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Allows reading Bio-Rad *.1sc image/analysis files.

Project description

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

Documentation at:

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

Also installs the following command-line executables:


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


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


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. :)


# 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_inverted_brightness.tif", invert=True)
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)

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