biorad1sc_reader

Python Package to read, parse, convert *.1sc files generated by Bio-Rad Quantity One software.

Documentation at: http://biorad1sc-reader.readthedocs.io/

An optional dependency: numpy. If present, image operations in biorad1sc_reader will run 4x to 5x faster.

Also installs the following command-line executables:

bio1sc2tiff

converts *.1sc files to *.tif images. (type bio1sc2tiff --help)

bio1scmeta

reports all metadata contained in each *.1sc file to a text file. (type bio1scmeta --help)

bio1scread

reports details on a *.1sc file's internal structure. (type bio1scread --help)

Current Status

• "Alpha" quality software
  • API subject to change
  • No known problems in operation.
• Reading Image Data OK
• Saving Image from file to new TIFF file OK
  • Reader.save_img_as_tiff()
  • Reader.save_img_as_tiff_sc()
• Reading all metadata OK
  • Reader.get_metadata()
  • Reader.get_metadata_compact()
• Reading certain image Metadata from Data Block 7 OK
  • Reader.get_img_summary()
  • Includes:
    • Scanner Name: <Scanner Name>
    • Number of Pixels: (<img_size_x> x <img_size_y>)
    • Image Area: (<img_size_x> mm x <img_size_y> mm)
    • Scan Memory Size: <total_img_size> Kb
    • Old file name: <old_file_name>
    • New file name: <new_file_name>
    • <File Directory>
    • New Image Acquired
    • Save As...
    • Quantity One <Quantity One Version String>
• python2 (lack of) support
  • I'm currently unwilling to support python2
  • If you'd like python2 support, it's DIY. :)

Examples

# setup reader with input file
import bio1sc_reader
myreader = bio1sc_reader.Reader("my_biorad_file.1sc")

# get list/dict of all metadata in 1sc file
my_img_metadata = myreader.get_metadata()

# get a more succinct data structure of all metadata in 1sc file
my_img_metadata = myreader.get_metadata_compact()

# get a quick summary of some metadata about the image in the 1sc file
my_img_metadata = myreader.get_img_summary()

# Different options for writing image data out as a TIFF file
myreader.save_img_as_tif("unscaled_brightness.tif")
myreader.save_img_as_tif("unscaled_inverted_brightness.tif", invert=True)
myreader.save_img_as_tif_sc("scaled_brightness.tif")
myreader.save_img_as_tif_sc("scaled_brightness_more.tif", scale=0.8)
myreader.save_img_as_tif_sc("scaled_inverted_brightness.tif", invert=True)

File Format Documentation

• File Specification for Bio-Rad 1sc files

Related Info

• Bio-Rad Image Lab Software
  • For Mac, only version 5.x supports 1sc files. (Click on the Download tab to find it.)
• Bio-Rad Quantity One Software
  • Generates 1sc files from Bio-Rad instruments.
• Bio Formats: Bio-Rad Gel 1sc file format
• BioRadGelReader.java source
• Forum post: Bio-Format 1sc to jpg batch conversion
• reStructuredText Syntax