Acquisition Templates - how do you handle these?
Posted: Wed Nov 20, 2019 3:43 pm
Hi all,
How do you currently program the acquisition template into the CyTOF software?
e.g. I'm thinking of the following scenarios / options:
1) User sits with operator @ CyTOF and verifies that acquisition panel is correct.
2) User creates template using "offline" copy of CyTOF software and operator loads the .tem file from this.
3) User provides operator with Excel template.
4) User simply e-mails a list to the operator.
In cases 1 & 2, the user is thus responsible for ensuring their panel is correct.
In cases 3 & 4, the operator could be blamed for any mistakes.
Case #1 = Probably easiest and I would guess most common?
Case #2 = Easiest for operator. Potentially annoying for user.
Case #3 = Potentially annoying for Operator, easy for user.
Case #4 = Potentially very annoying for operator. Easiest for User?
I've devised a method that I hope achieves the following:
1) Easy for user.
2) Provides some guidance / basic checks to both the user and operator (e.g. if they've forgotten to add Ir / Pt / bead channels / all barcodes, presence of illegal characters).
3) Easy for operator (load a .tem file, rather than program the template in the CyTOF software).
4) Ensures that the user is primarily responsible for ensuring panel is correct.
UPDATE - web app built and tested - see post below.
So far, I've built a spreadsheet that the user fills out by marking which isotopes are in their panel and what they want them named / labelled.
It includes all the existing Fluidigm isotopes (including the new Cd).
It's "pre-loaded" with the compulsory bead channels, Ir and Pt, but the user could change these if they wish.
It provides some basic instructions to the user, as well as some "sanity checks" (e.g. the illegal symbols in CyTOF software are found and the user alerted)
Once sent to the operator, an R-script reads the Excel file, re-runs the sanity checks and spits out a .tem file that the operator simply opens on the CyTOF.
Intrigued at other's input to what method they currently use and whether my method would be useful for anyone else? (I don't know how common R would be for operators, but I've found it both useful and fun!).
How do you currently program the acquisition template into the CyTOF software?
e.g. I'm thinking of the following scenarios / options:
1) User sits with operator @ CyTOF and verifies that acquisition panel is correct.
2) User creates template using "offline" copy of CyTOF software and operator loads the .tem file from this.
3) User provides operator with Excel template.
4) User simply e-mails a list to the operator.
In cases 1 & 2, the user is thus responsible for ensuring their panel is correct.
In cases 3 & 4, the operator could be blamed for any mistakes.
Case #1 = Probably easiest and I would guess most common?
Case #2 = Easiest for operator. Potentially annoying for user.
Case #3 = Potentially annoying for Operator, easy for user.
Case #4 = Potentially very annoying for operator. Easiest for User?
I've devised a method that I hope achieves the following:
1) Easy for user.
2) Provides some guidance / basic checks to both the user and operator (e.g. if they've forgotten to add Ir / Pt / bead channels / all barcodes, presence of illegal characters).
3) Easy for operator (load a .tem file, rather than program the template in the CyTOF software).
4) Ensures that the user is primarily responsible for ensuring panel is correct.
UPDATE - web app built and tested - see post below.
So far, I've built a spreadsheet that the user fills out by marking which isotopes are in their panel and what they want them named / labelled.
It includes all the existing Fluidigm isotopes (including the new Cd).
It's "pre-loaded" with the compulsory bead channels, Ir and Pt, but the user could change these if they wish.
It provides some basic instructions to the user, as well as some "sanity checks" (e.g. the illegal symbols in CyTOF software are found and the user alerted)
Once sent to the operator, an R-script reads the Excel file, re-runs the sanity checks and spits out a .tem file that the operator simply opens on the CyTOF.
Intrigued at other's input to what method they currently use and whether my method would be useful for anyone else? (I don't know how common R would be for operators, but I've found it both useful and fun!).