Do you mean a stand alone program? We use psoc Creator to make the program source and use it to program the device or board.. There is a stand alone Cypress programming program also. I am not clear what you want to do.
I did try Psoc programmer, but seems it does not support CapSense CY8CMBR3.
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MBR3 devices are preprogrammed and cannot be re-programmed.
You can configure the MBR3 devices using I2C.
Please refer the design guide: http://www.cypress.com/file/46366/download [Section '5. Configuring CY8CMBR3xxx']
Is there any command line interface software for configuring CapSense CY8CMBR3 by using Miniprog3 or USB/I2C cable? Thanks.