biorad1sc-reader 0.1

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

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

Also installs bio1sc2tiff command-line executable to convert *.1sc files to *.tif images.

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

Current Status

• Version 0.1

• “Alpha” quality software

  • API subject to change

  • No known problems in operation.

• Installs command-line executable: bio1sc2tiff (type ‘bio1sc2tiff –help’)

• Reading Image Data OK

• Saving Image from file to new TIFF file OK

• Reading Image Metadata from Data Block 7 OK

  • 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

  • So far code works with python2 if you remove the maxsplit argument from split

  • I’m currently unwilling to support python2

  • If you’d like python2 support, it’s DIY. :)

Documentation

• File Specification for Bio-Rad 1sc files

Examples

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

# get dict of metadata in Data Block 7 of 1sc file
my_img_metadata = myreader.get_img_metadata()

# 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)

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