The answer to this question depends on what type of interrupts you are using.
The legacy line-based interrupts used on PCI based devices will perform this task just fine.
The MSI interrupt scheme, used on PCIe based devices, will not support separate interrupts on separate channels from separate application threads. It will, however, support MSI interrupts for separate channels from a single application thread.
For Windows users who wish to field separate MSI interrupts from separate application threads on separate channels, you must modify the device .inf file to force the card that uses MSI interrupts to instead use line-based interrupts to achieve that goal. Refer to this
For Linux or other OS users, we do not have that option at this time.