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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: 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

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Filename, size & hash SHA256 hash help File type Python version Upload date
biorad1sc_reader-0.6-py3-none-any.whl (33.9 kB) Copy SHA256 hash SHA256 Wheel py3 Nov 15, 2017
biorad1sc_reader-0.6.tar.gz (27.8 kB) Copy SHA256 hash SHA256 Source None Nov 15, 2017

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