)?  As described here:


http://www.macbiophotonics.ca/imagej/t.htm#t_deltaF


Michael


?
Michael J. Schell, Ph.D., CIV, USUHS
Assist. Professor
Dept. of Pharmacology
Uniformed Services University
4301 Jones Bridge Rd.
Bethesda, MD  20814-3220
tel:  [phone]
[hidden email]
>>> "Rainer M. Engel"  12/08/11 12:52 PM >>>
Am 08.12.2011 18:24, schrieb John Oreopoulos:
> Hello ImageJ users:
>
> I'd like to create a macro or plugin that generates a sequence of difference images from a time-lapse image sequence. For example, suppose I have a time-lapse sequence of 1000 images. I'd like the macro/plugin to create a new sequence of 999 images where each frame is the resultant subtraction of the next frame minus the previous frame (Frame[N+1] minus Frame[N]). I think this operation is simple enough that I could code it myself, but I just wanted to check and see if anyone else knew of an existing ImageJ plugin or macro that already does this. No sense in re-creating the wheel.
>

Hey.. I don't know if this has exactly been done before but you find
useful fragments to create your own macro here.

Simply hit Strg+Shift+N to paste the macro into editor..


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

imageCalculator
http://rsb.info.nih.gov/ij/macros/ImageCalculatorDemo.txt


Maybe someone else has even more hints or you find better starting
points in the docs.

Regards,
Rainer

--
Rainer M. Engel
www.scientific-media.de


Classification:  UNCLASSIFIED
Caveats: None


Classification:  UNCLASSIFIED
Caveats: None

[John Oreopoulos]

Yes you're right, I even had this plugin already installed from the macbiophotonics package and didn't realize it was there. Thanks for pointing this out.

John Oreopoulos


On 2011-12-08, at 1:27 PM, Michael Schell wrote:

> Isn't this just plugins-stacks-deltaFdown (or deltaF up)?  As described here:
>
>
> http://www.macbiophotonics.ca/imagej/t.htm#t_deltaF
>
>
> Michael
>
>
> ?
> Michael J. Schell, Ph.D., CIV, USUHS
> Assist. Professor
> Dept. of Pharmacology
> Uniformed Services University
> 4301 Jones Bridge Rd.
> Bethesda, MD  20814-3220
> tel:  [phone]
> [hidden email]
>>>> "Rainer M. Engel"  12/08/11 12:52 PM >>>
> Am 08.12.2011 18:24, schrieb John Oreopoulos:
>> Hello ImageJ users:
>>
>> I'd like to create a macro or plugin that generates a sequence of difference images from a time-lapse image sequence. For example, suppose I have a time-lapse sequence of 1000 images. I'd like the macro/plugin to create a new sequence of 999 images where each frame is the resultant subtraction of the next frame minus the previous frame (Frame[N+1] minus Frame[N]). I think this operation is simple enough that I could code it myself, but I just wanted to check and see if anyone else knew of an existing ImageJ plugin or macro that already does this. No sense in re-creating the wheel.
>>
>
> Hey.. I don't know if this has exactly been done before but you find
> useful fragments to create your own macro here.
>
> Simply hit Strg+Shift+N to paste the macro into editor..
>
>
> BatchConvert
> http://rsb.info.nih.gov/ij/macros/BatchConvert.txt
>
> imageCalculator
> http://rsb.info.nih.gov/ij/macros/ImageCalculatorDemo.txt
>
>
> Maybe someone else has even more hints or you find better starting
> points in the docs.
>
> Regards,
> Rainer
>
> --
> Rainer M. Engel
> www.scientific-media.de
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>
> Classification:  UNCLASSIFIED
> Caveats: None

[Adrian Daerr-2]

> I'd like to create a macro or plugin that generates a sequence of
> difference images from a time-lapse image sequence [..] where each frame
> is the resultant subtraction of the next frame minus the previous
> frame (Frame[N+1] minus Frame[N]).

You can check out this plug-in of mine,

http://www.msc.univ-paris-diderot.fr/~daerr/tmp/Stack_Differentiator.class
(GPLed source at:
http://www.msc.univ-paris-diderot.fr/~daerr/tmp/Stack_Differentiator.java
)

which offers a preview, different formulas and adjustable parameters:
     static final String[] ops = {"([n] - [n-a])*b + c",
                                  "[n] - [n-a]*b + c",
                                  "([n] - [a])*b + c",
                                  "[n] - [a]*b + c",
                                  "([n] - c):b + [n-a]",
                                  "[n] + [n-a]*b - c",
                                  "([n] - c):b + [a]",
                                  "[n] + [a]*b - c"};

It was written back in 2002, so it doesn't make use neither of Java
1.5's Enumerations, nor ImageJ's own preview mechanism (through the
ExtendedPlugInFilter interface). In particular it will not make use of
multi-threading. But it works nicely, and we use it regularly as a nice
way of detecting changes. Just drop the .class file into ImageJ's
plugins directory, and restart ImageJ, as usual.

hth
Adrian