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.
Also installs bio1sc2tiff command-line executable to convert *.1sc files to *.tif images.
Also installs bio1scmeta command-line executable to report all metadata contained in each *.1sc file to a text file.
An optional dependency: numpy. If present, image operations in biorad1sc_reader will run 4x to 5x faster.
Documentation at: http://biorad1sc-reader.readthedocs.io/
Current Status
- “Alpha” quality software
API subject to change
No known problems in operation.
- Installs command-line executables
bio1sc2tiff (type bio1sc2tiff --help)
bio1scmeta (type bio1scmeta --help)
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 Image Metadata from Data Block 7 OK
Reader.get_img_summary()
- Current info
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)
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