Shannon Entropy Analysis
To characterize microscope performance, we calculate the Shannon Entropy across a time series of maximum intensity projections. Here, we describe our script to perform this analysis.
Running the Python script
To run the script, please provide the filenames where the data is saved (parentfolder) and where the Excel file with the Shannon Entropy values should be saved.
parentfolder = "~/timeseriesfolder"
result_xlsxfile = "~/analysis/ShannonEntropyValues.xlsx"
The data in the parentfolder should be organized in the following way:
.
|-- timeseriesfolder
| |-- t00000.tif
| |-- t00001.tif
| |-- t00002.tif
| |-- t00003.tif
....
Output
The script will generate a plot of the Shannon Entropy values over time and save the plot and the data as an Excel file.
Testdata set for PSF characterization
Test data is available for the calculating the Shannon Entropy of bead images in the folder Exemplary_ShannonEntropy/timeseries.
- on Synapse:
- or Zenodo: