Imaging (41)

17 Feb 2014


Kandisky's painting

Mondrian's paintings

Dr Shigeru Watanabe at Keio University is an unique scientist in that he believes that birds and mice have an ability to distinguish fine art. He has published that sparrows and pigeons have the ability to distinguish one form of painting from the other. This might be a basic pattern recognition by the animals but in his recent work, he has shown that though the animals did not possess a preference for one painting vs. the other, they could form relationships between stimuli and paintings. He treated mice with one pleasurable drug, morphine, when exposed to one kind of painter and saline when exposed to another form of painting. Works from Mondrian and Kandinsky were the two painters that were chosen for this experiment. See if you can tell the obvious difference in styles.

Over time, the mice learnt to distinguish the paintings that were linked to the pleasurable drug. This could be a version of the Pavlovian reflex but it does show that the pattern recognition and the analysis machinery in mice eye and brain are advanced enough to distinguish patterns of different painters.

11 Feb 2014

2014-02-11-blender imageIt is always amazing to see that there are several options available for users as they develop 3D models for imaging. The one that is open source and has been gaining significant following is Blender. There are several choices for users for software and there are several websites that will compare the different offerings. The one that seems most impressive is Blender because of the capability, user community and the shear amount of information that is available from the community. Blender enables not only the creation and support of 3D models but makes it possible to create animation, graphics and game character development. It is equivalent or even superior to some of the commercial products that are available. The tutorials are superb and they are of a good variety that are available by individual users as well as the Blender foundation. This product is worth investigating if you are into 3D printing or any other 3D related activity.

29 Aug 2013

Cell change shape frequently as they move and divide but the measurement of the thickness is difficult. Current microscopy techniques can measure the dimensions in X and Y axis very accurately but cannot measure the cell thickness. Confocal microscopy, that is usually used with fluorescence dyes can measure the thickness of the cell but it requires fluorescent label. However, if you need to account for the thickness and enhance the image dependent on thickness then looking through a phase contrast microscope will serve the purpose.

However, it is still useful to get an exact number on the thickness and one company is creating an instrument that will allow the measurement of thickness in real time. Their link is below but they have used their prototype instrument to measure the movement of a paramecium in real time where the colors represent the thickness of the paramecium.

25 Jul 2013

Weather prediction requires significant investment in sensors, computers to predict and calculate and then experts who would interpret the data. However, a group of entrepreneurs have made an app that predicts the weather in the short term with very little investment.

First, what does the application do ? It predicts rain in the short term – is it going to rain in the next hour or so ? That information is most important for many people. Sometimes, when you are waiting to go home and it is raining outside, the question that you have is – will it stop raining in the next 2 hours. That is exactly what the group at Dark sky does.

How they do it? They do image processing of publicly available images of radar weather and use that to calculate how the clouds will behave at that specific location in the short time. Interestingly, this weather calculation only works in the short term and that is exactly what they have been doing for the app. The imaging algorithm first located where you are. Then it looks up the radar images in your location. From there, it figures out how the clouds are moving near you and what the precipitation has been near you.

The imaging algorithms have been the real winner in this app. Look at the groups Kickstarter link to find out more.

24 Jul 2013

The problem: When staining tissues, it is difficult to see through tissue and so most of the time what is done is to section the tissue and then stain for specific proteins to see their distribution within the tissue. Sectioning also enables the tissue to become accessible for the reagents that are used to stain the tissue.

However, for brain as a tissue, it will be great to see the connections between within the neurons and see the whole brain.

Solution: Treat the tissue to make it transparent. Karl Diesseroth from Stanford have enabled the brain tissue to become transparent and enables antibodies to stain the entire brain. The cool factor is the ability to see the distribution of any specific protein all over the brain in glorious three dimensions. They have created an hydrogel that replaces the lipid in the brain and then removed the lipid with electrophoresis. Once that is done then the entire organ like the brain can be stained and looked at whole.

The images look fantastic. Look at the link below for more details but the video from NATURE is very impressive.

18 Jul 2013

ImageJ is one of the popular image analysis programs along with Fiji, Bioimage and Icy. There is another program that is used for image analysis that has several qualities that make it very useful. It is written completely in Java and so can run on multiple platforms, is object oriented for image storage that enables the annotation and the image data to be stored such that they can be addressed independently. It can read multiple formats of images and has more than 140 image processing operations.

Even the user interface is unique. It is available for free and overcomes several limitations in ImageJ and commercial software packages. Definitely, a program to check out…

17 Jul 2013

A Japanese group has compiled images that correspond to those seen by the person in a dream enabling researchers to reconstruct the dreams. In short, this was accomplished in two passes: first recording the images that are relevant to people and then correlating it with the specific areas of brain stimulated, as seen through MRI. Next time, when the people are dreaming, the computer figures out which areas of the brain that were stimulated and then looking up images that were associated with the image in the first pass.

Thus, Horikawa’s group has figured out the images that are seen in the dream. They have published a paper in Science that involved confirming that the subjects were indeed watching/dreaming the images .

16 Jul 2013

It is known that eyes of the common fly is a compound eye with multiple detectors and multiple lenses. It has always been thought that the 180 degree vision would be very useful and could be very high resolution. Though interesting to think about in terms of camera’s, it has been difficult to create multiple camera’s in that orientation. A team at University Urbana Champaign has created the eye purely out of curiosity and has determined two applications of value : Endoscopes and Surveillance. It is interesting that though the compound eye has been known for quite some time, single camera with wide lenses have been used much more.

It will be good to see how these compound eye camera’s get used.

13 Jul 2013

Robert Dudley was trying to design a system that would pick out the ripe cauliflowers that were ripe amidst the leaves. However, he ended up discovering a system that can decide when the strawberries are ripe for picking. His system uses imaging with microwave, light and terahertz radiation. He found that the microwave radiation, that is very sensitive to water, is ideal for picking up the ready to eat ripe strawberries. Of course, the red strawberries can be picked out well when they are under a light camera but covered by leaves, it was difficult for a light imaging system to pick out. However, with microwave radiation could see through relatively dry leaves and spot strawberries easily.

The catch here is that though the farmers may not have the advanced imaging tools, it is possible that such a system coupled with robotic arms could automatically pick strawberries. This would save a lot of labor of picking strawberries.

22 Jun 2013

There have been many ways that people use standards for fluorescence but the one big one that has been used in flow cytometry and imaging. The one area that has developed a lot is the use of plastic fluorescent beads as controls. There are obviously many companies that have developed that but the one company that has developed many beads in this area is called spherotech.

Usin’Life scientists use these beads (pdf here) to set up their controls and standards. This helps in standardizing the instrumentation but also makes them comparable with other companies and customers.

The bead technology has developed substantially, such that now beads come pre-labeled with fluorescent tags of different varieties and they can be managed easily, without worrying about photobleaching, or other complications.

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