Command-line Utilities

Accompanying this python package are the following command-line utilities, which enable some of the same tasks to be accomplished without writing python code.


bio1sc2tiff

Convert input 1sc file(s) to TIFF image(s).

Usage

bio1sc2tiff [-h] [-s] [-i] [-o OUTPUT_FILENAME] src_1sc_file [src_1sc_file ...]

Positional Arguments

src_1sc_file
Source 1sc file.

Optional Arguments

-h, --help
show this help message and exit
-s, --scale
Scale brightness of output image to maximize dynamic range between darkest and lightest pixels in input file.
-i, --invert
Invert brightness scale of image.
-o OUTPUT_FILENAME, --output_filename OUTPUT_FILENAME
Name of output image. (Defaults to <input_image>.tif) in same directory as source file.

bio1scmeta

Print all metadata contained in 1sc file(s).

Usage

bio1scmeta [-h] [-v VERBOSITY] [-o OUTPUT_FILENAME] src_1sc_file [src_1sc_file ...]

Positional Arguments

src_1sc_file
Source 1sc file.

Optional Arguments

-h, --help
show this help message and exit
-v VERBOSITY, --verbosity VERBOSITY
Verbosity of report, number, 0, 1, or 2 (default 0).
-o OUTPUT_FILENAME, --output_filename OUTPUT_FILENAME
Name of output text file. (Defaults to <filename>_meta.txt in same directory as source file.

bio1scread

Read/Parse Bio-Rad *.1sc file(s) and produce reports detailing their internal structure. Reports for <filename>.1sc are placed in <filename>_reports directory.

Usage

bio1scread [-h] [-S] srcfile [srcfile ...]

Positional Arguments

srcfile
Source 1sc file(s).

Optional Arguments

-h, --help
show this help message and exit
-S, --omit_strings
Do not include Type 16 String fields in reports. (But include the strings when listing references to them.)