nCounter Knowledge Base: Assays & Applications

To prepare for delivery and installation of your CosMx SMI instrument, download, review, and sign the CosMx SMI Site Preparation Guide available in NanoString University. Additionally, the CosMx SMI Site Readiness Portal provides an interactive checklist to ensure that you, and your site, are ready for your new instrument.

IT specifications and requirements for the CosMx SMI system are found in the CosMx SMI Site Preparation Guide. For additional AtoMx IT requirements, see the AtoMx SIP User Manual. Note, to use your CosMx SMI the system must be networked so it is crucial that IT specifications are met.

The maximum number of FOVs allowed per flow cell depends on several factors that contribute to the run time of the instrument: the number of flow cells on the instrument, the assay being run, and the software version of the instrument. A CosMx SMI run should not exceed 14 days, with runs of 7-10 days being optimal for the best data quality generation. A CosMx SMI turnaround time estimation table is provided in the CosMx SMI Instrument User Manual for each software version. This table allows you to determine the recommended and maximum number of FOVs per run based on total run time. Please note that the number of FOVs listed in the turnaround time table is the total number of FOVs across all flow cells (not per flow cell). That information can be used to calculate the number of FOVs per slide. The user manual for each software version of the instrument is available in NanoString University.

The run time, or turnaround time, depends on several factors: the software version of the instrument, the assay being run, the number of flow cells, and the number of fields of view (FOV) selected per flow cell. A CosMx SMI turnaround time estimation table has been provided in the CosMx SMI Instrument User Manual for each software version. This table will allow you to determine the estimated turnaround time for your run based on the software, assay, and total number of FOVs selected.