Tag Archives: anatomy

The Biodiversity Heritage Library made over 150,000 illustrations and 55 million pages of research free to download

The world’s “largest open-access digital library for biodiversity literature and archives” has made 55 million pages of literature and at least 150,000 illustrations open for the public to enjoy.

Illustration from the Transactions of the Entomological Society of London, 1911.
Image credits Biodiversity Heritage Library / Flickr.

Do you like life, science, cool art, or all three? Then the Biodiversity Heritage Library (BIH) has a treat for you. The BIH pools together diagrams, sketches, studies, and data pertaining to life on Earth from hundreds of thousands of journals and libraries, some of them from as far back as the 15th century. You can see it all, and download it all, without paying a dime.

Science for all

“To document Earth’s species and understand the complexities of swiftly-changing ecosystems in the midst of a major extinction crisis and widespread climate change, researchers need something that no single library can provide – access to the world’s collective knowledge about biodiversity,” the Library’s about page explains.

“Scientists have long considered this lack of access to biodiversity literature as a major impediment to the efficiency of scientific research.”

The sheer wealth of information that the BIH contains is staggering. However, this is a goldmine even if you’re not too keen on learning biology, even if you don’t need some citations for your degree paper — there is a lot of beauty to be found here. Illustrations of plants, animals, and the biological mechanisms that keep them going abound. They’re analyzed in hand-drawn diagrams, detailed in bright watercolors, and celebrated in dazzling lithography.

From “Report on the work of the Horn Scientific Expedition to Central Australia, pt. 2 – zoology, London: Dulau, 1896.”
Image credits Biodiversity Heritage Library / Flickr.
From “Beiträge zur Pflanzenkunde des Russischen Reiches. Lf. 10 (1857)”.
Image credits Biodiversity Heritage Library / Flickr.

Among the works in the BIH is a digitized copy of Joseph Wolf’s 19th-century The Zoological Sketches, two volumes totaling around 100 lithographs of wild animals kept in London’s Regent’s Park (which are drop-dead gorgeous). Dig around deep enough and you will find a DIY taxidermy guide, full with illustrated guides, published in 1833. Weird, but cool. One of my personal favorites is Osteographia, or the Anatomy of the Bones, a body of sketches published in London, 1733, looking at the human skeleton and its afflictions. Die Cephalopoden by one G. Fischer and Margaret Scott’s British sea-weeds could easily pass for surrealist artwork in my book. The striking yet translucent watercolors of The genus Iris make for an almost otherworldly look at the family of flowers.

From “Die Cephalopoden T.2”.
Image credits Biodiversity Heritage Library / Flickr.
From “British sea-weeds, v. 1”.
Image credits Biodiversity Heritage Library / Flickr.
From “The genus Iris”.
Image credits Biodiversity Heritage Library / Flickr.

Still, this is, when you get down to it, a resource aimed at scientists. As such, it comes with a wide range of tools to help navigation and assist research: these include features to monitor online conversations related to books and articles in the archive or to find works related to a particular species. But, if all you want to do is look at the pretty pictures (I don’t blame you), the BIH also has an Instagram and Flickr account that you can check out.

“Through Flickr, BHL provides access to over 150,000 illustrations, enabling greater discovery and expanding its audience to the worlds of art and design. BHL also supports a variety of citizen science projects that encourage volunteers to help enhance collection data,” the Library’s about page adds. “Since its launch in 2006, BHL has served over 8 million people in over 240 countries and territories around the world.”

“Through ongoing collaboration, innovation, and an unwavering commitment to open access, the Biodiversity Heritage Library will continue to transform research on a global scale and ensure that everyone, everywhere has the information and tools they need to study, explore and conserve life on Earth.”

That’s definitely a goal I can get behind.

Meet your new organ: the interstitium

Doctors have identified a previously unknown feature of human anatomy with many implications for the functions of most organs and tissues, and for the mechanisms of most major diseases.

Structural evaluation of the interstitial space. (A) Transmission electron microscopy shows collagen bundles (asterisks) that are composed of well-organized collagen fibrils. Some collagen bundles have a single flat cell along one side (arrowheads). Scale bar, 1 μm. (B) Higher magnification shows that cells (arrowhead) lack features of endothelium or other types of cells and have no basement membrane. Scale bar, 1 μm. (C) Second harmonics generation imaging shows that the bundles are fibrillar collagen (dark blue). Cyan-colored fibers are from autofluorescence and are likely elastin, as shown by similar autofluorescence in the elastic lamina of a nearby artery (inset) (40×). (D) Elastic van Gieson stain shows elastin fibers (black) running along collagen bundles (pink) (40×).

A new paper published on March 27th in Scientific Reports, shows that layers of the body long thought to be dense, connective tissues — below the skin’s surface, lining the digestive tract, lungs, and urinary systems, and surrounding arteries, veins, and the fascia between muscles — are instead interconnected, fluid-filled spaces.

Scientists named this layer the interstitium — a network of strong (collagen) and flexible (elastin) connective tissue fibers filled with fluids, that acts like a shock absorber to keep tissues from rupturing while organs, muscles, and vessels constantly pump and squeeze throughout the day.

This fluid layer that surrounds most organs may explain why cancer spreads so easily. Scientists think this fluid is the source of lymph, the highway of the immune system.

In addition, cells that reside in the interstitium and collagen bundles they line, change with age and may contribute to the wrinkling of skin, the stiffening of limbs, and the progression of fibrotic, sclerotic and inflammatory diseases.

Scientists have long known that more than half the fluid in the body resides within cells, and about a seventh inside the heart, blood vessels, lymph nodes, and lymph vessels. The remaining fluid is “interstitial,” and the current paper is the first to define the interstitium as an organ in its own right and, the authors write, one of the largest of the body, the authors write.

A team of pathologists from NYU School of Medicine thinks that no one saw these spaces before because of the medical field’s dependence on the examination of fixed tissue on microscope slides. Doctors examine the tissue after treating it with chemicals, slicing it thinly, and dyeing it in various colorations. The “fixing” process allows doctors to observe vivid details of cells and structures but drains away all fluid. The team found that the removal of fluid as slides are made makes the connective protein meshwork surrounding once fluid-filled compartments to collapse and appear denser.

“This fixation artifact of collapse has made a fluid-filled tissue type throughout the body appear solid in biopsy slides for decades, and our results correct for this to expand the anatomy of most tissues,” says co-senior author Neil Theise, MD, professor in the Department of Pathology at NYU Langone Health. “This finding has potential to drive dramatic advances in medicine, including the possibility that the direct sampling of interstitial fluid may become a powerful diagnostic tool.”

Researchers discovered the interstitium by using a novel medical technology — Probe-based confocal laser endomicroscopy. This new technology combines the benefits of endoscopy with the ones of lasers. The laser lights up the tissues, sensors analyze the reflected fluorescent patterns, offering a microscopic real-time view of the living tissues.

When probing a patient’s bile duct for cancer spread, endoscopists and study co-authors Dr. David Carr-Locke and Dr. Petros Benias observed something peculiar — a series of interconnected spaces in the submucosa level that was never described in the medical literature.

Baffled by their findings, they asked Dr. Neil Theise, professor in the Department of Pathology at NYU Langone Health and co-author of the paper for help in resolving the mystery. When Theise made biopsy slides out of the same tissue, the reticular pattern found by endomicroscopy vanished. The pathology team would later discover that the spaces seen in biopsy slides, traditionally dismissed as tears in the tissue, were instead the remnants of collapsed, previously fluid-filled, compartments.

Researchers collected tissues samples of bile ducts from 12 cancer patients during surgery. Before the pancreas and the bile duct were removed, patients underwent confocal microscopy for live tissue imaging. After recognizing this new space in images of bile ducts, the team was able to quickly spot it throughout the body.

Theise believes that the protein bundles seen in the space are likely to generate electrical current as they bend with the movements of organs and muscles, and may play a role in techniques like acupuncture.

Another scientist involved in the study was first author Rebecca Wells of the Perelman School of Medicine at the University of Pennsylvania, who determined that the skeleton in the newfound structure was comprised of collagen and elastin bundles.

Browse the brain one cell at a time in the most detailed atlas ever made

The new Allen Brain Atlas combines neuroimaging and detailed cell studies to create the most detailed ever map of the brain.

Image credits Ed S. Lein et al., 2016.

Image credits Ed S. Lein et al., 2016.

One of the biggest hurdles neuroscientists face today is the incredible complexity of the organ they work with. Because so many different parts come together to make it work (and because so many of those parts are so tiny) there isn’t an exact template of where each piece starts and where it ends. But now, after a five-year-long effort, Ed Lein and his colleagues from the Allen Institute for Brain Science in Seattle have put together a comprehensive, open-access digital atlas of the human brain — think of it as the Google map of the brain, complete with markers and street-view.

Where’s what

“Essentially what we were trying to do is to create a new reference standard for a very fine anatomical structural map of the complete human brain,” says Ph.D. and Lead Investigator at the Allen Institute for Brain Science Ed Lein.

“It may seem a little bit odd, but actually we are a bit lacking in types of basic reference materials for mapping the human brain that we have in other organisms like mouse or like monkey, and that is in large part because of the enormous size and complexity of the human brain.”

The project was based on a single healthy postmortem brain of a 34-year-old woman. The team started by taking full scans of the organ in magnetic resonance and diffusion weighted imaging to capture the overall structure and the way fibers connect inside the brain. Then, it was time to look inside. The brain was sliced up into 2,716 thin sections for cellular analysis. Parts of these sheets of brain were dyed with Nissl stain, and their cell architecture was examined. The team then used two other stains to selectively label certain aspects of the brain, such as structural elements of cells, fibers in the white matter, and specific types of neurons.

Based on the Nissl-stained slides, the team cataloged 862 distinct brain structures, finding some novel subregions of the thalamus and amygdala and two other structures that have previously only been described in non-human primates.

When the team put the overall high-resolution data together with the detailed, cellular-level structure of each area, they annotated the atlas with the brain structure they identified. Lein explains that the atlas is available online so people can “navigate it, and move from the macro level all the way right into the cellular level.”

He says that the atlas will become an invaluable tool for neuroscientists to use as common starting material — a set of well-defined areas on which they can later add more levels of annotation based on the criteria they need.

“To understand the human brain, we need to have a detailed description of its underlying structure,” says Lein.

One brain to map them all

Mapping the human brain has long been a major goal of neuroscientists who are trying to make heads and tails of how it works, what its parts are and what these parts actually do. Last year, researchers from the Human Connectome Project released a detailed brain map based on multiple MRI measurements recorded from 210 healthy patients. Lein and his colleagues chose to concentrate their efforts on only one brain to go into a lot more detail with their work.

“Because of the labor intensiveness of doing this, it always lives in the scale of a single brain,” Lein says, “and you really go to town in trying to understand everything you can about that one individual.”

But going in-depth on a single specimen also has its drawbacks. Human Connectome Project researcher Matthew Glasser thinks that the Allan Brain Atlas is “impressive” particularly on a neuroanatomical level, but points out that it might be hard to generalize the findings to the whole human race.

“The thing that’s a challenge is relating a single brain like this that’s very intensively studied to other brains,” Glasser says.

But the thing to remember is that before these two datasets became available, the best reference material we’ve had was put together in 1909, when German anatomist Korbinian Brodmann used Nissl staining to create a cellular-scale brain map. Most brain-mapping efforts to date are still based on Brodmann’s work — hopefully, the new Allen Brain Atlas will speed up such efforts in the future.

“There simply hasn’t been a complete map of the human brain as a reference piece of material for anyone studying any part of the brain,” Lein says, “and this is a completely essential part of doing research.”

[button url=”http://brain-map.org/” postid=”” style=”btn-danger” size=”btn-lg” target=”_self” fullwidth=”false”]Browse the Allen Brain Atlas[/button]

The full paper “Comprehensive cellular-resolution atlas of the adult human brain” has been published in The Journal of Comparative Neurology.


How the eye works


Image via flickr. 

Doing some light reading

Touch interprets changes of pressure, texture and heat in the objects we come in contact with. Hearing picks up on pressure waves, and taste and smell read chemical markers. Sight is the only sense that allows us to make heads and tails of some of the electromagnetic waves that zip all around us — in other words, seeing requires light.

Apart from fire (and other incandescent materials), bioluminiscent sources and man-made objects (such as the screen you’re reading this on) our environment generally doesn’t emit light for our eyes to pick up on. Instead, objects become visible when part of the light from other sources reflects off of them.

Let’s take an apple tree as an example. Light travels in a (relatively) straight line from the sun to the tree, where different wavelengths are absorbed by the leaves, bark and apples themselves. What isn’t absorbed bounces back and is met with the first layer of our eyes, the thin surface of liquid tears that protects and lubricates the organ. Under it lies the cornea, a thin sheet of innervated transparent cells.

Behind them, there’s a body of liquid named the aqueous humor. This clear fluid keeps a constant pressure applied to the cornea so it doesn’t wrinkle and maintains its shape. This is a pretty important role, as that layer provides two-thirds of the eye’s optical power.

Anatomy of the eye.
Image via flikr

The light is then directed through the pupil. No, there’s no schoolkids in your eye; the pupil is the central, circular opening of the iris, the pretty-colored part of our eyes. The iris contracts or relaxes to allow an optimal amount of light to enter deeper into our eyes. Without it working to regulate exposure our eyes would be burned when it got bright and would struggle to see anything when it got dark.

The final part of our eye’s focusing mechanism is called the crystalline lens. It only has half the focusing power of the cornea but its most important function is that it can change how it does this. The crystalline is attached to a ring of fibrous tissue on its equator, that pull on the lens to change its shape (a process known as accommodation), allowing the eye to focus on objects at various distances.

Fun fact: You can actually observe how the lens changes shape. Looking at your monitor, hold your up hands some 5-10 centimeters (2-4 inches) in front of your eyes and look at them till the count of ten. Then put them down; those blurry images during the first few moments and the weird feeling you get in your eyes are the crystalline stretching to adapt to the different focal vision.
Science at its finest.

After going through the lens, light passes through a second (but more jello-like) body of fluid and falls on an area known as the retina. The retina lines the back of the eye and is the area that actually processes the light. There are a lot of different parts of the retina working together to keep our sight crispy clear, but three of them are important in understanding how we see.

  • First, the macula. This is the “bull’s eye” of the retina. At the center of the macula there’s a slight dip named the fovea centralis (fovea is latin for pit). As it lies at the focal point of the eye, the fovea is jam-packed with light sensitive nerve endings called photoreceptors.
  • Photoreceptors. These differentiate in two categories: rods and cones. They’re structurally and functionally different, but both serve to encode light as electro-chemical signals.
  • Retinal pigment epithelium. The REP is a layer of dark tissue whose cells absorb excess light to improve the accuracy of our photoreceptors’ readings. It also delivers nutrients to and clears waste from the retina’s cells.

So far you’ve learned about the internal structure of your eyes, how they capture electromagnetic light, focus it and translate it into electro-chemical signals. They’re wonderfully complex systems, and you have two of them. Enjoy!

There’s still something I have to tell you about seeing, however. Don’t be alarmed but….

The images are all in your head

While eyes focus and encode light into the electrical signals our nervous system uses to communicate, they don’t see per se. Information is carried by the optical nerves to the back of the brain for processing and interpretation. This all takes place in an area of our brain known as the visual cortex.

Brain shown from the side, facing left. Above: view from outside, below: cut through the middle. Orange = Brodmann area 17 (primary visual cortex)
Image via wikipedia

Because they’re wedged in your skull a short distance apart from each other, each of your eyes feeds a slightly different picture to your brain. These little discrepancies are deliberate; by comparing the two, the brain can tell how far an object is. This is the mechanism that ‘magic eye’ or autostereogram pictures attempt to trick, causing 2D images to appear three dimensional.  Other clues like shadows, textures and prior knowledge also help us to judge depth and distance.

[YOU SHOULD  ALSO READ] The peculiar case of a woman who could only see in 2-D for 48 years, and the amazing procedure that gave her stereo-vision

The neurons work together to reconstruct the image based on the raw information the eyes feed them. Many of these cells respond specifically to edges orientated in a certain direction. From here, the brain builds up the shape of an object. Information about color and shading are also used as further clues to compare what we’re seeing with the data stored in our memory to understand what we’re looking at. Objects are recognized mostly by their edges, and faces by their surface features.

Brain damage can lead to conditions that impair object recognition (an inability to recognize the objects one is seeing) such as agnosia.  A man suffering from agnosia was asked to look at a rose and described it as ‘about six inches in length, a convoluted red form with a linear green attachment’. He described a glove as ‘a continuous surface infolded on itself, it appears to have five outpouchings’. His brain had lost its ability to either name the objects he was seeing or recognize what they were used for, even though he knew what a rose or a glove was. Occasionally, agnosia is limited to failure to recognize faces or an inability to comprehend spoken words despite intact hearing, speech production and reading ability.

The brain also handles recognition of movement in images. Akinetopsia, a movement-recognition impairing condition is caused by lesions in the posterior side of the visual cortex. People suffering from it stop seeing objects as moving, even though their sight is otherwise normal. One woman, who suffered such damage following a stroke, described that when she poured a cup of tea the liquid appeared frozen in mid-air, like ice. When walking down the street, she saw cars and trams change position, but not actually move.


Breathtaking digital images probe human anatomy like never before


Often called  a “Digital Age Leonardo da Vinci”, Alexander Tsiaras is a digital innovator, technologist and artist. You might know him from his work that showcases beautiful digital images of the human body, made using cutting edge imaging software along with artsy tweaks. Guided by a passion for the human form and insides, Tsiaras founded the TheVisualMD, an extensive online library that documents human anatomy and illness, as well as Anatomical Travelogue, a company specialized in creating digital works of art that faithfully show the workings of the human body. He also authored a number of well received books like From Conception to Birth: A Life Unfolds, The Architecture and Design of Man and Woman: The Marvel of the Human Body, Revealed, The InVision Guide to a Healthy Heart and The InVision Guide to Sexual Health. 


Tsiaras and his team create the works using full-body scans, ultra-powerful microscopes and molecular modeling tools that allow them to illustrate the body in vivid detail, for both 3-D pictures and animations. Thus we can now marvel at things like fetuses, bones wrapped in muscle or a baby exiting the birth canal with unprecedented detail, all while being anatomically faithful and scientifically accurate. It’s not an understatement to say Tsiaras’ works have inspired and educated a new generation of physicians and laymen, alike.


“Most of this is just about information,” he says. “I look at myself as a storyteller who works with artists and technologists.”


“My goal is to visualize life in all its glory. And to see how daily lifestyle decisions affect the choreography of all of our cellular activity, causing disturbances stored in trillions of X, Y, Z coordinates.”


“In my earlier days, I marveled at the symbiotic relationship that the developing child and mother shared. I saw only unbridled potential… the mother as a magnificent mobile heart/lung/immunology protector. Now I view pregnancy not as a perfectly loving mobile spa, but rather, as a fragile environment, one that must be kept healthy at all costs if a developing fetus is ever to be allowed to experience the delicate imperative of each of its genes.”






The anterolateral ligament (ALL). (c) University of Leuven

New ligament discovered in the human knee

The human body is a complex biological entity in seemingly perfect harmony as thousands of components play their part in tandem. Discovering, describing and understanding how each of this body parts function and work together is the primary role of human anatomy. Some of you might be surprised to find that human anatomy is yet from being exhaustively described, as new body parts are discovered ever so often. For instance, doctors at University of Leuven, Belgium recently report they’ve discovered a new ligament in the human knee. Moreover, its function has also been revealed.

The anterolateral ligament (ALL). (c) University of Leuven

The anterolateral ligament (ALL). (c) University of Leuven

Termed the anterolateral ligament (ALL), and located in the human knee, the ligament’s existence was first proposed in 1879 by a French surgeon but couldn’t be proven until recently. Deep anatomy studies are made on cadavers, and death has the nasty habit of spoiling bodies and making observation difficult especially of subtle body parts. The researchers led by  Dr. Steven Claes, an orthopedic surgeon and study co-author at the University of Leuven, Belgium performed an in-depth analysis of 41 cadaver knees and found the ligament in 40 of the bodies.

“The anatomy we describe is the first precise characterization with pictures and so on, and differs in crucial points from the rather vague descriptions from the past,” Claes said. “The uniqueness about our work is not only the fact that we identified this enigmatic structure for once and for all, but we are also the first to identify its function.”

So what’s the ALL good for? One common injury to the knee is related to another ligament, the anterior cruciate ligament (ACL), which causes what’s known as a “pivot shift”. Basically, do the intense stress your knee stays in position while the rest of the leg moved, causing severe complications least not to mention excruciating pain.  The study suggests that one type pivot shift might actually caused by injury to the ALL, which helps to control the rotation of the tibia, one of the two bones in the lower leg, Claes said.

Like I said earlier, new body parts are discovered fairly often. In June scientists found a new eye layer, named Dua’s layer after its discoverer, that sits at the back of the cornea.

Shorties: the Google body browser

You should know that Google has a sort of Google Maps application, only it’s not for real maps, but for the human body. It’s a pretty awesome and nifty tool, especially if you’re into anatomy at a basic or intermediate level, or if you have problems visualizing the human body, or even if you’re just curious.

Here it is.

Some people report browser problems when using it, getting this message: Welcome to Google Body. You need a Web browser that supports WebGL. I tried it in Firefox 4 and got the same message, I’m not sure what the problem is, but it works just fine with other browsers.

So, happy anatomy browsing !