Alternate Entrypoints to PalmettoBUG Tutorials

Besides the core imaging pipeline, there are alternate ways of starting a PalmettoBUG analysis, such as directly from FCS files from solution-mode CyTOF or from a CSV file exported by PalmettoBUG (which allows the easy transfer of a single-cell analysis from one copy of PalmetotBUG to another). Note that loading from a CSV does not allow spatial analysis (only single-cell analysis).

Additionally, there are some side-functionalities of PalmettoBUG that are illustrated here – converting the back-up text files exported by the Hyperion system into .tiffs, and performing bead-normalization on CyTOF FCS files. These tutorial notebooks do not use example data, depending on your own data to test.

The order of these notebooks is not important for their execution, except the AnalysisFromCSV does depend on an exported CSV file from the “AnalysisFromFCS” tutorial.

Contents:

• Reading Back-up Text Files to TIFFs
• Bead Normalization through PalmettoBUG
  • CHANGE The following directory to match an existing directory on your computer if you are testing this tutorial on your own machine!
• Loading for Single Cell Analysis Directly from FCS files
  • CHANGE The following directory to match an existing directory on your computer if you are testing this tutorial on your own machine!
    • Create new CyTOF directory, fetch and load example FCS data:
    • Example Plots:
• Loading a Single-Cell Analysis from a CSV
  • CHANGE The following directory to match an existing directory on your computer if you are testing this tutorial on your own machine!
    • Set up CSV project directory and load from exported data
    • Do Analysis steps on loaded data!
    • The cell clusterings from the exported data are still available
    • But we can still re-cluster the data if we like