tm2od

Convert transmission to optical density for digitized micrographs

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Uses the proc2d program from the EMAN package to invert density and convert transmission values to optical densities for digitized micrographs scanned with Nikon scanners. Micrograph files should be in TIFF format.

061005 mktemp compatibility issue fixed

Usage example:

$ tm2od
Usage: tm2od [ -a ] [ -c ] [ -m ] [ -s ] file1 [ file2 file3 ... ]
This program uses proc2d from the EMAN package to invert density
and convert transmission values to optical densities for micrographs
scanned with Nikon scanners.

Options:
  -a    append filenames with 'o' or 'oi' to indicate treatment
  -c    don't invert density (for cryo)
  -m    output MRC format instead of IMAGIC
  -s    output SPIDER format instead of IMAGIC

Requirements:
Input file should be in 16-bit TIFF format.
Output files are in IMAGIC format by default.
proc2d must already be in the user's executable path.
$ tm2od -a 100.tif
tm2od: 100.tif: processing... inverting density... writing 100oi.img