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ref: -0 tags: optogenetics micro LED flexible electrodes PET rogers date: 12-28-2017 03:24 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-23580530 Injectable, cellular-scale optoelectronics with applications for wireless optogenetics.

  • Supplementary materials
  • 21 authors, University Illinois at Urbana-Champaign, Tufts, China, Northwestern, Miami ..
  • GaN blue and green LEDs fabricated on a flexible substrate with stiff inserter.
    • Inserter is released in 15 min with a dissolving silk fibrin.
    • made of 250um thick SU-8 epoxy, reverse photocured on a glass slide.
  • GaN LEDS fabricated on a sapphire substrate & transfer printed via modified Karl-Suss mask aligner.
    • See supplemental materials for the intricate steps.
    • LEDs are 50um x 50um x 6.75um
  • Have integrated:
    • Temperature sensor (Pt serpentine resistor) / heater.
    • inorganic photodetector (IPD)
      • ultrathin silicon photodiode 1.25um thick, 200 x 200um^2, made on a SOI wafer
    • Pt extracellular recording electrode.
        • This insulated via 2um thick more SU-8.
  • Layers are precisely aligned and assembled via 500nm layer of epoxy.
    • Layers made of 6um or 2.5um thick mylar (polyethylene terephthalate (PET))
    • Layers joined with SU-8.
    • Wiring patterned via lift-off.
  • Powered via RF scavenging at 910 Mhz.
    • appeared to be simple, power in = light out; no data connection.
  • Tested vs control and fiber optic stimulation, staining for:
    • Tyrosine hydroxylase (makes l-DOPA)
    • c-fos, a neural activity marker
    • u-LEDs show significant activation.
  • Also tested for GFAP (astrocytes) and Iba1 (activated microglia); flexible & smaller devices had lower gliosis.
  • Next tested for behavior using a self-stimulation protocol; mice learned to self-stimulate to release DA.
  • Devices are somewhat reliable to 250 days!

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ref: -0 tags: micro LEDS Buzaki silicon neural probes optogenetics date: 04-18-2016 18:00 gmt revision:0 [head]

PMID-26627311 Monolithically Integrated μLEDs on Silicon Neural Probes for High-Resolution Optogenetic Studies in Behaving Animals.

  • 12 uLEDs and 32 rec sites integrated into one probe.
  • InGaN monolithically integrated LEDs.
    • Si has ~ 5x higher thermal conductivity than sapphire, allowing better heat dissipation.
    • Use quantum-well epitaxial layers, 460nm emission, 5nm Ni / 5nm Au current injection w/ 75% transmittance @ design wavelength.
      • Think the n/p GaN epitaxy is done by an outside company, NOVAGAN.
    • Efficiency near 80% -- small LEDs have fewer defects!
    • SiO2 + ALD Al2O3 passivation.
    • 70um wide, 30um thick shanks.

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ref: -0 tags: Peter Ledochowitsch ECoG parylene fabrication MEMS date: 09-25-2014 16:54 gmt revision:0 [head]

IEEE-5734604 (pdf) Fabrication and testing of a large area, high density, parylene MEMS µECoG array

  • Details 5-layer platinum parylene process for high density ECoG arrays.

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ref: Ledochowitsch-2011.01 tags: Ledochowitsch transparent micro ECoG Peter date: 01-30-2013 07:01 gmt revision:2 [1] [0] [head]

PMID-22254956[0] A transparent μECoG array for simultaneous recording and optogenetic stimulation.

  • We present a 49-channel μECoG array with an electrode pitch of 800 μm and a 16-channel linear μECoG array with an electrode pitch of 200 μm.
  • The backing material was Parylene C. Transparent, sputtered indium tin oxide (ITO) was used in conjunction with e-beam evaporated gold to fabricate the electrodes


[0] Ledochowitsch P, Olivero E, Blanche T, Maharbiz MM, A transparent μECoG array for simultaneous recording and optogenetic stimulation.Conf Proc IEEE Eng Med Biol Soc 2011no Issue 2937-40 (2011)

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ref: Fontani-2007.12 tags: mental training skilled motor control date: 01-03-2012 02:33 gmt revision:2 [1] [0] [head]

PMID-18229536[0] Effect of mental imagery on the development of skilled motor actions.

  • with trained subjects (performing something called Ura-Shuto-Uchi (Japanese? but the researchers are Italian)) showed a decrease in reaction time and EMG activity, as well as a increase in movement speed, muscle strength, power, and work. These results did not apply to untrained individuals. EEG also apparently changed vs. the untrained condition.


[0] Fontani G, Migliorini S, Benocci R, Facchini A, Casini M, Corradeschi F, Effect of mental imagery on the development of skilled motor actions.Percept Mot Skills 105:3 Pt 1, 803-26 (2007 Dec)

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ref: -0 tags: artificial intelligence machine learning education john toobey leda cosmides date: 12-13-2010 03:43 gmt revision:3 [2] [1] [0] [head]

Notes & responses to evolutionary psychologists John Toobey and Leda Cosmides' - authors of The Adapted Mind - essay in This Will change Everything

  • quote: Currently the most keenly awaited technological development is an all-purpose artificial intelligence-perhaps even an intelligence that would revise itself and grow at an ever-accelerating rate until it enacts millennial transformations. [...] Yet somehow this goal, like the horizon, keeps retreating as fast as it is approached.
  • AI's wrong turn was assuming that the best methods for reasoning and thinking are those that can be applied successfully to any problem domain.
    • But of course it must be possible - we are here, and we did evolve!
    • My opinion: the limit is codifying abstract, assumed, and ambiguous information into program function - e.g. embodying the world.
  • Their idea: intelligences use a number of domain-specific, specialized "hacks", that work for limited tasks; general intelligence appears as a result of the combination of all of these.
    • "Our mental programs can be fiendishly well engineered to solve some problems because they are not limited to using only those strategies that can be applied to all problems."
    • Given the content of the wikipedia page (above), it seems that they have latched onto this particular idea for at least 18 years. Strange how these sorts of things work.
  • Having accurate models of human intelligence would achieve two things:
    • It would enable humans to communicate more effectively with machines via shared knowledge and reasoning.
    • (me:) The AI would be enhanced by the tricks and hacks that evolution took millions of years, billions of individuals, and 10e?? (non-discrete) interactions between individuals and the environment. This constitutes an enormous store of information, to overlook it necessitates (probably, there may be seriuos shortcuts to biological evolution) re-simulating all of the steps that it took to get here. We exist as a cashed output of the evolutionary algorithm; recomputing this particular function is energetically impossible.
  • "The long term ambition [of evolutionary psychology] is to develop a model of human nature as precise as if we had the engineering specifications for the control systems of a robot.
  • "Humanity will continue to be blind slaves to the programs evolution has built into our brains until we drag them into the light. Ordinarily, we inhabit only the versions of reality that they spontaneously construct for us -- the surfaces of things. Because we are unaware that we are in a theater, with our roles and our lines largely written for us by our mental programs, we are credulously swept up in these plays (such as the genocidal drama of us versus them). Endless chain reactions among these programs leave us the victims of history -- embedded in war and oppression, enveloped in mass delusions and cultural epidemics, mired in endless negative-sum conflict \\ If we understood these programs and the coordinated hallucinations they orchestrate in our minds, our species could awaken from the roles these programs assign to us. Yet this cannot happen if knowledge -- like quantum mechanics -- remains forever locked up in the minds of a few specialists, walled off by the years of study required to master it. " Exactly. Well said.
    • The solution, then: much much better education; education that utilizes the best knowledge about transferring knowledge.
    • The authors propose video games; this is already being tested, see {859}

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ref: notes-0 tags: blackfin LED kernel module linux BF537 STAMP tftp BF537 bridge date: 11-13-2007 17:59 gmt revision:4 [3] [2] [1] [0] [head]

so, you want to control the LEDs on a BF537-STAMP board? You'll need a linux box with a serial port, then will need to do a few things:

  1. get the blackfin build tools:
    1. download the RPM file from blackfin.uclinux.org and use alien (if you are on debian, like me) to install it.
    2. installation instructions
  2. get uClinux distribution and compile it. http://blackfin.uclinux.org/gf/project/uclinux-dist/frs/
    1. unpack it to a local directory
    2. 'make menuconfig'
    3. select your vendor & device
    4. make sure runtime module loading is enabled.
    5. 'make' (it takes much less time than the full linux kernel)
    6. this will result in a linux.bin image, which uBoot can use.
  3. you need to set up a tftp server for uboot, see http://linuxgazette.net/125/pramode.html
  4. attach the blackfin stamp to the serial port on your computer. configure kermit with:
    set line /dev/ttyS1
    set speed 57600
    set carrier-watch off
    set prefixing all
    set parity none
    set stop-bits 1
    set modem none
    set file type bin
    set file name lit
    set flow-control none
    set prompt "Linux Kermit> " 
    (this is assuming that your serial port is /dev/ttyS1)
  5. power on the stamp, at the uBoot prompt press space.
  6. issue the following commands:
    set serverip
    set ipaddr
    tftpboot 0x1000000  linux
    bootelf 0x1000000 
    to get the device to boot your new uClinux image from SDRAM. your IP addresses will vary.
    1. note: you can boot any ELF image at this point; for example, the 'blink' example in the blackfin tool trunk SVN, 'make' produces a ELF file, which can be loaded into SDRAM via tftp and executed. I'm not sure what part of L1 uboot uses for its instruction, but conceivably you could load into L1 / data ram and execute from there. see also {403} you would do something like:
set serverip
set ipaddr
tftpboot 0x1000000  blink
bootelf 0x1000000 
  1. at the uCLinux prompt : ifconfig eth0
  2. write a simple kernel module, for example:
    #include <linux/module.h>
    //#include <linux/config.h>
    #include <linux/init.h>
    #include <linux/fs.h>
    #include <asm/uaccess.h>
    #include <asm/blackfin.h>
    #include <asm/io.h>
    #include <asm/irq.h>
    #include <asm/dma.h>
    #include <asm/cacheflush.h>
    int major;
    char *name = "led";
    int count = 0;
    ssize_t led_write(struct file* filp, const char *buf, size_t size, loff_t *offp)
    	printk("LED write called "); 
    	if (size < 2) return -EMSGSIZE;
    	if (!buf) return -EFAULT;
    	printk("led_write called with: %s ", buf); 
    	if(buf[0] == '0') {bfin_write_PORTFIO_CLEAR(1<< 6); }
    	else{ bfin_write_PORTFIO_SET(1<<6); }
    	return size;
    int led_open(struct inode *inode, struct file *file){
    	printk("led opened"); 
    	return 0; 
    int led_release(struct inode *inode, struct file *file){
    	printk("led released"); 
    	return 0; 
    struct file_operations fops = {
    	 .owner = THIS_MODULE,
    	.read = NULL,
    	.write = led_write,
    	.open = led_open,
    	.release = led_release
    int __init init_module(void)
    	// Set PF2 as output -- clear the FER bit.
    	bfin_write_PORTF_FER(bfin_read_PORTF_FER() & (~(1 << 6))); 
    	bfin_write_PORTFIO_SET(1<< 6);
    	bfin_write_PORTFIO_DIR(bfin_read_PORTFIO_DIR() | (1<<6)); 
    	major = register_chrdev(0, name, &fops);//hope it succeeds!
    	printk("registered, major = %d ", major); 
    	printk("portF = %d", bfin_read_PORTFIO()); 
    	printk("portF_FER = %d", bfin_read_PORTF_FER()); 
    	printk("portF_DIR = %d", bfin_read_PORTFIO_DIR()); 
    	return 0;
    void __exit cleanup_module(void)
    	unregister_chrdev(major, name);
    	printk("led: cleanup "); 
  3. write a makefile for this module, for example:
            make -C /uClinux-dist/linux-2.6.x/ M=`pwd`
  4. setup apache on your computer, e.g. 'apt-get install apache2'
  5. 'ln -s' your build directory to /var/www/, so that you can wget the resulting kernel module
  6. rm led.ko
    wget (for example)
    insmod led.ko
    rm /dev/led
    mknod /dev/led c 253 0
    chmod 0644 /dev/led
    echo 1 >> /dev/led