Preprocessing

The original images were in .C01 microcopic format stored on Swestore.

Access to Swestore

For accessing Swestore, we have used two different tools.

First, we have used lftp through terminal:

lftp https://username@webdav.swestore.se/snic/folder/

For downloading whole plate we used:

get plate_number.tar.gz

For uploading files we have used:

put plate_number.tar.gz

The other way to access files on Swestore was winscp tool which is a win-based tool.

WinSCP

For extracting and converting the format of images we have used “bfconvert” function of bftools command line tool.

This is conducted through command line or preprocessing/extract_conversion.py script and subprocess library.

The following command should run over images after bfconvert command to normalize images to 8-bit format,

ls *.png ; while read file; do convert file -auto-level  -depth 8 -define quantum:format=unsigned -type grayscale file; done

or through extract_conversion.py script.

For a correct, complete plate we should have A-P rows as well as 01-24 columns (6144).

plate

with the following command we could see if each well (A01-P24) and 16 images per well exist.

ls | cut -d _ -f 3 | cut -b 1-3 | sort |  uniq -c 