This script is a modified version of https://github.com/johnabel/per2py written by John H. Abel and Yongli Shan. It formats the output table generated by Luminoskan Ascent plate reader from Thermo Scientific for use in per2py, which then analyzes circadian oscillatory data. For installation notes, see per2py_installation.txt.

1. Prepare data for analysis:

   Change LUMINOSKAN output xls file to csv in Excel (save as - text file with separators). Not needed for 2020 and older envs, where xlrd package works.

   Open file PREPARE_LUMINOSKAN.py, for 96-well plate set plate = 96, for 384-well plate set plate = 384. Run by pressing F5, select the path to output (i.e. the unformatted csv table from Luminoskan) and close the selection window, the script will generate file with the same ID_signal.csv in .\data\analysis_output__
   It will also copy the correct XY file from templates folder and rename it.

2. Open file START_ALL.py in IDLE (via conda-per2py environment or using batch file, see per2py_installation.txt.)

3. Change INPUT_FILES = ['ID'] to match your file names ID_signal.csv (ID can be any character string)

4. Change time_factor if needed (for 96 well usually 0.25, for 384 well 1 hour).

5. Change treatment and end_h variables as needed (i.e. start and end times in hours for analysis of selected time intervals).

6. Run by pressing F5 or via menu Run - Run module. It can take a long time on weaker PC and with many traces, be patient. Should beep once everything finished OK.

7. Plots are saved as png (for viewing) and svg (import to Corel Draw), output tables as csv files in .\data\analysis_output__\

8. Remove the analyzed files from .\data\analysis_output__\ before new analysis, otherwise they will be ovewritten.