During a sequencing run, blocking of the nanopores can occur. In such cases, the pore activity plot will show an increase in inactive channels over time and the pore scan plot will show an increase in unavailable pores (in turquoise). Below is an example.

This increase in unavailable pores means the nanopores are becoming blocked over time. This indicates an issue with the sample (extraction, library prep). If you experience this and you would like to recover the nanopores being lost to this state, then a wash is recommended to digest the DNA in the flow cell, including that which is blocking the nanopores.

The flow cell wash kit, which is designed to wash MinION and PromethION Flow Cells, contains a nuclease and removes 99.9% of the initial library. Please see here for the full protocol for washing a flow cell.

For further considerations on blocking, unblocking, and flow cell output, please see this post on the Community.