How to test algorithms

[Adrián Villalba]

Dear colleagues,

How can i test different algorithms simoultaneously in one step?

For example, if i want to test which algorithm of threshold adjusting fits
better in my pic i have to do that manually one by one. Is it possible to
test all at the same time?

Thanks

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[ctrueden]

Hi Adrián,

> if i want to test which algorithm of threshold adjusting fits better
> in my pic i have to do that manually one by one. Is it possible to
> test all at the same time?

For thresholding specifically, the Fiji distribution of ImageJ includes the
Image > Adjust > Auto Threshold command, which lets you "Try All",
producing a mosaic.

For image filtering algorithms in general, one option is to use ImageJ2's
notebook.mosaic method. Here is an example Groovy script which performs
N-dimensional Gaussian blur with various settings, and displays the results
side-by-side in a 2x2 grid:

  // @ImageJ ij
  // @Dataset image
  // @OUTPUT Object mosaic

  // Smudge it up horizontally.
  double[] horizSigmas = [8, 0, 0]
  horizGauss = ij.op().filter().gauss(image, horizSigmas)

  // And now vertically.
  double[] vertSigmas = [0, 8, 0]
  vertGauss = ij.op().filter().gauss(image, vertSigmas)

  // We can also blur the channels.
  double[] channelSigmas = [0, 0, 1]
  channelGauss = ij.op().filter().gauss(image, channelSigmas)

  int[] grid = [2, 2]
  mosaic = ij.notebook().mosaic(grid, image, horizGauss, vertGauss,
channelGauss)

And here is sample output from a downsampled Fluorescent Cells sample:

Of course, you can also just show the resulting images in separate windows.

Regards,
Curtis

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Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
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On Sun, Apr 9, 2017 at 3:48 PM, Adrián Villalba <[hidden email]> wrote:

> Dear colleagues,
>
> How can i test different algorithms simoultaneously in one step?
>
> For example, if i want to test which algorithm of threshold adjusting fits
> better in my pic i have to do that manually one by one. Is it possible to
> test all at the same time?
>
> Thanks
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[gankaku]

Dear Adrián,

if you mean compare with test and you use the Fiji distribution of ImageJ,
then you can have a look at the BioVoxxel Toolbox which offers the
"Threshold Check" comparing the automatic thresholds Curtis already
mentioned and it offers to do that in a visual/qualitative as well as a
semi-quantitative way. There is currently no implementation to test
user-chosen manual thresholds, but I can have a look in my old
repositories. I might still have something like this.
If you wnat to compare image filters you can equivalently have a look at
the "Filter Check" which gives you the chance to run multiple radii for one
specific filter making a comparison somewhat faster.

For more information, please have a look here:
http://imagej.net/BioVoxxel_Toolbox

Kind regards,
Jan

2017-04-09 22:48 GMT+02:00 Adrián Villalba <[hidden email]>:

> Dear colleagues,
>
> How can i test different algorithms simoultaneously in one step?
>
> For example, if i want to test which algorithm of threshold adjusting fits
> better in my pic i have to do that manually one by one. Is it possible to
> test all at the same time?
>
> Thanks
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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CEO: Dr. Jan Brocher
phone:  [phone]
mobile: [phone]
e-mail: [hidden email]
info: [hidden email]
inquiries: [hidden email]
web: www.biovoxxel.de

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