Hi Jonathan,
you might remember that we initially had to set the sample exchange to 1 sample for the CryoARM300, since we could not directly communicate from your software or SerialEM with the specporter.
By now there is a semi-official executable floating around which can, if not for all at least for most CryoARMs, control the sample specporter. In particular it can query the content of the stage, sample storage and magazine. It also can send commands to change the samples based on the ID in the storage system.
I think it would be great if this can be incorporated in your system, so that JEOL user can also benefit from the full sample storage.
What we currently do is in SerialEM call a shell script with a set of commands and that script communicates with the CryoARM. So either, your software can call the same script or if JEOL is willing (and I can get you in contact with the right people) just send the proper commands directly through your software (i.e. rewriting that shell scripts in your software).
Let me know
Cheers
Marcus