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A hardware implementation of the Izhikevich model of a spiking neuron

Home Page: https://open-labware.net/projects/spikeling/

License: MIT License

OpenSCAD 0.52% Prolog 0.81% C++ 30.39% MATLAB 14.65% Jupyter Notebook 25.86% C 27.77%

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spikeling's Issues

add Spikeling to Open-neuroscience

Hello!

We are reaching out because we would love to have your project listed on Open Neuroscience, and also share information about this project:

Open Neuroscience is a community run project, where we are curating and highlighting open source projects related to neurosciences!

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The reason why we have the form system is that it makes it open for everyone to contribute to the website and allows developers themselves to describe their projects!

Also, there are so many amazing projects coming out in Neurosciences that it would be impossible for us to keep track and log them all!

Please get in touch if you have any questions or would like to collaborate!

Issue with PCB (?)

Hi,

ordered myself some Spikeling PCBs from Elecrow last week using the Gerbers you provide for download. Today they wrote saying there's some holes that have both a round and a square shape and which one of those should they use - see the image they sent:

Looking at the photo you provide it seems to me like that's the mechanical/GND connectors for dials 1-4, so I told them it's a round hole (that's what my eyes think they see there).

Anyways, even if it was the wrong choice, it'll probably be easy enough to work around it. Still wanted to let you know. Thank you for a very interesting project, looking forward to soldering it!

Cheers,

Jonathan

Nano Every

I am making some Spikelings for the Neurophysiology lab that I am teaching for the spring. I made two to test and they are awesome!
To scale up, I got the pin-equivalent Nano Every that was much cheaper from Arduino in a pack of 6.
I am getting an error that I do not understand how to troubleshoot myself (see below).
It seems like there are some differences in some of the code needed for this Processor.
(for example, in FlyPi, I had to change "B00001111" to "0B00001111" in the matrix pattern specification to get it to work).
The following seems like a more complicated modificaiton:
Do you have any suggestion?
Thank you!

Arduino: 1.8.15 (Mac OS X), Board: "Arduino Nano Every, ATMEGA328"

In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h: In function 'void ADC_init()':
SettingsArduino.h:90:2: error: 'ADMUX' was not declared in this scope
  ADMUX   = _BV(REFS0); // Reference voltage = Vcc (5V)
  ^~~~~
In file included from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/io.h:99:0,
                 from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/pgmspace.h:90,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/String.h:31,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/IPAddress.h:24,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/ArduinoAPI.h:30,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/Arduino.h:23,
                 from sketch/Spikeling.ino.cpp:1:
SettingsArduino.h:90:16: error: 'REFS0' was not declared in this scope
  ADMUX   = _BV(REFS0); // Reference voltage = Vcc (5V)
                ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:90:16: note: suggested alternative: 'VREF_t'
SettingsArduino.h:91:7: error: 'ADCSRA' was not declared in this scope
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
       ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:91:3: note: in expansion of macro 'sbi'
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
   ^~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:91:7: note: suggested alternative: 'ADC_t'
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
       ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:91:3: note: in expansion of macro 'sbi'
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
   ^~~
SettingsArduino.h:91:14: error: 'ADPS2' was not declared in this scope
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
              ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:91:3: note: in expansion of macro 'sbi'
   sbi(ADCSRA,ADPS2);    // Prescaler 1 MHz
   ^~~
SettingsArduino.h:92:14: error: 'ADPS1' was not declared in this scope
   cbi(ADCSRA,ADPS1);
              ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:92:3: note: in expansion of macro 'cbi'
   cbi(ADCSRA,ADPS1);
   ^~~
SettingsArduino.h:93:14: error: 'ADPS0' was not declared in this scope
   cbi(ADCSRA,ADPS0);
              ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:93:3: note: in expansion of macro 'cbi'
   cbi(ADCSRA,ADPS0);
   ^~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:93:14: note: suggested alternative: 'ADC0'
   cbi(ADCSRA,ADPS0);
              ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:93:3: note: in expansion of macro 'cbi'
   cbi(ADCSRA,ADPS0);
   ^~~
SettingsArduino.h:94:16: error: 'ADEN' was not declared in this scope
  ADCSRA |= _BV(ADEN);  // Enable ADC
                ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:94:16: note: suggested alternative: 'ADC0'
In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h: In function 'uint16_t ADC_read(uint8_t)':
SettingsArduino.h:103:2: error: 'ADMUX' was not declared in this scope
  ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
  ^~~~~
In file included from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/io.h:99:0,
                 from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/pgmspace.h:90,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/String.h:31,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/IPAddress.h:24,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/ArduinoAPI.h:30,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/Arduino.h:23,
                 from sketch/Spikeling.ino.cpp:1:
SettingsArduino.h:103:18: error: 'MUX3' was not declared in this scope
  ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                  ^
SettingsArduino.h:103:30: error: 'MUX2' was not declared in this scope
  ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                              ^
SettingsArduino.h:103:42: error: 'MUX1' was not declared in this scope
  ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                                          ^
SettingsArduino.h:103:54: error: 'MUX0' was not declared in this scope
  ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                                                      ^
In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
SettingsArduino.h:105:2: error: 'ADCSRA' was not declared in this scope
  ADCSRA |= _BV(ADSC);
  ^~~~~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:105:2: note: suggested alternative: 'ADC_t'
  ADCSRA |= _BV(ADSC);
  ^~~~~~
  ADC_t
In file included from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/io.h:99:0,
                 from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/pgmspace.h:90,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/String.h:31,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/IPAddress.h:24,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/ArduinoAPI.h:30,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/Arduino.h:23,
                 from sketch/Spikeling.ino.cpp:1:
SettingsArduino.h:105:16: error: 'ADSC' was not declared in this scope
  ADCSRA |= _BV(ADSC);
                ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:105:16: note: suggested alternative: 'DDRC'
In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
SettingsArduino.h:107:10: error: 'ADC' was not declared in this scope
   return ADC;
          ^~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:107:10: note: suggested alternative: 'ADC0'
   return ADC;
          ^~~
          ADC0
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h: In function 'void initializeHardware()':
SettingsArduino.h:129:3: error: 'TCCR2B' was not declared in this scope
   TCCR2B = TCCR2B & 0b11111000 | 0x01; // sets PWM pins 3 and 11 (timer 2) to 31250 Hz
   ^~~~~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:129:3: note: suggested alternative: 'TCB2'
   TCCR2B = TCCR2B & 0b11111000 | 0x01; // sets PWM pins 3 and 11 (timer 2) to 31250 Hz
   ^~~~~~
   TCB2
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h: In function 'void housekeeping()':
SettingsArduino.h:147:5: error: 'ADMUX' was not declared in this scope
     ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
     ^~~~~
In file included from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/io.h:99:0,
                 from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/pgmspace.h:90,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/String.h:31,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/IPAddress.h:24,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/ArduinoAPI.h:30,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/Arduino.h:23,
                 from sketch/Spikeling.ino.cpp:1:
SettingsArduino.h:147:21: error: 'MUX3' was not declared in this scope
     ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                     ^
SettingsArduino.h:147:33: error: 'MUX2' was not declared in this scope
     ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                                 ^
SettingsArduino.h:147:45: error: 'MUX1' was not declared in this scope
     ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                                             ^
SettingsArduino.h:147:57: error: 'MUX0' was not declared in this scope
     ADMUX  &= ~(_BV(MUX3) | _BV(MUX2) | _BV(MUX1) | _BV(MUX0));
                                                         ^
In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
SettingsArduino.h:149:5: error: 'ADCSRA' was not declared in this scope
     ADCSRA |= _BV(ADSC);
     ^~~~~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:149:5: note: suggested alternative: 'ADC_t'
     ADCSRA |= _BV(ADSC);
     ^~~~~~
     ADC_t
In file included from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/io.h:99:0,
                 from /Users/kperks/Library/Arduino15/packages/arduino/tools/avr-gcc/7.3.0-atmel3.6.1-arduino5/avr/include/avr/pgmspace.h:90,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/String.h:31,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/IPAddress.h:24,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/api/ArduinoAPI.h:30,
                 from /Users/kperks/Library/Arduino15/packages/arduino/hardware/megaavr/1.8.7/cores/arduino/Arduino.h:23,
                 from sketch/Spikeling.ino.cpp:1:
SettingsArduino.h:149:19: error: 'ADSC' was not declared in this scope
     ADCSRA |= _BV(ADSC);
                   ^
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:149:19: note: suggested alternative: 'DDRC'
In file included from /Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/Spikeling.ino:10:0:
SettingsArduino.h:151:32: error: 'ADC' was not declared in this scope
     ADCData[iADCData[i] -A0] = ADC;
                                ^~~
/Users/kperks/OneDrive - wesleyan.edu/Teaching/Neurophysiology/Spikeling/Arduino/Spikeling/SettingsArduino.h:151:32: note: suggested alternative: 'ADC0'
     ADCData[iADCData[i] -A0] = ADC;
                                ^~~
                                ADC0
exit status 1
'ADMUX' was not declared in this scope


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