Remote lab and 3D reconstruction of confocal images

 

The technological advancements of the age have enabled us to do things which were considered almost impossible just over a few years ago.

For the first time, last month, I started setting up remote access to lab experiments for monitoring and control of experiments. This enables monitoring and administration of operations at night without being in the lab physically.

I have experimented with machine learning methods for image classification and tracking, though it is still in its infancy and the technology needs improvement.

The use of 3D reconstruction of amyloid fibril structure obtained from confocal imagery will provide better information about the structure of fibrils.

Confocal image of fibril
Confocal Z-slice image of fibril
3D reconstructed fibril
3D reconstructed fibril 

 

 

 

 

 

 

 

 

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Deep convolutional neural network for unbiased classification of amyloid fibrils from salt crystals

Image source: “New clues illuminate Alzheimer’s roots”- http://news.rice.edu/2013/07/19/new-clues-illuminate-alzheimers-roots-2/

I am using machine learning in python along with the use of libraries such as Tensorflow and scikit-learn. Recently I re-trained the Google’s inception model to learn and classify what microscopic images look like for amyloid fibrils and for samples one thinks as fibrils but are salt crystals from a buffer solution of NaCl.  The system was designed to provide an unbiased classification(removing expert bias). The Google’s inception model v3 was re-trained on thousands of images of amyloid fibrils and salt crystals taken from peer reviewed journals.

 

Results of running sample cases

 

IOT devices and prototyping boards changing the way we do research

Image source: http://techfactslive.com/

 

Internet of things (IOT) devices has made data acquisition, remote real-time monitoring and remote control. With the advent of new and productive prototyping boards such as the Arduino, Raspberry Pi, and Particle Photon, being IOT capable has revolutionized the way modern day research can be performed. The ease of how they can be customized to the specification of a given project makes it simple enough for anyone with basic programming and electronics experience to develop cutting edge solutions within a span for few hours.

The recent introduction of remote labs around the globe, where people can monitor research work remotely and control devices, has enabled researchers to control and monitor experiments hazardous locations and while traveling. Such remote labs also enable collaboration through remote sharing with investigators around the globe who can access data in real-time and even engage in control of experiments.

The simplicity and infrastructure in the current era also support the use of IOT based devices almost anywhere in the world and for a low cost. Most of the climate control systems, home appliances, etc. have all become IOT devices. With integration of real-time data acquisition and analytics,  we can make conclusions for improvement in a variety of areas including improvement in research methods and reduction of energy consumption not just in labs, but also in our homes

 

 

 

Ease, customizability and security of using linux os

Most of us are familiar with Windows and Mac OSes, and a growing number for Linux based distros.

The sheer ease of use, customizability, and security has led mostly geeks to use Linux based distros.

When Windows 10 came out, most of us believe is higher levels of security in comparison to its past releases. However, even Windows 10  had its flaws, and was never free of viruses or spyware even with its enhanced security features. Mac OSes, OS X, based on UNIX is secure compared to Windows, but comes with expensive hardware and is closed source. Linux distros, however, has all the advantages of UNIX based OSes and is open source with a large number of contributors around the world, including software engineers in major tech firms.

There are various distros with a specific application like Scientific Linux developed by CERN for physic and other scientific research.

Linux is also highly customizable that we can use a stripped down version for own use and which is specific for our purposes. Most of the today’s closed source application also have their Linux variants, like Skype, which makes it suitable for use for our day to day use.

 

Moi linux desktop from Fayaz Rasheed on Vimeo.

Do we actually use all those publications in journals in real life?

Image source: spectrumcenter.umich.edu

It is quite an intriguing question I was asking myself, despite numerous publication in high-quality journals about new research in science, technology, management and psychology; we rarely use them. Be it at the universities that submit the papers to journals or in the people in their real life.

A simple example would be in management, how a school manages or mismanages student experience or how a team in the University administers a conference. How they utilize research in human psychology to avoid anxiety, stress, and harassment to train the students well enough to enable to contribute to the society. The absence of which makes such academic institutions mouthpieces to research with no use of its own.

A classic example of good management by the educational institution was that of the case of one of last year’s APS  conference, where over 30 thousand people were well managed and taken the care off, and without any source of anxiety.

I have also had an exact opposite experience in another conference.

The belief that the productive use of research will benefit society is under question in such cases.

Few modest upgrades


The need of large data backup and for the safe storage of data without the voltage variations damaging USB hard disk drive, a WD cloud drive was found to be ideal . Memory upgrades with high speeds are required for processing of memory heavy datasets and hence the Vengance Pro memory cards with the solid performance and speeds was suitable. The requirement of processing and manipulation of large sets of data was solved by the 640 CUDA core Nvidia EVGA 750 Ti overclocked cards.

 

Finally my own copy of HONY-Humans of New York

Its things like TED talk and Brandon Stanton’s Humans of New York, that re-assures faith in Humanity. HONY tells stories of people not just from New York, but from around the world and makes us feel how similar we are to them. His recent visits to war-zones in world, showed us how misguided the world is about the outlook of the life of people there, through stories of people, kids, families… their simple lives. This captured the hearts of many, made us see a world in a different perspective and many of his Facebook followers, even insisted that he should show this to the world leaders, the U.N and which could hopefully make a difference.

I bought Stanton’s book called HONY Stories to own a piece of history in the making, to show my support to HONY. To remind myself of how simple life is and that everyone has their fair share of problems and moments of happiness in this complicated event called life.

The quality in the not so famous brands

Portable Fireplace. Source: Business Insider.
Portable Fireplace. Image Source: Business Insider.

Most of us, are fond of famous brand names for everyday use varying from clothing to the coffee we drink. Due to the mass production of the products and broad spectrum of services, the product or service might not keep up with the expected level of quality.

 

I recently came across a lot of smaller brands and startups which produced high quality products and provided high quality of service, most of the at cheaper costs than popular brands. The method and technology used by these small brands and startups left me intrigued. Some of the methods of production of commodity and service provided, increases in cost and/or loose quality when the production size is increased. The price range of the commodity of service can vary from being extremely expensive to really cheap in comparison with their popular counterparts.

These brands also have tier own unique identity, with most being designed and hand-crafted differently. It might the masterpiece of indie artists which come out from small studios to a specially designed cafe that serves medicinal tea along with an environment to use free wifi, read and work.