Re: Line Fit and Plane Fit

Posted by Michael Schmid on Jul 13, 2017; 8:00am
URL: http://imagej.273.s1.nabble.com/Line-Fit-and-Plane-Fit-tp5019057p5019058.html

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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