Extracting Height Profile from Interference Fringes

[cyang]

Hi all,

I've only recently started using ImageJ and am new to various image processing techniques. We were hoping to use ImageJ to to help us analyze interferometry fringe images (sample image attached) and generate height profiles.
NDFiltered.tiff
I was looking through the old ImageJ forum threads and some others had previously asked about plugins that could be used to help with image processing a long time ago but I could not find too much about it. Anyone have any suggestions?

Thank you!
Cassidy

[Romain Guiet]

Hi Cassidy,

If you want to measure height profile you should consider to take image without saturation.
The image you enclosed to your e-mail is highly saturated and thus measurements are not possible anymore.
You can have a look to : http://jcs.biologists.org/content/120/10/1703.full
where you can see that : "Similarly, if laser powers, lamps, PMT gains or camera exposures are set too high, detectors can be saturated and features within images can be lost. Most software programs offer a high/low or range finder look-up table (LUT) where blue pixels read zero intensity and red pixels are saturated. The image acquisition parameters should be set so that no detection channel shows pixels reading zero or saturated levels. "

Regarding generating height profile you can use imagej, draw a line and get a line profile (analyse -> plot profile). Is that what your are looking for ? or do you have something more specific in mind ?

Regards,

Romain



---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

________________________________________
De : ImageJ Interest Group [[hidden email]] de la part de cyang [[hidden email]]
Envoyé : samedi 8 août 2015 02:50
À : [hidden email]
Objet : Extracting Height Profile from Interference Fringes

Hi all,

I've only recently started using ImageJ and am new to various image
processing techniques. We were hoping to use ImageJ to to help us analyze
interferometry fringe images (sample image attached) and generate height
profiles.
NDFiltered.tiff
<http://imagej.1557.x6.nabble.com/file/n5013957/NDFiltered.tiff>
I was looking through the old ImageJ forum threads and some others had
previously asked about plugins that could be used to help with image
processing a long time ago but I could not find too much about it. Anyone
have any suggestions?

Thank you!
Cassidy



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View this message in context: http://imagej.1557.x6.nabble.com/Extracting-Height-Profile-from-Interference-Fringes-tp5013957.html
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[John Oreopoulos]

Hellow Cassidy,

I agree with the same comments by the previous poster - try to avoid saturation of the image. However, in other parts of the image you submitted, there are clear interference patterns which presumably are due to height differences within the sample and how the light interacts with it (is this a thin film of some material, or something else?).

I think what you're doing here is a version of what is known as "Reflection Interference Contrast Microscopy" (RICM) or "Interference Reflection MIcroscopy" (IRM). Do a google search on that and you'll find many publications that describe the mathematical framework on how to extract height information from these types of images.

In terms of using ImageJ to do this, as far as I know, there are no plugins written specifically for that type of analysis, but it should be straightforward to write a macro or a plugin to do that for you. Ie: the tools to perform the necessary calculations on a RICM/IRM image are there on a pixel-by-pixel basis.

John Oreopoulos
Staff Scientist
Spectral Applied Research Inc.
A Division of Andor Technology
Richmond Hill, Ontario
Canada
www.spectral.ca



On 2015-08-10, at 4:25 AM, Romain Guiet wrote:

> Hi Cassidy,
>
> If you want to measure height profile you should consider to take image without saturation.
> The image you enclosed to your e-mail is highly saturated and thus measurements are not possible anymore.
> You can have a look to : http://jcs.biologists.org/content/120/10/1703.full
> where you can see that : "Similarly, if laser powers, lamps, PMT gains or camera exposures are set too high, detectors can be saturated and features within images can be lost. Most software programs offer a high/low or range finder look-up table (LUT) where blue pixels read zero intensity and red pixels are saturated. The image acquisition parameters should be set so that no detection channel shows pixels reading zero or saturated levels. "
>
> Regarding generating height profile you can use imagej, draw a line and get a line profile (analyse -> plot profile). Is that what your are looking for ? or do you have something more specific in mind ?
>
> Regards,
>
> Romain
>
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP)
> Ecole Polytechnique Fédérale de Lausanne (EPFL)
> Faculty of Life Sciences
> Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
> http://biop.epfl.ch/
> ---------------------------------------------------------------
>
> ________________________________________
> De : ImageJ Interest Group [[hidden email]] de la part de cyang [[hidden email]]
> Envoyé : samedi 8 août 2015 02:50
> À : [hidden email]
> Objet : Extracting Height Profile from Interference Fringes
>
> Hi all,
>
> I've only recently started using ImageJ and am new to various image
> processing techniques. We were hoping to use ImageJ to to help us analyze
> interferometry fringe images (sample image attached) and generate height
> profiles.
> NDFiltered.tiff
> <http://imagej.1557.x6.nabble.com/file/n5013957/NDFiltered.tiff>
> I was looking through the old ImageJ forum threads and some others had
> previously asked about plugins that could be used to help with image
> processing a long time ago but I could not find too much about it. Anyone
> have any suggestions?
>
> Thank you!
> Cassidy
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Extracting-Height-Profile-from-Interference-Fringes-tp5013957.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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