iltering) is a tool for denoising and pre-segmenting noisy electron microscopy tomograms. It could also be successfully applied to X-ray tomography and other imaging techniques where gray scale images are used. XMS supports both 2D and 3D images and is able to deal with different image formats including SPIDER
, IMAGIC, etc.. File name extensions are used to infer which file format is being used for both reading and writing.
Getting the software
XMSF can be obtained in two different ways:
- As a stand-alone statically compiled executable: executables are provided for Linux. Just copy to any destination folder you want, add specific environment variables and use it.
- As part of the Xmipp image processing software package: Go to Xmipp page, download the software and compile it following instructions. The program will the be invoked as 'xmipp_mean_shift'.
XMSF is a command-line application. Whether you are invoking it from the Xmipp installation or from the stand-alone application, the set of arguments to pass to it are:
- -i [image in] OR [volume in] Input image or volume to be filtered. Different image formats are admitted (image format is inferred from file name extension)
- -o [image out] OR -o [volume out] Where the result is written. Different image formats are admitted (image format is inferred from file name extension)
- -hs Maximum distance between neighbor pixels to be taken into account. If not provided, a default value of '6' is used.
- -hr Maximum color distance between adjacent pixels to be taken into account. If not provided, stddev is calculated for the input image and is used as the default value.
- -thr Number of threads to use. If not provided, one (sequential algorithm) is used
- -use_gauss Use gaussian normal kernels instead of the faster computing method. This method implements the original mean-shift algorithms without performance improvements.
- -iters Number of iterations to be performed. If not provided one is used.
- -save_iters Save resulting filtered volume after each iteration. If not provided, just an output volume is created at the end of the process.