tm2od

Convert transmission values 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. Micrograph files should be in 16-bit TIFF format.

The proc2d operation used is calibrated specifically for Nikon Coolscan scanners, so tm2od should not be used for images digitized using other scanners.

10.05.06 Update: 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 Coolscan 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