[3dem] Help running ccderase

[Cedric Bouchet-Marquis]

Your model is wrong. You have to place a model point on each pixel you want to "erase" and not place points surrounding your bad pixel area.

If you want to avoid making errors when writing the commands, do everything in the GUI of Etomo it is simpler.

Cheers and
Good luck.

Cedric

Sent from my iPhone

On Dec 3, 2012, at 2:06 AM, "Manikandan KARUPPASAMY" <mkaruppa at embl.fr> wrote:

> Hi,
> 
> There are some bad pixels areas in the images collected at 100 kV.
> I would like to replace those pixels by the average value of the 
> neighboring pixels in the image. I tried running the program 'ccderase' 
> of IMOD and could not succeed.
> I made the boundary model in IMOD (please see the attachment, 
> imod_mod.jpg) and run the program as follows.
> 
> $ccderase -model badpixels.mod -boundary input.mrc corr_input.mrc
> 
> The program did not change the pixel values to the average value of the 
> neighboring pixels.
> 
> The ctf correction of the raw image shows spurious rings around these 
> pixels that hinders particle picking.
> 
> Please help me to run ccderase and let me know about any other program 
> which can replace those pixel values.
> 
> with kind regards
> 
> Mani.
> <imod_mod.jpg>
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