Line Fit and Plane Fit

[Mahesh Kakuturu]

Hi group,

I am using ImageJ application(1.48v) along with Micro-Manager.
I have an AFM image generated with my controller raw data. I want to apply
and see the difference with Line fit or Plane fit to that image from ImageJ.
I am not quite sure what the Bandpass Filter is doing, but it's doing
something to eliminate dark pixel data. Can some one explain me how to
apply the line fit and Plane fit to the image.
Hopefully this functionality is already existed through menu items
available or through some plug-Ins.
Any help is greatly appreciated.

--
Best Regards,
Mahesh Kakuturu
Sr. Software Engineer
Angstrom Science, Inc.

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

[Michael Schmid]

Hi Mahesh,

well, I don't know much about MicroManager (does it also control AFMs?),
but there is an ImageJ plugin for fitting polynomials. It can also do
plane fits if you select 1st order:
   http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start

The 'Fit Polynomial' plugin also allows you to select which part of the
image you want to use for fitting; e.g. if you have some islands in the
AFM image, you can create a selection excluding them (three widely
separated background patches might be enough) and only use the
background for fitting.


If you want to use Process>FFT>Bandpass filter for a line-by-line
background, you would typically set the following parameters:
- Filter large structures: a large number, larger than your image size
- Filter small structures up to: 0
- Suppress stripes: Horizontal
- Tolerance of direction: about 2% for 256x256 or 512x512 pixels, 1%
above for 1024x1024 pixels and up. A higher number will also suppress
low-frequency wiggles along each scan line (similar to fitting a
higher-order polynomial to each line)
- Checkboxes off

To better see what the Bandpass Filter does, duplicate your image first,
then apply the filter and use Process>Image Calculator (32-bit output)
to subtract the filtered from the original, then you will see what the
background looks like.

If you have 16-bit data that use much of the dynamic range, convert them
to floating point (32 bits) first, otherwise some minima or maxima may
get saturated.

I am not aware of a plugin for a simple line-by-line background ignoring
the slope of the lines; but it should be very easy to write one.

Michael
________________________________________________________________

On 13/07/2017 00:23, Mahesh Kakuturu wrote:

> Hi group,
>
> I am using ImageJ application(1.48v) along with Micro-Manager.
> I have an AFM image generated with my controller raw data. I want to apply
> and see the difference with Line fit or Plane fit to that image from ImageJ.
> I am not quite sure what the Bandpass Filter is doing, but it's doing
> something to eliminate dark pixel data. Can some one explain me how to
> apply the line fit and Plane fit to the image.
> Hopefully this functionality is already existed through menu items
> available or through some plug-Ins.
> Any help is greatly appreciated.
>

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