Find ROIs with maximal intensity increase in a time series

[Bertrecht]

Hello everybody,

in one of my experiments I obtain a time series of one frame, which can be opened with imagej as a stack. I would like to find out, which ROIs within this frame show the strongest increase in intensity. For example, I want to divide the image into small rectangular ROIs and then compare each mean intensity ratio from the end frame to the first frame. Ideally, the macro will give me a normalized colour-coded intensity map on the basis of the ratios. Maybe there are already macros available for this purpose or you can help me by creating such macro, since I'm not very experienced with imagej until now.

Best

Bertrecht

[fabrice senger-2]

Hi,

I guess if you do a Z-projection and go for standard deviation the siganl
should be the highest were the intensity increases the most.

Fabrice.

2015-06-25 12:55 GMT+02:00 Bertrecht <[hidden email]>:

> Hello everybody,
>
> in one of my experiments I obtain a time series of one frame, which can be
> opened with imagej as a stack. I would like to find out, which ROIs within
> this frame show the strongest increase in intensity. For example, I want to
> divide the image into small rectangular ROIs and then compare each mean
> intensity ratio from the end frame to the first frame. Ideally, the macro
> will give me a normalized colour-coded intensity map on the basis of the
> ratios. Maybe there are already macros available for this purpose or you
> can
> help me by creating such macro, since I'm not very experienced with imagej
> until now.
>
> Best
>
> Bertrecht
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Find-ROIs-with-maximal-intensity-increase-in-a-time-series-tp5013282.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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[Bertrecht]

Hi Fabrice,

thank you for the quick response! The Z Project command is absolutely what I was looking for...nevertheless, with the default settings it is not possible to determine the area with the maximum increase in intensity - I guess. I was checking the spots with the highest standard deviation and they can be correlated to areas with the highest decrease in intensity...if there would be a setting like "normalized Intensity". Anyway, thank you a lot and I will look for additional options using the "Z Project"

Bertrecht

[Michael Schmid]

Hi Bertrecht,

what about the following idea:
- Duplicate the first and last slice
- Subtract or divide these two images, with floating-point(=32-bit) output (Image>Process>Image Calculator)

You can also create a mask of your ROIs and then run the 'Particle Properties to Image' macro to replace the particles with their mean intensity. Thereafter subtract or divide.
  http://imagejdocu.tudor.lu/doku.php?id=macro:particle_properties_to_image

Michael
________________________________________________________________
On Jun 25, 2015, at 12:55, Bertrecht wrote:

> Hello everybody,
>
> in one of my experiments I obtain a time series of one frame, which can be
> opened with imagej as a stack. I would like to find out, which ROIs within
> this frame show the strongest increase in intensity. For example, I want to
> divide the image into small rectangular ROIs and then compare each mean
> intensity ratio from the end frame to the first frame. Ideally, the macro
> will give me a normalized colour-coded intensity map on the basis of the
> ratios. Maybe there are already macros available for this purpose or you can
> help me by creating such macro, since I'm not very experienced with imagej
> until now.
>
> Best
>
> Bertrecht

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[fabrice senger-2]

In addition you may try "Find maxima" this will find you the brightest
spots.

2015-06-25 14:53 GMT+02:00 Bertrecht <[hidden email]>:

> Hi Fabrice,
>
> thank you for the quick response! The Z Project command is absolutely what
> I
> was looking for...nevertheless, with the default settings it is not
> possible
> to determine the area with the maximum increase in intensity - I guess. I
> was checking the spots with the highest standard deviation and they can be
> correlated to areas with the highest decrease in intensity...if there would
> be a setting like "normalized Intensity". Anyway, thank you a lot and I
> will
> look for additional options using the "Z Project"
>
> Bertrecht
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Find-ROIs-with-maximal-intensity-increase-in-a-time-series-tp5013282p5013290.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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