Table of contents

Overview

NSpike NDAQ Hardware Overview
NSpike Computer Hardware Overview
Things to Buy

Computer Hardware Requirements
Connecting the Data Acquisition System and the Computers

Building the Clock Cable
Connecting the Data Acquisition System components
Connecting the Computers

Installing Linux

Linux Installation

Networking Setup
Kernel Networking Setup
Direct Rendering Check

Istalling and Compiling the NSpike Code
Running the NSpike Code

NSpike Configuration Files
Running NSpike on One Computer
Running NSpike on Two Networked Computers

Collecting Data with the NSpike Hardware and Software

Setting up Your Configuration File

DSP Channel Mapping
Electmap Section of Config File
Hostname and Channel Section of Config File

Using the NSpike GUI

Menus

Master Menu
File Menu
Display Menu
Digital IO Menu
Position Menu
Tetrode Settings Menu
Status Information

Continuous Mode Display
Spike Mode Display

Extracting Data from NSpike
Working with Extracted Data

Troubleshooting
Working with the NSpike Code

Overview

This is the documentation for the NSpike Neural Data Acquisition hardware and associated open source software. This documentation includes descriptions of the data acquisition front end (the amplifier, digitial to analog converter, DSP processors and digitial input/output system) as well a set of instructions for setting up a network of computers to run the nspike data acquisition software.

Conventions: Instructions are in normal typeface, while commands that should be typed into a terminal window or into a file are in fixed width typeface. Directories are in bold face.

NSpike NDAQ Hardware Overview

The NDAQ hardware system consists of the following:




NSpike Computer Hardware Overview

The NSpike software package is designed to run on 1 or more computers. For the purpose of these instructions, we are assuming that are four computers, although additional slave computers can be added and we are currently experimenting to determine whether a single non-RT slave computer is sufficient. The computers consist of

1 main computer and 2 slave computers.

These instructions should generalize to an arbitrary number of slave computers, as long as there is exactly one master computer. Each computer handles part of the data processing, displaying or saving as described below.

Tasks are divided among the computers as follows:

The non-RT slave computer(s)


The master computer




Things to Buy

 You need to purchase or make






Computer Hardware Requirements

The computer hardware consists of a minimum of two computers (we use either two or three) and several auxillary devices. Below are recommended specifications:

Computer specifications:

If you want to include video, you will also need

Other devices







Connecting the Data Acquisition System and the Computers

The diagrams below shows the overall organization of the data acquisition system as it is used in our lab, including the networking setup and the resulting data flow.



Network Connections:



Data Flow:






Building a Clock Cable

If you want to synchronize your system with some other hardware you can do so witha  clock cable that connects the 10 KHz output of the Master DSP to a counter (e.g. a PCI-CTR05 card) in some other computer.  Take a 6 foot or longer BNCcable, chop off one end, and strip the other so that you have access to both the signal and ground lines. Solder the lines to the female DB37 as follows:


Use hot glue gun glue to cover the solder cups of all of the pins of the connector after soldering to pin 36 and wrap aluminum foil around the back of the connector and the BNC cable. You may want to fill the space around the back of the connector with hot glue. Make sure the foil makes good contact with the shielding of the cable and the metal outside of the connector. Finally, wrap the foil with electrical tape. If you have synchronization problems, check the shielding of the cable.





Connecting the Data Acquisition System components

Additional specifications can be found in NSpike_NDAQ_Setup.doc.


Amplifier / Analog to Digital Converter Boxes:
The amplifier and the A/D box should be eventually placed in or at the ceiling, but for initial testing purposes we recommend putting them on a table top. The back of the Amplifier box has four 50 pin SCSI connectors on it and one input for a power cable. Make sure the power supply is off and attach the bare wire end of the power cable to the one of the 6V power supplies and the other to the Amplifier box.  Repeat for the A/D box. Plug one SCSI cable into each connector on the Amplifier box and attach the other end of each cable to the A/D box. Make sure output 1 from the Amplifier connects to input 1 on the A/D box, output 2 goes to input 2 and so on.

The Amplifier box has four rows of connectors on the front panel. These can be either Mill-max connectors (2x15 pins) and SMA connectors or DB-37 connectors. Here we assume you have the Mill-max version, each of which carries 27 channels of data, +5V and ground. The other connectors can be connected to either neural signals or line level signals (+/- 5V) but the amplitude ranges must be specified when you order the system. The pin numbers for each Mill-max and the mapping to the DSP channels is given in Appendix 1. Plug your fine wire cables into the Mill-max inputs.

Plug the long fiber optic cable into the TX fiber optic connector on the A/D box.

Master and Aux DSP Boxes:
Plug the other end of the long fiber optic cable into the RX fiber optic connector on the Master DSP box. Use the short fiber optic cable to connect the TX connector of the Master DSP box to the RX connector of the Aux DSP box. Connect the power supplies for the Master and Aux DSP boxes. Use Cat5, Cat5e or Cat6 ethernet cables to connect the ethernet ports on the Master DSP and on each Aux DSP to the 16 port hub.


Video
If you are using one camera, run a BNC line from the camera to a T connector attached to the video sync 1 input on the back of the Master DSP box. The other video sync input should be terminated.  Run another BNC from the free end of the T connector to your frame grabber card.


Connecting the Computers

This document assumes you know how to put the computers together and hook up the KVM switch. Below are the instructions for the networking and clock cable connections.


Master Computer:
There are three ethernet ports on the master. Generally the number of the corresponding ethernet device will increase as you move from the top to the bottom of the case, so the port closest to the top of computer is usually the first ethernet device (eth0). Plug the cable connecting the Master to the rest of your network into the first ethernet port. Plug the cable connecting the Master to the 16 port data hub into the next port (eth1) and the cable to the smaller, computer only hub into the last port (eth2).

Slave computers
Plug the cable connecting each computer to the 16 port data hub into topport (eth0) and the cable to the smaller, computer only hub into the last port (eth1).


Installing Linux

 This document assumes some familiarity with linux installation. The goal of this process is to




Linux Installation 

Get a DVD withthe latest version of your favorite distribution (we use Mandriva linux). Start the installation process. We recommend the following for installation:





Networking Setup
Set up the network settings as follows. Here we assume there are four machines: drizzle (the master), rain (slave 1) and mist (slave 2).

drizzle (master)
eth0 10.1.1.110  #connection to outside world; This is your ethernet address on your global network
eth1 10.1.2.1    #data connection for DSPs
eth2 10.1.3.1    #local network
netmask 255.255.255.0
gateway your_gateway (e.g. 10.1.1.1 for us)
name server your_nameserver (also 10.1.1.1 for us)

rain (slave 1)
eth0 10.1.2.2     #data connection to DSPs
eth1 10.1.3.2     #connection to drizzle
netmask 255.255.255.0
gateway 10.1.3.1
gateway device eth1
name server 10.1.3.1

mist (slave 2)
eth0 10.1.2.3     #data connection for DSPs
eth1 10.1.2.3     #connection to drizzle
netmask 255.255.255.0
gateway 10.1.3.1
gateway device eth1
name server 10.1.3.1


Once the networking setup is complete, boot each machine into linux.

Edit /etc/hosts on each machine to include the other machines and the DSPs.  It is best not to put the 10.1.2.x addresses for the computers in the /etc/hosts file.

/etc/hosts should look something like this:
127.0.0.1 localhost

10.1.3.1 drizzle
10.1.3.2 rain
10.1.3.3 mist
10.1.3.4 fog


10.1.2.10 dsp0
10.1.2.11 dsp1
10.1.2.12 dsp2
10.1.2.13 dsp3
10.1.2.14 dsp4
10.1.2.15 dsp5
10.1.2.16 dsp6
10.1.2.17 dsp7
10.1.2.18 dsp8
10.1.2.254 fakedsp

Note that it is essential that you have fakedsp listed.  As UDP packets are not acknowledged, your ethernet switch can lose track of the location of the computers and start broadcasting packets to all ports after some time (in our case about 9 minutes).  The code prevents this by sending empty packets to fakedsp once a minute.


Kernel Networking Setup

As superuser, add the following four lines to /etc/sysctl.conf:

net.core.rmem_max=8388607
net.core.rmem_default=8388607
net.core.wmem_max=8388607
net.core.wmem_default=8388607

Alternatively, you can open /etc/rc.d/rc.local in a text editor and add the following lines at the end:

sysctl -w net.core.rmem_max=8388607
sysctl -w net.core.rmem_default=8388607
sysctl -w net.core.wmem_max=8388607
sysctl -w net.core.wmem_default=8388607

These settings increases the socket buffer read and write sizes so that we will not lose data if any of the programs fall temporarily behind. 


Direct Rendering Check
Open up a terminal window and run the glxinfo program. There should be a line near the top of the output that says

Direct Rendering: Yes

If so, try runningglxgears and look at the framerate that the program reports. You should see > 500 frames/sec (ideally you'll see a few thousand or more).

If not, you need to get it working by installing the correct driver for your card.






NFS Setup
Now set up the shared filesystems. The home directory (/home/lorenlab for us) should be exported from drizzle and nfs mounted by the other systems.  The following assumes you are making these changes in the main text files.  You can also make them using the control panel for your distribution (drakconf for Mandriva).

Edit /etc/exports on drizzle to be

/home rain(rw,no_root_sqaush,sync) mist(rw,no_root_squash,sync) fog(rw,no_root_squash,sync)
/usr/local rain(rw,no_root_sqaush,sync) mist(rw,no_root_squash,sync) fog(rw,no_root_squash,sync)

Add the following line to /etc/fstab on rain, mist, and fog:

drizzle:/home /home nfs rw,suid,bg 1 1
drizzle:/usr/local /usr/local nfs rw,suid,bg 1 1

Now set up the data directory exports so you can copy the data off the system. Edit /etc/exports on the non-RT slaves to be

/data drizzle(rw,no_root_squash,sync)

Add the following lines to /etc/fstab on drizzle:

mist:/data /mistdata nfs rw,suid,bg 1 1
rain:/data /raindata nfs rw,suid,bg 1 1

In a terminal window on drizzle, create those directories:

mkdir /mistdata
mkdir /raindata





Installing and Compiling the NSpike Code (without DSPs)

The NSpike code has two debug modes, and you should first get the code working in the debug modes before you try to interact with the DSPs.  Note that you will need to have set up networking correctly as described in the computer setup section before the code can be run on multiple machines. You will also need to have nfs exported /home and /usr/local directories that are available on all machines. All of the commands below assume that “.” (the current directory) is in your path. If it is not, add a “./” before each local command (e.g. make and configure).

First, unpack the compressed tar archive in the directory where you would like it to live. On our systems we store the source in /home/lorenlab/, so the commands are

cd /home/lorenlab
tar xvzf NSpike_x.x.x.tgz
ln -s NSpike_.x.x.x NSpike

This will create the NSpike_x.x.x directory, a link called NSpike and the various subdirectories. 0

If you plan to use video, you will need to install the mpeg encoding library on the computer that you will be using to compile the code (this is normally the master computer). The version of this library used for the code is included in the tar archive and is called “libfame-0.9.1.tar.gz”. libfame also exists in rpm form for most linux distributions, so if possible, download the rpm and install it. If not, not that the version of libfame provided doesn't compile on 64 bit systems. If you have a 32 bit system, you may want to move the libfake-0.9.1.tar.gz file somewhere else to unpack it (/usr/src for example). Unpack the archive and compile it (more detail instructions are in the INSTALL file that is extracted into the libfame-0.9.1 directory). tar xvzf libfame-0.9.1.tar.gz
cd libfame-0.9.1
If you are on intel system that supports the MMX instruction set, run

configure

If you are on an AMD system (the type we use), use

configure --disable-mmx

next, become root and enter

make install


Return to the directory where you installed nspike (for us /home/lorenlab/NSpike). 

First examine the file “spike_defines.h” in the include subdirectory. Near the top of the file you will see a line that says 

#define NO_DSP_DEBUG

When that line is present (e.g. not commented out) the code will compile without the sections that interact with the DSPs. Make sure this line is not commented out (e.g. it should look exactly as it does above).

Below that line you will see another line that says

#define NO_POS_DEBUG

When that line is present the code will compile without the sections that interact with the framegrabber card.  return to the nspike base directory and run the QT Makefile generating utility



qmake

to create the local Makefile. This depends on having qt installed, so if this doesn't work, make sure that the qt and qt development libraries are installed. Now do

makeallclean

to get rid of old files and

make

to compile the main program. This will compile the nspike code in the NSpike base directory and some, but not all of the code in the Modules subdirectory. You should see a few warnings but no errors. The warnings result from the -Wall compiler flag and can be ignored. If there are errors, they are most likely due to the absence of libraries that are necessary, and you will have to track these down and install them.

NOTE: For reasons that are not clear to me, the make utility does not always properly detect cases when the header files (e.g. spike_defines.h) are changed, so after changing a header file, make sure to do “makeallclean” and then “make” or “makeall”.

Now change to the Modules subdirectory and configure the makefile:

cd Modules
configure

If configure gives errors they are once again likely to be due to the absence of necessary libraries. Once it works it will generates the local makefile for the modules using Makefile.am as the automake template file.

If you are not using video you can copy Makefile.am.novideo to Makefile.am:

cp Makefile.am.novideo Makefile.am

Now run

 
automake
make

to compile the modules.

When both nspike and the modules have been compiled, go back to the Nspike directory and install the code in /usr/local/nspike by running the makeallinstall script as root. Note that for future reference, the makeall script is available to compile both nspike and the modules in one command.

cd /home/lorenlab/Nspike
makeallinstall

Check to see that the follow files exist in /usr/local/nspike (Note that the “*” after each file means that it is executable and is not part of the name):

ls /usr/local/nspike

should produce a listing like this:

nspike spike_behav spike_fixpos spike_process_posdata
nspike_matlab spike_daq spike_matlab spike_rgbcolor
spike_extract spike_posdaq spike_save_data






Running the NSpike Code


Make sure that /usr/local/nspike is in your path.



NSpike Configuration files

The majority of the program configuration is specified in the configuration files. nspikeconfig is the default name of the main configuration file. The various options for each item are given within that file.
 
NOTE: at the moment, while it is possible to save configuration files within the main program, those saved configuration files can only be edited (and then used) if you delete the binary characters at the beginning and end. The program write out all files using the zlib compression library, and the header and final binary code need to go away if the contents of the file change. If you edit the file without removing the necessary characters and then try to run the program with the new configuration, it will die with a segmentation fault.

To get the program working, you will need to designate a master machine and some number (0-n) of slave machines. That designation, along with port numbers for communication between the machines, is given near the top of configuration file.

If you have 1 or more slaves, note that they will not begin acquisition until they recieve a message from the master, and similarly, exiting from the program requires exiting on the master machine.

The NSpike directory has a number of example configuration files which are named “nspikeconfig#”. These files are internally documented (comments begin with '%') and contain all of the configuration information to set datatypes, channel numbers, position tracking variables and behavior / digital IO variables. 

Running the Program on One Computer

First modify all of the nspikeconfig* files, changing the names of the machine(s) to fit your local setup. For nspikeconfig1-2, there is only one machine. For nspikeconfig3-4 there are two machines, so make sure to change all instances in both files to the two machines on your network.
Start in the NSpike directory and try the software with “nspikeconfig1”:

nspike –config nspikeconfig1

You will see quite a bit of output, as shown below.  This is normal, but can be changed so that each program sends output to its own configuration file by changing the #define STATUSFILE in NSpike/include/spike_defines.h.  The module numbers refer to numbers for each program defined in NSpike/include/spike_defines.h.

spike_main: Reading config file
machine num 0, type 0
Launching modules
spike main program getting client /tmp/spike_message_16_to_14
spike_daq: starting
spike_daq: starting messaging
module 12 starting server /tmp/spike_message_16_to_12
spike_save_data: starting messaging
module 14 starting server /tmp/spike_message_16_to_14
module 14 starting display client /tmp/spike_message_14_to_16
spike main program got client /tmp/spike_message_16_to_14
spike main program getting client /tmp/spike_message_16_to_12
spike main program got client /tmp/spike_message_16_to_12
spike main program getting server /tmp/spike_message_14_to_16
module 12 starting display client /tmp/spike_message_12_to_16
spike main program got server /tmp/spike_message_14_to_16
spike main program getting server /tmp/spike_message_12_to_16
spike main program got server /tmp/spike_message_12_to_16
getting data server /tmp/spike_data_12_to_16 from 12
sent message for data server /tmp/spike_data_12_to_16
program 12 got message 8, socket name /tmp/spike_data_12_to_16, protocol 0, type 1, connection from virga 12 to virga 16
sending START_NETWORK_SERVER to 14 for 16 to 14 DATA socket
getting client server /tmp/spike_data_16_to_14 from 16
program 14 got message 7, socket name /tmp/spike_data_16_to_14, protocol 0, type 1, connection from virga 16 to virga 14
sending START_NETWORK_SERVER to 14 for 12 to 14 DATA socket
sending START_NETWORK_CLIENT to 12 for 12 to 14 DATA socket
Waiting for CONNECTION_ESTABLISHED message on 14
got CONNECTION ESTABLISHED message from 14
program 14 got message 7, socket name /tmp/spike_data_12_to_14, protocol 0, type 1, connection from virga 12 to virga 14
Waiting for CONNECTION_ESTABLISHED message on 12
program 12 got message 8, socket name /tmp/spike_data_12_to_14, protocol 0, type 1, connection from virga 12 to virga 14
program 12 got message 2, socket name , protocol 0, type 0, connection from  0 to  0
program 12 sending out CONNECTION ESTABLISHED message to main program
Finished establishing messaging in program 12
program 14 got message 2, socket name , protocol 0, type 0, connection from  0 to  0
program 14 sending out CONNECTION ESTABLISHED message to main program
Finished establishing messaging in program 14
got CONNECTION ESTABLISHED message from 12
Finished establishing messaging in program 16
Sending system config
QLayout "unnamed" added to SpikeMainForm "unnamed", which already has a layout
Programming DSPs
Programming Master DSP
Programming Aux DSP 1
Programming Aux DSP 2
Programed DSPs
Status message: Clock Reset
Starting acquisition
Acquistion started

 You should now have a simulated EEG display with 24 channels. Every channel should have a 8 or so Hz sinewave on it. If it doesn’t work, the problem is likely to be in your modification to the config file, and you should carefully look through the output of the program to identify any errors it caught. To quit, select "Quit" from the Master menu.

Similarly,

nspike –config nspikeconfig2

should bring up a simulated spike display with four tetrodes per screen (6 total) and the opportunity to switch between spiking and continuous modes using the tabs near the bottom of the window. The data are once again a simulated sine wave, so the spike windows show the part of the sine wave above threshold.  





Running the Program on Two Networked Computers

Now you should test the networking between machines. Run

nspike –config nspikeconfig3

on both the master and a slave machine (the names must, of course, match the names you put into nspikeconfig3, and you will need to run it from a directory where you can see spikeconfig3 on both machines e.g. /home/lorenlab/NSpike for us). You should see 8 channels of EEG on the master and simulated spike data on the slave.

Finally, try

nspike –config nspikeconfig4

on the master and
 

You should get a position and EEG display on the master. 


Collecting Data with the NSpike Hardware and Software



Setting up Your Configuration File

As discussed above, the configuration files set most of the parameters associated with data collection.  The remaining parameters (e.g. the number of points to collect when a threshold crossing is detected) are defined in the spike_defines.h file in the include subdirectory.  If you want to change those parameters, substantial recoding of a number of files will be required. 

An example of an actual configuration file for a microdrive with 8 tetrodes (6 spike tetrodes, one eeg tetrode, and one reference tetrode) is in the franklab8tetconfig file.  This configuration file sets the master (snow) to display 7 channels of EEG data (one channel from each tetrode with the exception of the reference), position data from the frame-grabber on the rtslave (graupel) and behavioral data (digital I/O) from the UEI card on graupel.  Hail, the non-rt slave, processes spike data from the 6 spike tetrodes (24 channels of data total).  Here we go through the most complex parts of the configuration file, the mapping from the tetrodes on the animal to the dsp channels and the specification of channels for each machine.

To understand the mapping it is important to know that each channel of input on the front end Amplifier box corresponds to 1 of 127 channels on the fiber optic bus.  These channels (refered to as DSP channels) are numbered 0 to 126, and each Aux DSP has access to all of these channels and can filter and send out up data from and arbitrary set of up to 16 of these channels at 30 KHz per channel (the fixed sampling rate of the A/D box).  The "electmap" lines in the configuration file define the relationship between individual input channels and DSP channels.  This mapping is given in the DSP Channel Mapping section below.



DSP Channel Mapping

Looking down into the inputs to the preamplifies, the dsp channels for each pin on each Mill-max connector are as follows:
headstage map

Notes:

The above mappings can also be applied to the connectors on the top of the microdrive array, omitting the +V pin which only goes into the preamplifier.

The Group Number corresponds to the number of the row of connectors (Mill-max and SMA or a single DB-37) on the front of the Amplifier box.

The J1-8 designations refer to the SMA connectors on the front panel of the Amplifier box.

DSP Channel 127 is the block count, which counts the high work of the current sample number (16 bit).  This channel is used by the DSPs to remain synchronized and is not used for neural data.  


Alternatively, from the front of the Amplifier box, the Mill-max pin numbers and their associated DSP channls are as follows:
mill max pinout


DSP Channel

Group Number

Mill-max

00

1

22

01

1

14

02

1

6

03

1

J1

04

2

22

05

2

14

06

2

6

07

2

J1

08

3

22

09

3

14

10

3

6

11

3

J1

12

4

22

13

4

14

14

4

6

15

4

J1

16

1

21

17

1

13

18

1

5

19

1

J4

20

2

21

21

2

13

22

2

5

23

2

J4

24

3

21

25

3

13

26

3

5

27

3

J4

28

4

21

29

4

13

30

4

5

31

4

J4

32

1

23

33

1

15

34

1

7

35

1

J7

36

2

23

37

2

15

38

2

7

39

2

J7

40

3

23

41

3

15

42

3

7

43

3

J7

44

4

23

45

4

15

46

4

7

47

4

J7

48

1

24

49

1

16

50

1

8

51

1

J5

52

2

24

53

2

16

54

2

8

55

2

J5

56

3

24

57

3

16

58

3

8

59

3

J5

60

4

24

61

4

16

62

4

8

63

4

J5

64

1

26

65

1

18

66

1

10

67

1

J8

68

2

26

69

2

18

70

2

10

71

2

J8

72

3

26

73

3

18

74

3

10

75

3

J8

76

4

26

77

4

18

78

4

10

79

4

4

80

1

25

81

1

17

82

1

9

83

1

1

84

2

25

85

2

17

86

2

9

87

2

1

88

3

25

89

3

17

90

3

9

91

3

1

92

4

25

93

4

17

94

4

9

95

4

1

96

1

27

97

1

19

98

1

11

99

1

3

100

2

27

101

2

19

102

2

11

103

2

3

104

3

27

105

3

19

106

3

11

107

3

3

108

4

27

109

4

19

110

4

11

111

4

3

112

1

28

113

1

20

114

1

12

115

1

4

116

2

28

117

2

20

118

2

12

119

2

4

120

3

28

121

3

20

122

3

12

123

3

4

124

4

28

125

4

20

126

4

12

127

 

Block count

Electmap Section of Config File

The electmap section of franklab8tetconfig is shown below:

%           electrode  channel#  dsp_channel
electmap    1            0        96
electmap    1            1        80
electmap    1            2        32
electmap    1            3        16
electmap    2            0        112
electmap    2            1        64
electmap    2            2        48
electmap    2            3        0
electmap    3            0        97
electmap    3            1        81
electmap    3            2        33
electmap    3            3        17
electmap    4            0        113
electmap    4            1        65
electmap    4            2        49
electmap    4            3        1
electmap    5            0        98
electmap    5            1        82
electmap    5            2        34
electmap    5            3        18
electmap    6            0        114
electmap    6            1        66
electmap    6            2        50
electmap    6            3        2
electmap    7            0        99
electmap    7            1        83
electmap    8            0        115

There is one entry (row) for each electrode wire that is connected to the input side of your preamp.  The ground is pin 2 of the mill-max connector, and is hard wired.

The electrode number column contains the numbers you have assigned to your tetrodes.  This must start with 1, but all other numbers are 0 based.  It should be possible to skip electrode numbers, although we have not tested this.

The channel number column indicates the channel (eg. wire) within each tetrode.  For tetrodes that will be used for spike data there are a total of 4 channels (0, 1, 2 and 3).  For us, EEG tetrodes have two connected channels (e.g. tetrode 7, channels 0 and 1) and reference tetrodes have a single channel (e.g. tetrode 8, channel 0). 

The DSP channel number column indicates the number of the dsp channel that contains data from the specified channel of the specified electrode.  This is derived from the channel map above.




Hostname and Channel Section of Config File
 The next sections of the file specify the order in which channels are to be processed and displayed on each machine.

Each machine that gets data from the dsp should have it's own section that begins with

hostname      machine_name

Follwing that line, there should be a set of channel definitions.  The first line of each definition is the channel number, which specifies where this channel will be displayed on the computer.  \

Channel numbers

Thus, for the seven channels of EEG data processed by the master machine in franklab8tetconfig, the channel numbers go from 0 to 6.

If you are collecting EEG/LFP data, each tetrode should have a single entry where you have chosen a single channel from that tetrode for EEG data.  If you specify multiple channels from the same tetrode the data will not extract correctly, so ... don't.

Channel 1 is specified as follows:
    channel     1
        dspnum           1
        dspchan          112
        refelect         8
        refchan          0
        number           2
        electchan        0
        depth            0
        thresh           40
        maxdispval       1000
        filter           300    6000
        color            0

This means that the second trace (channel 0 is the first trace) that will be displayed will be processed by dsp 1 and corresponds to tetrode 2, channel 0, which is dsp channel 112.


If you are collecting spike data from tetrodes, each set of four channels (in order) should correspond to the four channels from a single tetrode, and thus they should all have the same
number entry but should have electchan numbers that are 0, 1, 2 or 3. 

e.g.
% tetrode 1
    channel     0
        dspnum        2
        dspchan       96
        refelect      8
        refchan       0
        number        1
        electchan     0
        ...

    channel     1
        dspnum        2
        dspchan      80
        refelect     8
        refchan      0
        number       1
        electchan    1
        ...

    channel     2
        dspnum        2
        dspchan       32
        refelect      8
        refchan       0
        number        1
        electchan     2
        ...

    channel     3
        dspnum        2
        dspchan       16
        refelect      8
        refchan       0
        number        1
        electchan     3
        ...

These channels should also all have the same depth (and, for scientific reasons, the same filter settings) but can have different thresholds, maximum displayed values, and colors.

Using the NSpike GUI

 
Menus

Master Menu Items (Available only on the Master machine):

   

File Menu Items (Available on all machines):


Display Menu Items (Available on all machines):


Digital IO Menu Items (Available only on digital IO system):

Position Menu Items (Available only on position system):


Tetrode Settings Items (Available only on spike systems):

This menu allows you to tie together settings across tetrodes, so that a change on one tetrode is propogated to all tetrodes on this machine. 





Status Information





Continuous Mode Display

A snapshot of the Continuous / Position mode looks like this:  EEG Position Screen

The two sections with sine waves show simulated EEG data, and the upper right section shows simulated position data. 

The numbers in large font are derived from the number specified in the config file. 

Each button next to the number displays

Clicking on a button (e.g. the button for tetrode 14) brings up the following window:
EEG Settings Window 
This window allows you to change the settings for this tetrode.




Spike Mode Display
Spike Mode Window

This tab of the spike mode window shows four tetrodes at a time.  Any wave form that exceeds the threshold (yellow line) on any one of the four channels is displayed on all four, and a point representing the peak amplitude on each pair of channels is plotted in each of the six projection boxes.  The left row of boxes represent channel 0 vs. 1, 0 vs. 2 and 0 vs. 3, while the right row represents 1 vs. 2, 1 vs. 3, and 2 vs. 3. 

The top gray area above the waveform windows shows

The bottom gray area below the waveform windows shows the settings for each channel.

When the M, T or F buttons are depressed, changes in the corresponding setting will be propogated to all channels of the tetrode.  When the buttons are not depressed, changes are local to the changed channel.

Note that the maximum displayed value (MDV) sets the size of the traces in both the spike and projection windows.  This setting does not affect data storage, however, so traces that exceed the MDV are not trucated on disk, and increases in the MDV will allow a redraw of the projection windows to include points that were previously too large. 


Audio buttons




Collecting Data

The following represents the sequence we use to collect data:

  1. Turn on the power to the Amplifier and the A/D box by toggling the switch on the FlyBat box.

  2. Turn on the power to the DSPs

  3. Start nspike on the master and slaves

  4. Start nspike_rt on the RT system

  5. Select the appropriate camera. 
    Note that it is essential to stop acquisition before switching cameras.

  6. Check light levels / position threshold so that only the diodes on the head exceed a threshold (We like a threshold around 225 - 240).

  7. Enter depths on all tetrodes

  8. Check / adjust references, thresholds and filters

  9. Reset clocks

  10. Check  time synchronization

  11. Open files on all machines

  12. Start save on all machines

  13. Collect Data

  14. Stop save on all machines

  15. Close files on all machines

...This list could also include launching behavior programs and/or triggering digital outputs.






Extracting Data from NSpike

Once you have finished collecting data you will need to extract it from the data file or files.  To do so, we usually move the data to its own directory on a separate workstation.  We then run

nspike_extract -all datafilename

on each data file.  

nspike_extract

will give you a list of available options for extraction.  




Working with Extracted Data

Once extracted, the data are stored in files with relatively straight forward formats.  Note that all timestamps are in 100 µsec units, so there are 10000 timestamps per second.

Spike data:
    Spike data are stored in .tt files which are extracted into subdirectores, one per tetrode.  Tetrode #2, at a depth of 110, would be in a file called 02-110/02-110.tt.  Within the tt file there is an ASCII header which starts with
%%BEGINHEADER
and ends with
%%ENDHEADER
followed by binary records of each spike.  Each spikes is stored as follows:
timestamp    unsigned integeter (32 bit)
data              160 signed shorts

The file readtt.m in the Matlab subdirectory will read in all of the spikes from a ttfile.


Continuous Data (EEG or LFP):
    Continuous data are stored in a .eeg file, so the data from tetrode #2 at depth 110 is stored in 02-110.eeg.  The continuous data have a header similar to that of the tt files, followed by data records with the following format:
timestamp        unsigned integer (32 bit)
nsamples          int
sampling_rate   double
samples            nspikes signed shorts

The mex code readeeg.c in the Matlab directory will read in the eeg data from a file.  Compile within matlab as follows:

mex -o readeeg readeeg.c fileiomat.c

Position Data:
    Position data are extracted to two files, named as the directory name where the extraction occured (e.g. rat5day1) followed by .mpeg or .postimestamp.  The .mpeg file is a normal mpeg file that can be played with any mpeg player.  The .postimestamp file has the complete header from the data file followed by a list of timestamps (all unsigned integers), one for each frame of the mpeg.  We use nspike_fixpos to compute the locations of the large and small diode arrays on our animals' heads.  See the top of spike_fixpos.c for usage.


Digital IO Data
    Digital IO data are extracted in text format to a file that is named as the currect directory followed by .dio (e.g. rat5day1.dio).  This corresponds to the -diotext option for extraction.  The file contains two colums.  Column 1 is the timestamp and Column 2 is the state of the all digitial IO lines at that time.  


Event Data
    Events (disk on only at this moment) are written to disk, and the event type is given in spike_defines.h.  Other events will be written to disk in the future.


Configuration Data
    Each datafile also has a header which is the configuration file used to collect those data.  This is extracted to datafilename.config.

Troubleshooting

Problem:

The NSpike code fails to start with an error that indicates there is a problem opening a socket on a particular port.


Solution:  

Change the port number in the config file to some other unused port and run kspike to kill off the other processes.
We have had problems with the Gnome window manager not allowing us to open ports, so you may want to avoid using Gnome for nspike.


Problem:

The NSpike code fails to start with an error that indicates there is a problem looking up a machine number.


Solution:  

Check the config file to make sure that the machine on which the error was seen is listed as either master or a type of slave.



Problem:

The NSpike code hangs after the line
Programming DSPs


Solution:  

There is an error communicating with the DSPs.  This probably means that the network that the DSPs are on is down or that the DSPs are not powered up.  You may need to kill (kspike) and then restart the software.


Problem:

The NSpike code reports very large numbers of lost packets and / or hangs.

Solution:

 This appears to occur on some systems and not others, and results from broadcast messages (usually ARP requests) on the DSP network.  If this happens on your machine, do the following:
Add the following lines to sysctl.conf:

net.ipv4.neigh.eth1.mcast_solicit=0
net.ipv4.neigh.eth1.ucast_solicit=1
net.ipv4.conf.default.forwarding=0

where you replace eth1 with the name of the ethernet interface on each machine that communicates with the DSPs.  Our sysctl.conf is in the NSpike directory for reference.

Move the setupnet script to /usr/local/bin (or some other directory in root's path).  Modify the script to select the DSP ethernet interface on each machine.  Become root and run this script each time the DSPs are turned on.

That combination fixes the problem for us.

Working with the NSpike Code

To be written....