conversion of a bunch of xmipp particle files (.xmp) into a multi-image purdue image format (.pif) file

Submitted by dieter on Thu, 2011-05-19 10:10

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Electron Microscopy and Image Processing

Hi,
I need to convert a bunch of picked single particle images (from each micrograph) from Xmipp (.xmp = Spider format) into the multiple-image Purdue Image Format (.pif). I have so far used em2em that gives me a file looking fine in bshow. At least all images are displayed and the grey values seem OK. However, when looking at the file with robem (the GUI for particle picking etc. of the Purdue package Auto3dem) I just see one single image that is essentially black and white without any grey values. Does anybody know how to convert these formats into each other? I'd like to process images pre-processed with xmipp by using auto3dem.
Thanks a lot for hints,
Dieter

dieter Mon, 2011-05-23 11:19

Hi Alexis,
thanks for the hint! Yes, I tried bsoft but did not find out how to tell the program to use a bunch of files instead of just one. "*.mrc" does not work and giving the filenames in a row (one after the other) does not work either. I managed to split a multi-image file (e.g. an imagic file) into the single files but did not manage the contrary!
Best, Dieter

Alexis Mon, 2011-05-23 11:30

Hi Dieter,
I often use the bcat command to "merge" many mrc files into a single img file. Something like "bcat -output test.img input*.mrc".
You could then try something like "bimg test.img test.pif" or equivalent with bconvert.
HTH

dieter Mon, 2011-05-23 17:07

Hi Alexis,
this is indeed a very easy way of conversion of single images into a multi-image file. However, although all images appear in bshow and seem to be correct, robem appearently fails to recognize them as 'true multi-image pif'. It simply says "can't read image"....
I have also tried to convert the xmipp particle files into mrc files with em2em and then to use the conversion tool in autopp (also from auto3dem) but again, robem cannot read it!
Dieter

dieter Wed, 2011-10-19 00:47

Hi Javier,
sorry for not having answered your forum post so far. I must have overlooked the original mail but got a reminder by Niko now:

I am sorry to tell you that we have not found a solution. As pointed out above, something must be wrong with the converted files since the .pif files (stack of single particle images) made with bconvert from the single particle .spi files extracted from a micrograph do not look ok in Robem, which is the GUI for CTF correction etc. contained in the Auto3dem package. Interestingly, though, they appear identical to the original images when viewed in bshow (at least by visual inspection).

After having switched from Auto3dem to Xmipp, I just wanted to see whether the preprocessed single particle Xmipp files would give the same reconstruction when using Auto3dem upon their (necessary) conversion into the .pif format. Since the conversion did not work, I finally gave up and thus could not find out why the results obtained with Auto3dem were different from those obtained with Xmipp (that are correct).

Best, Dieter