APM Help Files

119 Pages·2014·6.27 MB·English

What's New Page 1of 2
What's New in Software Version 2.07
(cid:122) Added the option to selectively read digital inputs only when a strobe event occurs.
(cid:122) Added the option to synchronize the spike and strobe event timestamps such that even if spikes
undergo a greater amount of processing than strobe events, they are sent out via TCPIP or saved in
the data file in the same order in which they are received.
February 2012
Version 2.06
(cid:122) Fixed issue related to the digital inputs not working.
August 2011
Version 2.05
(cid:122) Windows certified APM-02 driver.
(cid:122) Eliminated the possibility of missing received strobes.
March 2011
Version 2.04
(cid:122) Fixed serial buffer overflow while data acquisition was temporarily disabled.
(cid:122) Fixed inconsistent timestamps for serial data and digital events received at the beginning of a
recording or a trial or whenever timers were reset.
June 2009
Version 2.03
(cid:122) Implemented a non-linear adaptation of the stimulus artifact/line noise replica that operates under
input saturation condition.
(cid:122) Implemented multi-byte messaging for the APM serial port.
(cid:122) Implemented cancelling of the waveform acquisition in progress when resetting timers though
software or hardware, such that waveforms triggered before reset but ending up after the reset will
not be recorded any more. This affected a small number of waveforms that happen to be acquired
right when timers were reset.
(cid:122) Updated the APMReadData Matlab script to allow returning a single LFP vector containing all LFP
data on first trial only, which is now the default option when calling the function.
January 2009
Version 2.02
(cid:122) Implemented an option to adjust the Spike Acceptance Pulse duration.
(cid:122) Implemented an algorithm to delay the Spike Acceptance Pulse duration with a specified amount of
time.
(cid:122) Timestamps (without waveforms) can be now saved into the data files in Plexon format on a
separate event channel. At the same time, they are streamed over TCPIP for online analysis.
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What's New Page 2of 2
(cid:122) Fixed incorrect voltage calibration displayed at startup.
(cid:122) Occasional failure of the firmware upgrade process due to non-hardware causes has been fixed.
(cid:122) Additional information has been added to the recorded files: firmware type and version, digital filter
settings, adaptive line noise filter on/off, channel's serial number.
(cid:122) Fixed missing information (incuding trigger level and discriminator window position) in the data
files, when recording in gated mode.
August 2008
Version 2.01
(cid:122) A problem with the application not working on a computer that did not have Microsoft Office
installed has been fixed.
May 2007
Version 2.00
(cid:122) The software version 2.00 supports the new APM hardware version 2. It implements all the
functionality of the APM-01, plus a number of other features.
(cid:122) Extended number of digital inputs: 16 digital inputs per channel that can be configured as a strobed
word (up to 16 bits), individual event inputs, or combined event/strobed inputs. The 16-bit digital
inputs come in addition to the standard Gate, Sync and Validate inputs.
(cid:122) Line and stimulus artifact suppressor sync signal inputs separate from the event inputs.
(cid:122) Enhanced USB communications, using high-speed USB2.0 standard.
(cid:122) Increased analog input range, up to +/-10V.
August 2005
©2005-2011 FHC, Inc
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Overview Page 1of 16
Overview
Features
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System Description
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Front Panel
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Back Panel
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Multichannel System
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APM Features
(cid:122) Two pre-programmed modes of neural spike discrimination:
(cid:123) Slope/Height Window Discrimination detects and records any waveform that passes through a
user-defined time/amplitude window.
(cid:123) Adaptive (follows changes in waveform shape, such as caused by electrode drift) Template
Matching detects and records up to four different spikes based upon their shape.
(cid:122) Records LFP (Local Field Potential) data simultaneously with spike data, on the same channel by
using selective digital filtering of the raw input signal.
(cid:122) Allows user to implement their own detection/processing algorithms. Growing downloadable library
of user-contributed algorithms in standard C programming language located at
www.neurocraft.com.
(cid:122) Built-in adaptive stimulus artifact suppression functionality.
(cid:122) Adaptive line noise suppression functionality when used with the LSG Line Sync Generator (ordered
separately).
(cid:122) 64 tap bandpass finite impulse response digital filter with continuously adjustable low-pass and hi-
pass filters. Frequency range of DC to 20kHz.
(cid:122) User selectable gain from x1 - x120 .
(cid:122) Upgradeable firmware through the user-programmable FLASH memory.
(cid:122) Trigger on positive/negative signal slope or on peak/valley. Automatic trigger mode aids in
searching for units.
(cid:122) Real-time advanced signal processing by a dedicated 32 bit Digital Signal Processor (DSP).
(cid:122) Up to 48 kHz sample frequency fine sampling of the analog signal, 16 bit resolution for input and
output.
(cid:122) Online waveform display; no additional oscilloscope is required.
(cid:122) 16 bit general-purpose digital input port.
(cid:122) Onboard high speed USB port for direct connection to PC. No need for add-on PC boards, no
interrupt or address conflicts.
(cid:122) Multiple data storage options: waveforms and/or timestamps. Data can be saved in several formats
for use with standard analysis programs. (Matlab, Neuroexplorer, etc.)
(cid:122) Built-in TCP/IP data server allows other applications to retrieve data, and insert digital messages
(ex. behavioral data) into the recorded data file.
(cid:122) Compact, modular, desktop or rack mountable.
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Overview Page 2of 16
(cid:122) Multi-channel backplane version available with built-in power and USB HUB's.
Description
The APM (Acquisition/Processor Module) is a stand-alone digital neural spike discriminator with integrated
digital gain and filtering capabilities. It can be used as a direct replacement for existing analog window
discriminators. It can detect any activity within an adjustable time/amplitude "window", or up to 4
individual spikes with template matching per channel. When used with the SCP Single Channel Preamp
components, the APM is a complete single channel neural recording system. (please refer to
www.neurocraft.com for more information on this system.)
All functions of the APM are implemented in the hardware and DSP firmware of the unit. The 32 bit DSP
allows real time processing of signals on board, with no data processing performed on the host PC. The
flexible architecture of the software allows the user to develop customized algorithms. The user-
programmable FLASH memory allows expansion of basic functionality by a simple firmware upgrade
process. A web-based users group is established (www.neurocraft.com) for a free exchange of software,
under an open-source policy.
Two modes of spike discrimination can be selected: Slope/Height Window Discrimination, or Adaptive
Template Matching (ATM). In window discrimination mode, an acceptance window is placed in an area
where only relevant waveforms pass through it. Only those waveforms will be recorded. The acceptance
parameters (trigger, amplitude etc.) can be changed at any time during the experiment (not allowable in
all recording formats). This allows for changes in spike shape due to electrode drift etc.
The ATM mode utilizes a user selected spike to build a template of the waveform shape to be recorded.
Acceptance criteria settings are fully adjustable. Parameters can be set to make the template adaptive to
automatically follow changes in spike shape.
Inputs are provided for interfacing with available behavioral systems. Trial Gate, Trial Validate, and Event
Input are used when recording in gated mode to record only valid trial sections. A Spike Acceptance TTL
level output is provided for recording when any waveform is accepted. Aditionally, 16 general-purpose
digital inputs can be configured as strobed word input or as individual event input.
Stimulus artifact suppression software option can be used to remove artifacts created by microstimulation
of related neurons. Suppression works by building a replica of the artifact, then subtracting it from the
recorded signal.
Input from the LSG Line Sync Generator accessory (ordered separately) is used with the line noise
suppression software option to build a replica of line noise artifacts, then subtract them from the
recorded signal.
Both line noise and stimulus artifact suppression can be set to adapt to changes in the artifact
characteristics.

Waveforms are displayed online on the host PC. No additional scopes are required. An analog output of
the signal is provided for monitoring (audio or other) or further processing of the conditioned signal.
Data is stored on the PC as timestamps, waveforms, or both simultaneously. The host PC's graphical user
interface displays the waveform and settings for the selected channel, as well as thumbnail views for all
active channels. (Only one channel is used for each APM) The parameters of spike acceptance can be
interactively changed at any time during the experiment to compensate for electrode drift, etc. The
interface can simultaneously display up to the last 256 triggered waveforms per channel.
By using a wideband preamplifier and selective digital filtering performed by the DSP on the raw input
data, LFP (Local Field Potential) and spike data can be recorded simultaneously on the same channel.
Data can be stored/converted in several formats for use by standard analysis software i.e. Matlab,
Neuroexplorer, etc. Acquired data can also be retrieved online over TCPIP networks through the built-in
data server. Code samples that retrieve data into Matlab and perform online analyses are provided.
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Overview Page 3of 16
The APM is designed as a one-channel standalone module, while APC is its multichannel version. Multiple
module combinations can be run from a host PC using either the two USB ports commonly found on most
PCs or commercially available USB hubs. Additional complimentary neuro/craft® modules are available to
expand the APM in order to form a complete microelectrode recording and electrophysiological analysis
system.
A multichannel APC (Acquistion/Processor Channel) system is also available with built in power and USB
hubs for larger electrode count recording applications. (please refer to www.fh-co.com for more
information on this system.
Illustrative Procedure
1. Install the hardware and software, as described in the Getting Started section (first time
only) and power up the APM. Once initialized the USB Status LED will turn green.
2. Start the main APM control application by clicking the APM icon on the host PC.
3. Enter username. Any changes made to the recording parameters during this recording session
will be saved under this username.
4. Initiate communication between the APM channel and the host PC by clicking the Select tab in
the Channel Select Window. Click the 1 channel button and wait for it to turn green.
5. Enable the record function by clicking the Record tab of the Channel Select Window. Click
the 1 channel button and wait for it to turn green.
6. Click the Settings button in the Main User Interface to access and change the Settings
dialog box. These settings will be saved under the username entered in step 2, and will not
have to be set each time.
7. Adjust the Triggering Threshold Level and Input Gain until a stable, reasonably large
signal is displayed. Alternately, the Auto Adjust function can be used to automatically have
the APM accomplish this.
8. Adjust the Bandpass Digital Filter settings to narrow the bandwidth of the displayed signal
to remove unwanted noise.
9. Adjust, in a drag and drop manner, the Acceptance Window so that only acceptable spikes
pass through it (they will turn green).
10. If Slope/Height Discrimination recording mode is used, skip to step 16.
11. If the Adaptive Template Matching recording mode is to be used, adjust the Acceptance
Window such that it captures only one spike shape.
12. Click the Templates button to open the template settings dialog box.
13. Enable the template and record function by clicking on the appropriate template buttons.
14. Adjust the settings for the adaptive criteria of the template (the bottom three sliders).
15. Click the Rebuild From Window button to set the template.(A thick colored line defines the
template in the Main Waveform Window and also in the Thumbnail Channel Window.)
16. Repeat steps 8 through 13 for up to three more templates.
17. If using the Line Noise Suppression feature, Ensure that the LSG is on and connected to the
Line Sing Input on the backpanel or feature connector.
18. For either Line noise or Stimulus artifact suppression, click in the On checkbox to enable. Click
Load Replica to start the suppression functionality. Check the On box and adjust the
adaptation weight slider to enable the replica to adapt with changes in the artifact. Click
Reset Replica at any time to build a new replica.
19. Click the File button in the Main User Interface to set the filename and path where data will
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Overview Page 4of 16
be collected.
20. Enable data collection by clicking the Recording button in the Main User Interface. Click
again to end the recording session at any time.

APM Front Panel Description

Connections:
(cid:122) Analog Output: 3.5mm mono jack outputs an analog version of the signal converted from the
digital output for monitoring (audio, oscilloscope) or further processing. This connector has an
analog ground connection. See audio modes configuration dialog for audio monitoring options.
(cid:122) Spike Accept Output: 3.5mm mono jack outputs a TTL pulse on acceptance of a waveform. If
gated mode is selected, the output is inactive as while gate input is low. See the description of the
window discrimination method for more information about the timing of the acceptance pulse.
(cid:122) Trial Gate Input: 3.5mm mono jack for TTL input of trial gate (trial start/stop) from behavioral
systems. When used, waveforms are recorded on the host computer only while the TTL input to this
jack is HIGH. See recording modes description and recording configuration dialog for more
information.
(cid:122) Trial Validate Input: 3.5mm mono jack for TTL input of trial validate (trial acceptance) from
behavioral systems. When selected in software, waveforms are recorded on the host computer only
when the TTL input to this jack goes HIGH after the end of a trial. Unvalidated trials are not
recorded on the host computer. See recording modes description and recording configuration dialog
for more information.
(cid:122) Event Input: 3.5mm mono jack for TTL input of event marker from behavioral systems. When
used, a HI input to this jack causes an event timestamp to be recorded. See file format description
for more information on how event codes are saved in the data file.
(cid:122) Analog Input: 3.5mm mono jack for input of low impedance analog signal from preamp. This
connector has an analog ground connection. See input configuration dialog for more information.
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Overview Page 5of 16
Display:
(cid:122) USB Status: Tri-color LED indicates status of the USB port.
(cid:123) Green: Indicates communication ready to send and receive.
(cid:123) Amber: Indicates module is not yet recognized/initialized as an USB device. This happens
primarily at startup. LED changes from amber to green when device is recognized/initialized
by the host computer.
(cid:123) Red: Indicates communication is busy.
(cid:122) Spike Acceptance Output: Red LED lights indicating a HIGH TTL pulse is being output through
this jack. Four more LED lamps indicate the status of the TTL inputs/outputs.
(cid:122) Trial Gate Input: Yellow LED lights indicating a HIGH TTL pulse is being input through this jack.
(cid:122) Trial Validate Input: Yellow LED lights indicating a HIGH TTL pulse is being input through this
jack.
(cid:122) Event Input: Yellow LED lights indicating a HIGH TTL pulse is being input through this jack.
(cid:122) On: Green LED indicates power is on.
APM Back Panel Description

(cid:122) On/Off: Rocker switch used to activate power.
(cid:122) USB: High speed USB 2.0 type B connector for interfacing with host computer. Backward
compatible with full speed USB 1.1
(cid:122) Line Sync Input: 3.5mm mono jack for TTL input sync signal from an LSG Line Sync Generator,
usef for line noise suppression. See adaptive filters controls in main panel for more information.
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(cid:122) Stim Sync Input: 3.5mm mono jack for TTL input sync signal from a stimulator, used for stimulus
artifact suppression. See adaptive filters controls in main panel for more information.
(cid:122) Digital Input/Ouptut: 40-pin (2x20) connector providing access to additional 16-bit strobed
digital inputs and 16-bit strobed digital outputs. See digital inputs configuration dialog for more
information.

Pinout
1. Digital Input 0
2. Digital Input 1
3. Digital Input 2
4. Digital Input 3
5. Digital Input 4
6. Digital Input 5
7. Digital Input 6
8. Digital Input 7
9. Digital Input 8
10. Digital Input 9
11. Digital Input 10
12. Digital Input 11
13. Digital Input 12
14. Digital Input 13
15. Digital Input 14
16. Digital Input 15
17. Strobe In - When it goes low, the values present on the digital inputs are sent to APM. While
maintained low, any change in the digital lines configured as event inputs triggers an event.
While maintained high, digital inputs are locked in their last state.
18. Reserved - do not connect
19. Reserved - do not connect
20. Reserved - do not connect
21. Reserved - do not connect
22. Digital Ground
23. Digital Output 0
24. Digital Output 1
25. Digital Output 2
26. Digital Output 3
27. Digital Output 4
28. Digital Output 5
29. Digital Output 6
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30. Digital Output 7
31. Digital Output 8
32. Digital Output 9
33. Digital Output 10
34. Digital Output 11
35. Digital Output 12
36. Digital Output 13
37. Digital Output 14
38. Digital Output 15
39. Digital Ground
40. Strobe Out - When low, marks stable digital outputs. Goes high while the digital outputs are
updated.

(cid:122) Serial Port 9-pin D-SUB male connector for receiving data from other devices. It is connected to
the APC module in slot 1.

Pinout
1. NC Not connected
2. RxD Serial data from mouse/touch panel to ECM
3. TxD Serial data from ECM to mouse/touch panel (when using a mouse, used only for
powering it)
4. DTR Data Terminal Ready, positive voltage to mouse/touch panel and reset/detection
5. Signal Ground
6. DSR Data Set Ready
7. RTS Request to Send (when using a mouse, used only for powering it)
8. CTS Clear to Send
9. NC Not connected

Shell - Protective Ground
(cid:122) Power In: 2.1mm female socket. 12VDC 2A input.
(cid:122) Power Out: 2.1mm female socket. 12VDC pass-through outlet for daisy chaining of modules.
Accessory Use
LSG - Line Sync Generator
The LSG is an external device designed for providing digital pulses synchronized with the 50/60 Hz AC
power (115/230 V), for use in the APM's line noise suppressor. Based on the digital pulses it receives, the
APM builds a replica of the line noise and substracts it from the input signal. The same principle of
operation is used for the electrical microstimulation artifact suppression. Please refer to the Reference >
Artifact Suppression section of the documentation for more details.
Controls and Connections – LSG Front Panel:
(cid:122) Sync Output: 3.5mm mono jack output of generated synchronization wave for interface with the
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APM Trial Validate Input.
(cid:122) Voltage Switch: Slider switch for selecting input voltage level. Shown value indicates line in
voltage. (shown is for 115V line voltage.)

Display – LSG Front Panel:
(cid:122) On: Green LED indicates power is on.
Controls and Connections – LSG Side Panel:
(cid:122) 0|I: Rocker switch used to activate power.
(cid:122) Line In: IEC 60320-C13 type male for line cord connection.

Multichannel Preamplifier
Please click here to view multichannel preamplifier manual in Adobe PDF format.
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