## 2 System Overview  
A typical cabled JSATS system consists of acoustic microtransmitters, four hydrophones, four cables, a signal conditioning interface/amplifier, JSATS detector using digital signal processing (DSP) + field-programmable gate array (FPGA), a Global Positioning System (GPS) receiver, data acquisition computer, and decoder software (Figure 1). The acoustic microtransmitter, surgically implanted in the fish [23, 24], translates a programmed binary code into an acoustic message. The acoustic signal is transmitted through freshwater at approximately 1,500 m/s. When the study fish implanted with the microtransmitters travel within the detection range of the deployed receivers, the acoustic signals in the form of sound pressure levels are converted into a very low analog voltage by the piezoelectric sensors at the tip of the hydrophones [25, 26]. The four hydrophones, deployed underwater in a known fixed geometry, have an internal preamplifier that amplifies the low analog voltage signal. These hydrophones are connected by cables to a signal conditioning interface. The pre-amplified analog signal is then transmitted to the signal conditioner for further amplifying and conditioning prior to being input to a DSP + FPGA card resident in the data acquisition computer for detection analysis. The signal conditioning interface and the JSATS detector using DSP + FPGA are both designed to simultaneously process the data from all four receiver hydrophones. The times of receipt of candidate encoded messages at hydrophones in a multisystem array are synchronized across the array to submicrosecond accuracy using GPS receivers (Meinberg GPS 170 PCI, Meinberg Funkuhren GmbH & Co. KG, Bad Pymont, Germany). _Detection_ is the decision whether to collect a portion of the incoming signals. The process of detection analysis is described in detail in Section 3.4. The first step in detection is digitization of the received analog signal. Processing algorithms evaluate the stream of digital data to identify candidate  
Figure 1: JSATS cabled system schematic showing main components and direction of signal acquisition and processing. microtransmitter messages. Portions of the signals entering the DSP + FPGA that do not pass candidate microtransmitter identification criteria are classified as noise and ignored. If criteria for a candidate microtransmitter message are met, the DSP grabs a high-resolution time stamp from the GPS clock that corresponds to the initial receipt of the candidate microtransmitter message. The data is now a digitized waveform represented as a series of short integers (16 bits) and a high-precision time stamp acquired from the GPS clock card. The digital candidate microtransmitter message waveform is sent to the data acquisition computer and saved to disk in a custom format called the binary waveform format. The structure for a candidate message waveform file contains a header and a data payload. The header describes the data payload and the instruments used to digitize the analog waveform (e.g., the analog-to-digital converter resolution or number of hydrophone data the file contains). The data payload is where the digitized signal is stored. A binary format is selected to save hard drive space. Once stored as a binary file, the candidate message data is available for decoding. The decoding software reads the binary file and converts the data from short integer format into double floating-point format for better accuracy. The decoding software then processes the saved waveform file searching for valid microtransmitter messages. Each detected message is given a relative and absolute TOA. The relative TOA is the start of the decoded microtransmitter message time in microseconds relative to the start of the complete candidate message waveform file. The absolute TOA is the time of the start of the decoded microtransmitter message in seconds from the start of the day with microsecond fractional time information.