castillohair
commented
6 years ago Hi Hanns-Martin,
Good to know you're interested in our LPA! We have actually built a 96-well version in the past. See photos below:
However, we run into significant heating issues. It turns out that having that many LEDs and TLCs close together generates a lot of heat, which is unevenly distributed throughout the board, which in turn results in unpredictable cell growth rates and very noisy gene expression data. We tried several heat dissipation methods, including heatsinks (which you can see in the figure) and fans, but nothing worked to our satisfaction. Therefore, we never published on this.
I don't know what your firmware issues could be. I'm attaching below the code of the config.h file that we used for the 96-well device. It's been a while since we used it, so I can't guarantee that it will work with the latest firmware version. Remember that a program.lpf file for a 24-well LPA will not be recognized in a 96-well LPA, and this could give rise to a "wrong SD file" error. Also, as an electronic circuit gets faster and more complicated, board design becomes an important variable in terms of trying to aviod electromagnetic coupling. This seems like a decent reference, although it is a little wordy. In short, a circuit with 12 TLCs might be beyond what can be achieved in a breadboard.
In summary, because of the overheating issues, I'd recommend to just stick with the 24-well version and avoid yourself some headaches.
/*
* config.h
*
* Created: 03/03/2014 02:29:05 PM
* Author: Sebastian Castillo
*/
// Global configuration variables
#define F_CPU 16000000UL
// Configuration for Tlc5941 module
#define Tlc5941_GSCLK_DDR DDRB
#define Tlc5941_GSCLK_PORT PORTB
#define Tlc5941_GSCLK_PIN PB0
#define Tlc5941_XLAT_DDR DDRB
#define Tlc5941_XLAT_PORT PORTB
#define Tlc5941_XLAT_PIN PB1
#define Tlc5941_SIN_DDR DDRD
#define Tlc5941_SIN_PORT PORTD
#define Tlc5941_SIN_PIN PD1
#define Tlc5941_MODE_DDR DDRD
#define Tlc5941_MODE_PORT PORTD
#define Tlc5941_MODE_PIN PD2
#define Tlc5941_BLANK_DDR DDRD
#define Tlc5941_BLANK_PORT PORTD
#define Tlc5941_BLANK_PIN PD3
#define Tlc5941_SCLK_DDR DDRD
#define Tlc5941_SCLK_PORT PORTD
#define Tlc5941_SCLK_PIN PD4
#define Tlc5941_TIMER 2
#define Tlc5941_USART_SPI 1
#define Tlc5941_N 12
#define Tlc5941_MANUAL_DC_FUNCS 1
#include <avr/io.h>
#include <avr/pgmspace.h>
#include "Tlc5941/Tlc5941.h"
/*static const Tlc5941_gsData_t well2channel[Tlc5941_numChannels] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107,
108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,
132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,
168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179,
180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191};*/
static const Tlc5941_gsData_t well2channel[Tlc5941_numChannels] PROGMEM = {
95, 94, 81, 80, 79, 78, 65, 64, 63, 62, 49, 48, 47, 46, 33, 32, 31, 30, 17, 16, 15, 14, 1, 0,
93, 92, 83, 82, 77, 76, 67, 66, 61, 60, 51, 50, 45, 44, 35, 34, 29, 28, 19, 18, 13, 12, 3, 2,
91, 90, 85, 84, 75, 74, 69, 68, 59, 58, 53, 52, 43, 42, 37, 36, 27, 26, 21, 20, 11, 10, 5, 4,
89, 88, 87, 86, 73, 72, 71, 70, 57, 56, 55, 54, 41, 40, 39, 38, 25, 24, 23, 22, 9, 8, 7, 6,
103, 102, 105, 104, 119, 118, 121, 120, 135, 134, 137, 136, 151, 150, 153, 152, 167, 166, 169, 168, 183, 182, 185, 184,
101, 100, 107, 106, 117, 116, 123, 122, 133, 132, 139, 138, 149, 148, 155, 154, 165, 164, 171, 170, 181, 180, 187, 186,
99, 98, 109, 108, 115, 114, 125, 124, 131, 130, 141, 140, 147, 146, 157, 156, 163, 162, 173, 172, 179, 178, 189, 188,
97, 96, 111, 110, 113, 112, 127, 126, 129, 128, 143, 142, 145, 144, 159, 158, 161, 160, 175, 174, 177, 176, 191, 190,};
// Time step scaling
#define stepSizeScaling 1.0
HMoerten
tlnagy
Hi,
my name is Hanns-Martin & and after reading your inspiring publication, I have successfully built the 24 well LPA. A little unusual though, since I am a molecular biologist by education, but neither an optogeneticist nor very familiar with coding or with the details of electrotechnical circuitry. I have some experience with the development of biotechnical devices though and was just enthusiastic about the possibility of building a small biotech device in the spirit of the DIY/ maker movement.
After building the device, I simply asked a few labs here in Germany if they were interested of testing the LPA. To make a long story short, I was asked if I could come up with a 96 well solution as well.
Since I am, as mentioned, not all too good at coding (though brave enough to change code here and there), I thought that daisychaining 12 TLC5941s would somehow be the simplest solution. After being able to programm .lpfs with the jupyter notebook files, I found the 96well config.h you put on github and saw no reason why that should not work. On the hardware side, I constructed a breadboard circuit that mirrors the 24 well LPA, with more TLC5941 elements though.
So here comes my problem: I can get an 88 well version with 2 channels each (so 176 channels and TLC 5941_N set to 11) to work with. no problems so far, but whenever I switch to N set to 12 (and 192 channels) I get status LED errors, mainly of the "wrong SD file" type. Neither the compilation of the firmware.elf nor of the program.lpf files show errors. I tried all sorts of things, but have the impression there might be a physical barrier (buffer overflow? SPI limitations?). I have gone through the "demystifying the tlc 5940" book and found that there might be some clocking issues when daisychaining too many controllers.
So...any ideas on the subject? Any kind of help would be greatly appreciated!
Thank you from Cologne, Germany,
Hanns-Martin