Life is a game, take it seriously

Archive for the ‘Serious Stuffs’ Category

Looking Into Neuron Activities: Light Controlled Mice and Crystal Skulls

In brain, Neural Science, Paper Talk, Serious Stuffs on April 2, 2017 at 9:50 pm

by Li Yang Ku (Gooly)

It might feel like there aren’t that much progress in brain theories recently, we still know very little about how signals are processed in our brain. However, scientists have moved away from sticking electrical probes into cat brains and became quite creative on monitoring brain activities.

Optogenetics techniques, which was first tested in early 2000, allow researchers to activate a neuron in a live brain by light. By controlling the light that activates motor neurons in a mouse, scientists can control its movement remotely, therefore creating a “remote controlled mouse” which you might heard of in some not that popular sci-fi novels. This is achieved by taking the DNA segment of an algae that produces light sensitive proteins and insert it into a specific brain neuron of the mouse using viral vectors. When light is shed on this protein, it opens its ion channel and activates the neuron. The result is pretty cool, but not as precise as your remote control car, yet. (see video below)

Besides the Optogenetics techniques that are used to understand the function of a neuron by actively triggering it, methods for monitoring neuron activities directly have also become quite exciting, such as using genetically modified mice with brain neurons that glow when activated. These approaches that use fluorescent markers to monitor the level of calcium in the cell can be traced back to the green fluorescent proteins introduced by Chalfie etc in 1994. With fluorescent indicators that binds with calcium, researcher can actually see brain activities the first time. A lot of progress have been made on improving these markers since; in 2007 a group in Harvard introduced the “Brainbow” that can generate up to 90 different fluorescent colors. This allowed scientists to identify neuron connection a lot easier and also helped them won a few photo contests.

To better observe these fluorescent protein sensors (calcium imaging), a recent publication in 2016 further introduced the “crystal skull”, an approach that replaces the top skull of a genetically modified mouse with a curved glass. This quite fancy approach allows researchers to monitor half a million brain neuron activities of a live mouse through mounting a fluorescence macroscope on top of the crystal skull.

References:

Chalfie, Martin. “Green fluorescent protein as a marker for gene expression.” Trends in Genetics 10.5 (1994): 151.

Madisen, Linda, et al. “Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance.” Neuron 85.5 (2015): 942-958.

Josh Huang, Z., and Hongkui Zeng. “Genetic approaches to neural circuits in the mouse.” Annual review of neuroscience 36 (2013): 183-215.

Kim, Tony Hyun, et al. “Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex.” Cell Reports 17.12 (2016): 3385-3394.

 

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Organizing Publications Visually: EatPaper

In Paper Talk, Serious Stuffs on January 13, 2013 at 2:44 pm

by Gooly (Li Yang Ku)

eatpaper.org

I always hoped that there would be a good app to organize the papers I read and show it graphically. I did Google for it but couldn’t find one that fits my need, so I started to build one about a year ago (EatPaper.org). I stopped working on it several times for various reasons but now it’s finally functional (not perfect, but enough for now). The website functions a little bit like Pinterest, we both use bookmarklet, a website book mark that executes javascript, to fetch your current webpage. So the following are the typical steps to use EatPaper.

1. Search on Google scholar.

2. Click the bookmark button I made. (You can get the button by clicking “Add a Node” in EatPaper.org)

3. A dialog pops up and you can store the publication information you found as a node in your graph.

I also made a Chrome extension that has the exact same function.

eatpaper.org

The website is built using Google App Engine + Google Web Toolkit. If it turns out to be a little bit slow occasionally, please be patient; I have to admit that I don’t have any funding and only pay the minimum amount needed to host the server. Please share it to your friends if you like it. I probably can get more resources if more people use it.

You can leave a message here if you have any opinions, problems or found a bug.

Why I didn’t blog for 6 month – Facebook App for Blog Promotion

In facebook, Serious Stuffs on November 28, 2011 at 12:01 am

written by Gooly

CheerRabbit

6 month ago I was very enthusiastic about blogging, I felt it was extremely wonderful to share all the stuffs I knew. I made up a long list of stuffs I planned to talk about in computer vision and also prepared to share my Matlab code that recognizes different objects in different angles. Since computer vision wasn’t a popular field, I got roughly 5 visitors a day and a few comments over all. I believe the number will grow and I was very satisfied with it.

CheerRabbit Promote Your Blog

One morning while I was driving along PCH to work and thinking about what other cool stuffs I could talk about,  I suddenly came up with a question “How should I let other people in computer vision find my blog?” It was almost impossible to find it through Google, and I never searched a blog in WordPress.com (so I don’t think others will). This question also bugged me when I thought of making an Android app that adjusts photo images taken in the dark; if I can’t advertise it, nobody will use it even if it’s free and good. Currently the best way to advertise is probably Google AdSense, something I never clicked on. There should be a better way for individuals to advertise in a simple way for free.

CheerRabbit Facebook Promotion I finally came up with a simple answer: Facebook. If I ask a friend to help me post my blog link on her Facebook, all of her friends can see it. And if I’m lucky, one of them might become my blogs loyal reader and share it on Facebook again. In return, I’ll also help my friend share her blog link on my Facebook.

If this is effective, we can extend beyond our friends to anyone who has a blog or even anyone who want’s to share something and exchange Facebook posts. I thought that was a good idea and started building an app that does this, and this is what I worked on in my spare time for the past 6 month.

Website: http://cheerrabbit.com

CheerRabbit is currently finished and public, but still needs to be adjusted to fit the market.

A Need to Change in Survival Strategy: the merge of world wide web and real world

In Serious Stuffs on April 15, 2011 at 9:57 am

written by Gooly

Since the big bang of the world-wide web, our world split into the real world and the virtual world. We all live in the real world physically, but could be spiritually in the virtual world “completely”. In the good old 2000s, there used to be a simple way to circle people from different professions into groups on the socially active axis, like the one below. However, recent year’s rapid change in social network makes this no longer true.

If you do regression on the graph above you would very likely get a negative slope; since with limited time and passion one could hardly be extremely active in both axis.

Back in the good old 2000s, you’ll probably do pretty good just by working hard in one world, this is due to the following success equation at that time.

As you can see, what you do in one world doesn’t affect your achievement in the other world. For example, even if you defeated the evil lord after a 10 hour war and step on others to obtain the glory to become the leader of your whole tribe in the virtual world, you still need to take the midterm tomorrow, and your professor won’t even praise on your epic accomplishment. This is why parents used to be the biggest enemy of online games. They simply believe that the parameter B in the equation is significantly small compared to A. Since parents definitely heard of the famous quote ” Everything is Optimization” by Stephen P. Boyd, they would know the best way to gain the most is to put all the efforts in the real world. I have to say they are probably right under this equation, but we’ll see that this is no longer true.

After the rapid change in the virtual world due to the thrive of one various social networks, the real world and the virtual world is merging. It’s harder to hide after nick names on the web, sites remember who you actually are. What happens on the virtual world directly affects your real world; saying something wrong on the web will very likely hit you hard in the real world. The old equation no longer reflects reality. This gives us the following more adequate success equation for the current world.

Now we have 3 parameters instead of 2 ( A B and C are usually positive, most people  have C > 1), which makes life even more complicated. To optimize success, we have to first estimate A B C and put the exact amount of effort on both world. However A B and C differs between people and changes with time, therefore we have to do a series of experiments and probably adjust the weights along the time.

But this is not the main point, what is significant is that the equation changed from addition to multiplication. What you do on the web will largely affect your total result. You can no longer be extremely success by just working hard in the real world; internet do matters. Politicians, doctors, lawyers all have to jump into the virtual world to get the most; if they don’t, their colleagues would.

This might also mean that in the near future, your professor probably would appreciate you for stopping an evil empire expanding to his tribe.

Life is a game, take it seriously

In Serious Stuffs on April 13, 2011 at 4:02 am

This page is here so I can modify it some time later pretending I said it the first day.