RFID system with Bpod

Noa

Hi,
I am considering using Bpod for an automated behavioral system for mice in the home cage environment.
Meaning that multiple mice can freely enter the behavioral corner (one at a time), and we are using the RFID tags in order to identify the individual mice performance, and to control different task parameters for individual mice according to their performance. The RFID reader emits digital output (unique string of digits per mouse), and should be constantly searching for reads.

My question is how to connect the RFID to the Bpod? in order both to sync the timing of the read with the Bpod events, and to trigger different task according to the individual reads.

Thank you!
Noa

Josh

Hello Noa

First you should interface your RFID reader with MATLAB. Which model are you using?
Once you have the ability to poll for reads from the MATLAB command line, you would create a loop. In pseudocode,

while(1)
If NewReadAvailable
MouseID = ReadRFID
RunMyProtocol(MouseID)
end
end

where RunMyProtocol is a custom function to set up and run the correct protocol from the command line with the correct settings.
At the moment, protocols are easy to initialize from the launch manager, but the command line launch tool is broken and needs to be updated, to be compatible with the latest improvements. Until it is ready, a protocol that isn't initialized from the launch manager will have to be set up in your code. To see how this is done, in the beta repository branch, see the LaunchProtocol function in /Bpod/Functions/Launch Manager/LaunchManager.m

Hopefully we'll have the single-command launch function fixed and standardized in the near future.

Josh

Noa

Josh wrote[quote='Josh' pid='176' dateline='1493556699']
Hello Noa

First you should interface your RFID reader with MATLAB. Which model are you using?
Once you have the ability to poll for reads from the MATLAB command line, you would create a loop. In pseudocode,

while(1)
If NewReadAvailable
MouseID = ReadRFID
RunMyProtocol(MouseID)
end
end

where RunMyProtocol is a custom function to set up and run the correct protocol from the command line with the correct settings.
At the moment, protocols are easy to initialize from the launch manager, but the command line launch tool is broken and needs to be updated, to be compatible with the latest improvements. Until it is ready, a protocol that isn't initialized from the launch manager will have to be set up in your code. To see how this is done, in the beta repository branch, see the LaunchProtocol function in /Bpod/Functions/Launch Manager/LaunchManager.m

Hopefully we'll have the single-command launch function fixed and standardized in the near future.

Josh

Thank you for your answer,
At the moment we are considering several options for the RFID reader, so I don't know yet what model we will be using. One options is the "ANT-C40 Circular Single Coil Antenna with 40 mm dia." of TROVAN. http://www.trovan.com/animal/fixed.html

Regarding your suggestion, I want to make sure I understood correctly - you suggest the RFID reader will not be connected to the Bpod but only to the PC? and will activate a protocol upon identification of a RF read?
If so, what so you think is the best way to sync the precise timing of the reads with the Bpod events?

Josh

Hi Noa

If the RFID reader is only used to start a behavior session, you won't need to synchronize its timestamp with Bpod events - you can use MATLAB's now() function to grab a MATLAB timestamp immediately after each read, and save it with your data (BpodSystem.Data.RFIDTimestamp = now; ). Bpod's data file automatically stores its own copy of now(), measured when the first trial of the session was started.

I would caution against using an RFID reader to measure behavioral events during a trial (i.e. choices between 2 spatial locations). My experience with this one was that large tags are read reliably, but with small (glass, implantable) tags, the reader did not always detect the tag immediately and would take a noticeably random amount of time to register. It was also bad at situations where there were multiple tags in range - instead of detecting two, it would read 1 at random and then ignore both until they were removed from its range. Definitely validate your reader before you rely on its timing.

-Josh