zeisstopnm

Convert a Zeiss cofocal file into either .pgm or .ppm format

$ zeisstopnm [path/to/file]

$ zeisstopnm -[pgm|ppm] [path/to/file]

zeisstopnm [-verbose] [-alphaout alphafile] [zeissfile]

-verbose
    Display progress and processing details on standard error

-alphaout alphafile
    Output an alpha channel mask as PGM or PNM to the specified file

zeisstopnm is a Netpbm utility that converts images from the proprietary Zeiss confocal microscope format to the portable PNM (Portable aNyMap) format, which encompasses PBM (bitmap), PGM (grayscale), and PPM (color) images.

Designed for researchers using Zeiss microscopy systems, it parses the Zeiss file header—containing metadata like dimensions, bit depth, and color information—and extracts pixel data for output. This enables seamless integration with open-source image processing tools in the Netpbm ecosystem, such as filters, converters, and viewers.

The tool reads from a file or standard input and writes to standard output, supporting pipeline workflows. It handles both grayscale and color Zeiss images, automatically selecting the appropriate PNM subtype. An optional alpha channel can be extracted separately for transparency or masking applications.

Zeiss format varies by microscope model and software version; test compatibility with sample files. No error correction for corrupted headers.

If no zeissfile given, reads from stdin; supports single-image Zeiss files.

Automatically PPM for color, PGM for grayscale, or PBM for bitonal based on source data.

Added to Netpbm suite in the late 1990s for scientific imaging support; contributed by researchers to handle Zeiss confocal data as part of ongoing Netpbm expansions for microscopy formats.

pnm(5), ppm(5), pgm(5), netpbm(1)