Denoising with nd-safir

Summary

DenoiseWeb

Drosophila embryonic epithelium depicted with the cell membrane protein Cadherin. Collaboration with Jose-Maria Urbano (Sanson Group)
 

nd-safir is an image sequence denoising software that can help to improve the signal to noise ratio of your images. 
CAIC has a license and you can find the software on the workstations of the centre.

The steps for using ndsafir on one image (2d or 3d stack) from the command line are:

  1. Open a command prompt (In windows press the Start button and type cmd)
  2. Type: cd C:\ndsafir-3.0-win64 (or replace the path with the directory of ndsafir )
  3. Type: ndsafir -i 'path1\input.tif'  -o 'path2\output.tif' (replace path1, path2, input and output with the values for your particular input image and the desired output image)


In case you would like to apply ndsafir to a timelapse of 3d stacks, open the file ndsafir.m in Matlab and customize the first six lines.

To denoise all 3d stacks in one folder run the matlab script ndsafirDir (in the same folder with ndsafir). The results will be written in the same folder (the filenames will be prefixed with Den). 

You can find more information (other optional parameters,  how to obtain your own licence, etc.)  in C:\ndsafir-3.0-win64\ndsafir_user_guide.pdf or on the  webpage.

Reference:

J. Boulanger, C. Kervrann, P. Bouthemy, P. Elbau, J.B. Sibarita, J. Salamero 

Patch-based non-local functional for denoising fluorescence microscopy image sequences. IEEE Trans. on Medical Imaging, 29(2): 442-454, 2010