xmipp_transform_downsample (v3.0)


Downsample a micrograph. For volumes use xmipp_transform_geometry. There are several downsampling methods. The most general and recommended is Fourier. Fourier downsampling puts a window in Fourier space. This is the best downsampling that can be performed. Altermatively, smoothing makes color dithering which is pretty good for visualization, but it modifies the particle spectrum. Binning with a rectangle kernel modifies the spectrum of the micrographs and is not recommended. You may see the effects of the different downsampling schemes at this article.

The downsampling factor (--step) is the factor by which the micrograph will be reduced. For instance, a downsampling by 2 will reduce the image size to one half. Using Fourier and smooth you may use non-integer downsampling factors, and the image size will be reduced by 1/factor

See also


-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
--label <image_label=image>
Label to be used to read/write images.
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".
--step <factor>
Downsampling factor. factor=2 reduces the image size to one half. Fourier and smooth support non-integer downsampling factors. Rectangular binning must use integer factors.
--method <mth=fourier>
Method for making the downsampling
where <mth> can be:
  • fourier <numThreads=1> Fourier supports non-integer downsampling factors
  • rectangle This is simple binning in a square of size factor x factor
  • smooth smooth and colordither

Examples and notes

xmipp_transform_downsample -i micrograph.tif -o downsampledMicrograph.tif --step 2

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