Sample Prep for ZellScanner

Detailed protocols for sample prep can be found at:

Generally, you need to section tissue at 5-7µm onto a coverslip (provided by Unified Flow Core or through Canopy).  If this is frozen tissue (FF), be sure to FIX the tissue before mounting the coverslip onto the chip.  If this is paraffin embedded tissue (FFPE), be sure to BAKE, DEPARAFFINIZE, and PERFORM ANTIGEN RETRIEVAL steps before mounting the coverslip onto the chip.

Do NOT prestain your tissue before bringing it to be scanned.  The procedure is to photobleach the tissue first, acquire a background image, THEN stain, and acquire.

When performing subsequent staining cycles please keep these guidelines in mind:

  • It's a good idea to photobleach and acquire background images within a few days of the NEXT staining cycle. 
  • Make sure your tissue is properly photobleached in each channel you intend to stain in before applying the next stain.
  • Do not acquire data when the sample is in storage buffer; always switch to wash buffer before scanning or bleaching.