A web-based (Shiny) interface to create CyTOF .tem files.
This allows (hopefully) easy creation of .tem files, which can then be loaded onto a CyTOF system for acquisition.
Last updated: 26th Feb 2021.
I no longer work with CyTOF data, so this is unlikely to be updated further
- It seems unnecessary to download and install (CyTOF) software on an offline system to create an acquisition template.
- Creating a template at the machine (based on an e-mail or Excel file from a user) is risky unless the user is present to verify.
- There is no error-checking in the CyTOF software (e.g. it's easy to miss essential channels, such as EQ beads).
- Just for fun! It's the first time I've built and uploaded a Shiny app.
- Default template containing common contaminants, barcodes and Cell ID (Live/Dead, Ir).
- Quickly create template for the Direct Immune Profiling Assay.
- Upload template from Excel file (file must have headers for columns and mass/element in first column; target/markers in second column).
- Upload template from existing tem file.
- Easy Add/Remove of Barcodes, Cell-ID, Bead (EQ), Contaminants and Blank (M +/- 1 plus isotopic impurities and +16 oxidation) channels.
- Easy swap of Live/Dead marker (Pt195 or Rh103).
- Lookup of isotope by mass or name.
- Sorting of Panel by mass or name.
- Save as .tem file ready for use on CyTOF.
Checks to ensure that:
- All essential normalisation channels are present.
- Illegal characters are not present in the Target names. (This is a limitation imposed by CyTOF software).
- Cell ID (Ir) is present.
As with any software, this may have bugs and is used at your own risk.
This is not an official product of nor endorsed by Fluidigm or anyone else.
Before acquiring any data on an instrument, you should double-check that all channels / parameters are present!
Having said that, this tool was specifically designed to reduce the likelihood of missing channels. It's more likely that you will acquire more data using this template creator!
Tested on a Helios running CyTOF software version 6.7.1014 and 7.0.8493, using default Event mode parameters.