biorad1sc-reader 0.7.0

Description:

biorad1screader 0.7.0

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