Recent Posts

Maximum Magnification of a Confocal Microscope? Factors Involved


The confocal microscope is an amazing and useful piece of equipment, allowing one to look into tissues with greater clarity and without the limitations of other microscopes.  Not only can it be used to exactly pinpoint your stained objects of interest, but the 3D stacks it is capable of producing can be turned into virtual 3D worlds and animations you can fly through as if you were inside the living tissue.

microscope objectives

However, even the most knowledgeable science professionals sometimes miss out on the essential details. You could own a piece of certain laboratory equipment and remain unsure of its full potential.  In this article I will discuss the maximum magnification of a confocal microscope and related items.

Continue reading “Maximum Magnification of a Confocal Microscope? Factors Involved”

How to Fix a Non Working Wacom Tablet?


Many of us who work with graphics including 3D are familiar with graphics tablets. Companies like Apple, Microsoft, Samsung, Wacom, and Huion sell different types of  tablets according to the needs of the users. Wacom’s graphics tablets are favored by many due to their ease of use and all the functions.

wacom tablet and pen

However, no product is perfect, and these devices can run into problems.  Let’s explore all the things you can do when your tablet stops working.

Continue reading “How to Fix a Non Working Wacom Tablet?”

How to do Deconvolution in ImageJ: The Easy Way


If you are having problems with blurring in your microscopy images, going through deconvolution is highly likely to improve your results.

confocal microscopy photograph

Deconvolution is not as difficult as it sounds, you just need to understand a few basic concepts and know which software can perform the task.  This article will answer such questions.

As a general rule, to perform deconvolution you use a calculated theoretical or extracted point spread function from your microscope, which you then apply in a deconvolution plugin to your image or image stack.  The result which may take several iterations is a deconvolved image with less blur and more accurate object dimensions for data analysis.

But let’s start at the beginning by getting familiar with the terms and then describe the steps.

What is deconvolution?

Just to be on the same page if anyone is new to the term deconvolution, here are the basics needed to perform the process.  Deconvolution is a computationally intensive process of clearing up a microscopy image which has undergone convolution or distortion due to the objective’s limited aperture.  It makes the image appear closer to the actual real life subject being viewed.  Deconvolution can involve increasing resolution, contrast, and deblurring.

Deconvolution can be used on images from various types of microscopes, including confocal,  multi photon and light sheet.   In addition, it can improve the quality of images which were affected by motion during capture.  Deconvolution is performed on an entire Z series of images.

microscope binocular

While it is said that the pinhole and nature of the confocal microscope eliminates the need for deconvolution later on by getting rid of the signal from other focal planes, this is often not the case.  True deconvolution uses algorithms on existing images and can likely help with the quality of confocal photos.  In confocal, deconvolution helps with elongation of spherical objects in the Z axis.

Deconvolution is important whenever image analysis will be involved (and in science that is most of the time).  If not performed, the results of image analysis may contain a systematic error.

What is a Point Spread Function (PSF)

The Point Spread Function is a function or shape of your optical system which describes the convolution.  It does so by describing the path light from a point source of light takes through the microscope.  It has a different shape depending on the type of imaging used.  The point spread function is much wider for air lenses and that is why they have lower resolution unlike oil immersion lenses.

If the point spread function can be measured, the image can be corrected.  During convolution, the point spread function is applied to every point in the sample which as a result gives the final, altered image.  Anotherwords the image you observe is a product of the point spread function times the real object.  Deconvolution reverses this.

To perform deconvolution you need to generate the point spread function for your specific system.  There are different ways to do this, discussed later.

Here is an online calculator if you are interested in calculating a PSF (not needed for the process of deconvolution itself).

2D or 3D Deconvolution?

Deconvolution can be performed on single images or 3D stacks (file with multiple images at different depths).  3D deconvolution is more computationally intensive.  However, as with many procedures that take more time, the results are often more accurate.  3D deconvolution works through iterations with better quality images resulting from each subsequent cycle.  Blur is treated on every layer available.

In terms of what you need for 2D vs 3D deconvolution, for a 3D stack you have to enter the Z spacing of your stack as well as the number of images in stack.

When you are acquiring your 3D stack, be sure to go beyond your object of interest so that deconvolution results are the best possible.  This is because you want to cover the PSF of not only the subject of interest but also other points in the slide.

What you need for deconvolution

To perform deconvolution you need one of the following:

  1. image/stack of point like objects/beads  taken on the same scope as your image of interest to extract the PSF via a plugin
  2. full specs of the imaging system/scope used including excitation/emission wavelength, refractive index of lens, and aperture to compute theoretical PSF via a plugin

Plugins for deconvolution

There are several programs and plugins out there specifically made for deconvolution which will make the process much easier.  Some work with ImageJ, others with Matlab, and still others are stand alone Java programs.  In certain cases, a single program can run on all of these.  You can experiment with which ones work best for you.

Point Spread Function Plugins:

PSF Generator

Mentioned earlier, PSF Generator is a Java program that can be used to generate a point spread function.    It has more than a dozen models and can work with ImageJ as a plugin.

Diffraction-PSF-3D plugin

Diffraction PSF 3D creates a theoretical z stack of the theoretical point spread function.  All you need to do is enter data into various windows based on the raw image, including specs such as slice spacing, image pixel spacing, width, height, wavelength used, numerical aperture and index of refraction of your media.

 

Deconvolution Plugins:

Parallel Spectral Deconvolution

Parallel Spectral Deconvolution is an ImageJ plugin for deconvolution which takes advantage of higher spec hardware and multi core processors.

Deconvolution Lab

DeconvolutionLab is nicely laid out open source GUI plugin with various deconvolution algorithms including Naive Inverse Filter,  Tikhnonov Inverse Filter, and Richardson-Lucy.  It can be linked to ImageJ or Matlab and runs as a stand-alone.

Iterative Deconvolve 3D plugin

The Iterative Deconvolve 3D plugin is an ImageJ plugin for both 2D and 3D deconvolution.  It is iterative and has a built in Wiener filter as a preliminary step.  The plugin uses a point spread function image Z stack.  It is an iterative plugin which works much better for noisy microscopy images.

Deconvolution in ImageJ

Deconvolution may be performed using ImageJ and associated plugins adequately depending on the condition of the source material and other factors.  It is best to try it and see if it meets your expectations.

deconvolution in progress

“File:Blind deconvolution illustration.png” by Huo Zhuoxi is licensed under CC BY-SA 3.0

 

Keep in mind that some plugins for deconvolution only work on grayscale images.  If you are using one of these plugins, you need to go in ImageJ to Image/Type/8 bit to convert your image to grayscale. If you have a color image, you just have to split the color image into a layer for each color channel and then put it back together after the deconvolution is done.

This is easier than it sounds.  With color image open, go to Image/Color/Split Channels, save the resulting images with names to remember which was which color, deconvolve them separately as described below, then go to Image/Color/Merge Channels.

 

Below are steps for performing deconvolution in ImageJ using theoretical PSF:

 

-Open your image dataset

-Go to plugins/3D/Diffraction PSF 3D

-Enter your microscope and specimen values to create PSF

-Go to plugins/Parallel Spectral Deconvolution and choose 3D or 2D

-Choose source image and created PSF file

-Select options such as algorithm (experiment with it) and click Deconvolve

-Compare deconvolved slice with original one

-Repeat deconvolution with different settings if necessary

 

Below are steps for performing deconvolution in ImageJ using PSF extracted from a stack:

 

-Open your stack of point like objects/beads

-Go to plugins/PSF Generator and run it

-Save PSF

-Open your image dataset

-Go to plugins/Parallel Spectral Deconvolution and choose 3D or 2D

-Choose source image and created PSF file

-Select options such as algorithm (experiment with it) and click Deconvolve

-Compare deconvolved slice with original one

-Repeat deconvolution with different settings if necessary

 

It is that simple.  In addition to experimenting with the various algorithms, you can try different plugins and free vs commercial software packages if you are not happy with the results.  So basically you can substitute plugins in the steps where plugins are mentioned to see what works best for you.

Deconvolution speed

Deconvolution can be very hardware intensive.  The deconvolution process takes several iterations.   You may need a high spec workstation and GPUs for certain stacks and deconvolution procedures.  It also matters which software you are using.  A GUI heavy program with easy to navigate graphics may not be your optimal solution, keep that in mind.

Below is a useful video on deconvolution from the Howard Hughes Institute which gives a more detailed explanation:

 

I hope this article made deconvolution easier to understand and took away any fear of the process.

 

Click the following link to learn how to improve MRI quality.

How Much Does 3D Printing Organs Cost? The Actual Numbers


Currently, thousands of people are waiting on the transplant list for organs like kidneys, heart, and liver. Unfortunately, there are not nearly enough donor organs available to fill that demand.  You also cannot donate an organ such as a heart while the patient is alive.  What if instead of waiting, we could create a brand new customized organ? That is the idea behind bioprinting.

kidney 3d model

 

This technology is still in development but there are already printers out there capable of performing the impossible a few years ago.  The consensus is that rather than printing cells layer by layer as in regular 3D printing, 3D printing of organs should be done by printing scaffolds on which cells can grow and develop into a full size organ.

As you can imagine with such an undertaking on the cutting edge combining 3d printing technology, medicine and biology, this is not something that comes at a low price.  Let’s discuss the costs of printing organs.  

The cost of 3D printing organs is changing as technology evolves.  Living tissue has been successfully printed with a $1000 3D printer while more specialized bioprinters cost upwards of $100,000.  Other costs involved include bioinks which start at hundreds of dollars, associated research and the cost of highly skilled operators for 10 weeks or more per organ.  It is not uncommon for the initial cost of bringing a bioprinting technology onto the market to be in the tens of millions of dollars.

According to the National Foundation for Transplants, a standard kidney transplant can cost up to 300,000 dollars. But compared to that if a kidney is printed through a printer and if they are suitable for use in the human body then the cost will be much less.  Companies such as Bioscience, Volumetric, FluidForm, Printivo are working on 3D-printed organ services.

It is not all easy going, and companies pioneering in this space have to face huge start up costs in the millions of dollars to bring their technology to market.  Operating losses can be very high.  Funds are usually obtained from grants and private investors.  Another limitation is getting through all the usual red tape and testing tissue first in animals and finally in humans years later if approved.

What are 3D printed organs made of?

The world of 3-dimensional bioprinting or 3D organ printing is very complex. Polymers such as Hydroxyapatite, Titanium, Chitosan, and collagen are used that need to be biocompatible and capable of having cells attach to their scaffold and grow into an organ.  

BioInk:

A bioink, which can be thought of as printer ink for bioprinting, is a a hydrogel material combined with cells.  Using bio-inks provides high reproducibility and precise control over the fabricated constructs in an automated manner.

Bioinks are able to support the growth of various cell types. They come as a ready-to-use gel for printing 3D tissue models. They are versatile and biodegradable. BioInk is usable for long-term tissue cultivation such as many weeks.

OsteoInk:

Calcium Phosphate material for 3D tissue printing is called as OsteoInk. OsteoInk is a ready-to-use calcium phosphate paste for structural engineering. OsteoInk is a highly osteoconductive biomaterial close to the chemical composition of human bone. It is used to make various types of hard tissues in the human body such as bones, cartilage, or structural scaffolds.

OsteoInk can be combined with BioInk to create complex 3D tissue mimetic models. It controls the uniqueness of the bioprinter by enabling freeform fabrication of the tissue model, creating tissue layers, pore formation, and biological structure.  BioInk is often used with OsteoInk to reduce opacity.

In addition to BioInk and OsteoInk, special ingredients like Agarose, Collagen, Alginate, Polyethylene, Glycol, and Gelatin are used for 3D Bio-printing.

Why is printing organs difficult?

Transplantation of 3d printed organs could be a revolution in medical science. However, many issues stand in the way. Researchers are working hard to create a directly replaceable organ.  Many companies are working day after day to make it possible. They are constantly facing many problems while doing this research. As with organ transplants in the human body and rejection, the recipient often faces some problems. What are those unresolved obstacles?  Let’s see what problems scientists have to go through in this work.

Limited options for Biomaterials:

Collecting the biomaterials that are used to support and structure the cells that make up a functional printed organ is a difficult task for scientists.

As mentioned earlier, Synthetic polymers and Hydrogel are used for 3D organ printing. Synthetic polymers are mechanically strong and suitable for printing but may lack cell adhesive properties to support cell growth. Meanwhile, natural polymers are not as strong as synthetic polymer polymers but are much more suitable for cell attachment, expansion, and differentiation.

Scientists have recently printed a heart using a 3D bioprinter. The main ingredient in the artificial heart was Alginate, and it was taken from a type of algae that lives in the deep sea. They chose nano cellulose and alginate because these plant-based materials naturally support the power of plant micro-architectures to aid cell growth.

Maintaining the shape of the soft material:

The key to printing three-dimensional functional organs is to maintain the structural integrity of the organ. The shape of the artificial organ often depends on the viscosity of the BioInk used in the printer.

Biodegradable scaffolds made from biomaterials have often been used to maintain the shape of bioprinted tissues and seed cells, but scaffolding defects include stimulating immune responses, as well as cell detachment from potential toxicity and decay by-products.

Bioprinters:

Printers have become one of the major problems for bio-printing. Some minor flaws in the use of printed organs in the human body can become a major problem. Often, the entire printing is ruined due to a printer hardware error. An error in organ printing occurs when the printer is interrupted for some other reason.

Below is a good TED Talk video on how bioprinting works:

Which 3D printers are used for organ printing?

Bioprinting can be done with inkjet based and extrusion based methods, as well as SLA, FDM and SLS.

BioInk is used as the main printing material for 3D organ printers. A bioprinter uses polymeric materials and cellular hydrogels, such as syringes or professional extrusion paste. But plastics are used as the printing material of ordinary printers. So a bioprinter should never be compared to a normal printer. Currently, many companies are working on making and improving bioprinters.

Bioprinters are available at different price points and qualities on the market.   The bioprinter made by ‘EnvisionTEC’ is the latest type of a bioprinter. This printer converts computer-aided tissue engineering 3D models and patient CT data into a physical 3D scaffold. This printer is called ‘ 3D Bioplotter’.

The ‘NovoGen MMX’ made by Organovo is a much better quality bioprinter. They have created this for their own use only. This bioprinter is only used to make beneficial tissues. Organovo does not sell its ‘NovoGen MMX’ technology.

Organovo printer

“Organovo BioPrinter” by NIH-NCATS is marked with CC PDM 1.0

RegenHU’s ‘3DDiscovery’ bioprinter is one of the most expensive printers.  The printer uses two printing methods and utilizes various hydrogels, bioactives, cells, and extracellular matrix materials.  It is capable of enabling dynamic protein networks as well as cell/cell interactions.

These are very advanced printers. Also, there are some less expensive printers available in the market. Typically, these start at 10,000 dollars. But, buying a good quality printer can cost up to 200,000 dollars. One of the less expensive printers, ‘Alpha & Omega’ is a 3D printer made by ‘3Dynamic Systems’. It works on syringe-based extrusion technology.

Developers are still working on some sophisticated and open-source models of 3D printers, which have not yet hit the market. However, the hope is that when they come on the market, 3D bioprinters can be used at a very low cost and open to all. 

Here is a price guide for some of the more expensive bioprinters.

Other uses for 3D printing in medicine

3D printing technology is very important in the field of medical science. 3D-printed organs have been used in many large and complex surgeries as reference.  From the human brain to the smallest bones of the body, 3D printing has been used.  3D printed anatomical models are important for medical improvement. Surgeons can take less time in surgery by planning and practicing an operation on a custom 3d printed copy of a patient’s organ. 

I hope that this article has given you some idea about what is involved in 3D printing of organs, including the costs.  Click the following link to learn how to 3D print wax.

Medical Imaging vs. Radiology: What’s the Difference?


Unless you are a trained medical professional, you may have trouble understanding the difference between medical imaging and radiology. It’s sometimes hard to differentiate between two similar ideas or practices within the medical field, and people often get these terms confused.

CT scan image

 

In this article I will describe each term in depth and explain how they differ.

While radiology and medical imaging are certainly very closely related, they are not the same thing. Radiology is the science of X-rays and other high-energy radiation technologies for the diagnosis and treatment of different conditions and diseases. Medical imaging technologies, on the other hand, are visual representations of the inside of the body.

Radiology, however, is not limited to just one area of practice. Below, I will highlight several different specialties and subspecialties that utilize different medical imaging techniques for various purposes.

Is Medical Imaging and Radiology the Same?

While medical imaging and radiology are very closely related and often are confused with each other, they are not the same thing. Radiology is a specific field of medicine, while medical imaging is a technology used by radiologists.  Medical imaging may be used by radiologists to monitor, diagnose, or treat various conditions within the body in a non-invasive way. Different types of radiologists specialize in and utilize different medical imaging technologies, depending on what field of medicine they’re in and what kind of patients they treat.

These technologies are used so physicians can view the inside of the body without needing to perform any exploratory surgeries. According to the FDA, this is crucial in allowing the radiologist and other doctors on a patient’s care team to learn and monitor information related to the diagnosis and treatment of diseases or injuries. It also allows physicians to check how the body is responding to previously administered medical treatment.

What is Medical Imaging?

The term “medical imaging” refers to a branch of technologies that allow a radiologist to diagnose, treat, or monitor diseases or injuries inside the body. It can also be used to keep track of the body’s response to a previously administered or ongoing medical treatment.

According to NPS MedicineWise, medical imaging includes technologies such as:

  • X-rays
  • Ultrasounds
  • CT Scans
  • MRIs
  • SPECT Scans
  • PET Scans

Each of these technologies is best suited to different purposes, depending on the patient’s condition and what part of the body the radiologist needs to view.

Types of Medical Imaging Technologies

There are many different types of medical imaging technologies that radiologists use. Here is what you can expect with each one:

X-Rays with Ionizing Radiation

X-rays are typically used to provide images of the bones inside your body. They use ionizing radiation and are most often used to tell if you have a bone break or sprain. They can also detect arthritis, osteoporosis, infections, cancer, or digestive problems.

X-rays are relatively quick and simple, taking just a few seconds to complete. Usually, an x-ray will be done while you are either standing or sitting, but you might be required to lay down in some instances.

CT Scans with Ionizing Radiation

CT scans take a series of X-rays to create images of the cross-sections within the body. Like x-rays, they use ionizing radiation and can detect broken and fractured bones, infections, and cancers. According to the University of Virginia, CT scans can:

  • Detect traumatic injuries
  • Detect vascular and heart diseases
  • Guide biopsies

While x-rays are typically done while you’re sitting or standing, and are only done while laying down in certain circumstances, a CT scan requires you to lay on a table that slides into a tube, rotating around you while it takes x-rays of your whole body.

Like x-rays, CT scans are fairly quick procedures. They take about 15 minutes to complete, though this can vary based on your condition.

MRIs with Magnetic Waves

Like CT scans, you’ll be required to lay on a table that slides into a scanner during an MRI, though MRI machines are usually more narrow and deeper than CT scanners. MRI machines use magnetic waves, and you may hear tapping or banging while the MRI is used.

These scans produce detailed images of organs and tissues. According to UVA, MRIs can detect and diagnose serious conditions and problems including:

  • Aneurysms
  • MS
  • Strokes
  • Spinal cord issues
  • Tumors
  • Joint and tendon injuries

Ultrasounds with Sound Waves

Most people are familiar with ultrasounds in terms of monitoring a pregnancy and checking an unborn baby’s development. However, ultrasounds also have a number of important diagnostics uses. The University of Virginia claims ultrasounds can guide biopsies and diagnose things like:

  • Blood flow problems
  • Joint inflammation
  • Breast lumps

As the name suggests, ultrasounds use sound wave technology to view different organs within the body.

When you get an ultrasound, the technician will first apply a gel to your skin to reduce the amount of air between your skin and the ultrasound probe. This is done because the ultrasound waves may be affected while traveling through the air, skewing the image they provide. The technician will then move the probe around the area until they find the area they need to see.

PET Scans with Radiotracers

Positron emission tomography (PET) scans are one of the more complicated medical imaging technologies. They use radioactive drugs called “radiotracers” to show organ and tissue function throughout the body.

Before you undergo a PET scan, you’ll need a dose of radiotracers. The radiologist will either give you a radiotracer pill to swallow or an intravenous injection of the substance prior to the scan, and this will allow the scanner to read the radiation given off by it.

PET scans can be used to diagnose a variety of serious conditions, including:

  • Cancer
  • Heart diseases
  • Alzheimer’s
  • Parkinson’s
  • Epilepsy

The machine used to administer a PET scan is similar to those used for CT scans and MRIs.

SPECT Scans with Radiotracers

Single-photon emission computerized tomography scans, or SPECT scans, are a type of nuclear imaging scan similar to PET scans. They produce images that show how well your organs work together, like how well your blood flows throughout your body or what areas of your brain are the most active.

According to the Mayo Clinic, SPECT scans can monitor and diagnose:

  • Heart disorders
  • Brain disorders
  • Bone disorders

Before the SPECT scan begins, you will be given an intravenous dose of a radiotracer similar to that administered during a PET scan.

Once your body has absorbed the substance, you will be scanned in a machine similar to an MRI machine. The length of time it takes can vary depending on your condition, but it’s typically a longer process than most other medical imaging procedures (Mayo Clinic).

What is Radiology? What are the Different Types?

Radiology is a branch of medicine that uses radiation technology, including medical imaging, to diagnose, treat, and monitor diseases and injuries. In some cases, radiology is also known as roentgenology.

Physicians who practice radiology are known as radiologists. They may specialize in one of three areas:

  • Diagnostic Radiology
  • Interventional Radiology
  • Radiation Oncology

Within the broader area of radiology as a whole, there are three distinct areas in which radiologists will practice, according to the American Board of Radiology. These areas include:

Diagnostic Radiology: Diagnosing and Treating Disease

As the name suggests, diagnostic radiology is mainly concerned with the diagnosis and treatment of disease. Diagnostic radiologists use all of the medical imaging technologies listed above in their work.

There are many subspecialties that diagnostic radiologists may work within. Some of these include neuroradiology, pain medicine, and pediatric radiology.

Interventional Radiology: Using Medical Imaging for Treatment

Interventional radiologists perform imaging, image-guided procedures and can diagnose or treat conditions within:

  • The abdominal region
  • The pelvic region
  • The thorax
  • The extremities

They may utilize therapies such as embolization, angioplasty, drainage, and stent placement in their work.

Interventional radiologists may subspecialize in a variety of subjects, including nuclear medicine and pediatric radiology.

Radiation Oncology: Treating Cancer with Radiation

Radiologists who practice radiation oncology use radiation technologies, including ionizing radiation, CT scans, MRIs, and ultrasounds to treat cancer.

People who receive radiation therapy for cancer treatment will typically be working with a radiation oncologist. They may also use hyperthermia, or heat treatment, in their work. Some subspecialties of radiation oncology include hospice and palliative medicine, and pain medicine.

Different Subspecialties within Radiology

Subspecialties are specialized areas within the three main branches of radiology. Diagnostic radiologists, interventional radiologists, and radiation oncologists all have different fields in which they may subspecialize. There are also a number of intersectional subspecialties that include radiologists from all three backgrounds.

These are the subspecialties in which a radiologist might have expertise in:

Hospice and Palliative Medicine: Providing End-of-Life Care

Radiologists in all three fields are able to subspecialize in hospice and palliative medicine. These radiologists help to prevent and ease the suffering of patients who have been diagnosed with life-limiting illnesses, such as late-stage cancer. They work to optimize a patient’s quality of life and may also offer support for families.

Neuroradiology: Treating the Neurological System

Neuroradiology is a subspecialty often practiced by diagnostic and interventional radiologists. Neuroradiologists work within the neurological system, which includes the brain, sinuses, spine and spinal cord, neck, and central nervous system.

Neuroradiology can help treat:

  • Aging and degenerative disorders
  • Cerebrovascular diseases
  • Cancer
  • Other traumatic injuries or conditions.

Radiologists in this field commonly use medical imaging techniques such as angiography and MRIs (American Board of Radiology).

Nuclear Radiology: Using Radioactive Substances for Medical Imaging

Nuclear radiologists typically work within the diagnostic and interventional radiology fields. These physicians use small amounts of radioactive substances, including radiotracers, to create images and get information to render a diagnosis. They typically use PET, and SPECT scans to do so (American Board of Radiology).

Nuclear radiology can be very helpful in treating thyroid conditions, including hyperthyroidism and thyroid cancer. It is also often used to treat other kinds of cancer, including lymphoma, and can help with the pain brought on by cancer (CDC).

Pain Medicine: Easing Pain with Radiation Therapy

Diagnostic radiologists, interventional radiologists, and radiation oncologists may all have a subspecialty in pain medicine. These physicians provide pain relief care for all patients, including those with acute, chronic, or even cancer pain, in both in-patient and out-patient environments. They also work closely with other types of doctors to properly coordinate a patient’s ideal pain relief regimen.

Pediatric Radiology: Safely Providing Radiology for Children

Pediatric radiologists in the diagnostic and interventional radiology fields diagnose and monitor congenital disorders, and those present mainly in children and infants. They also work with children who have conditions that can cause more problems later in life.

An important part of a pediatric radiologist’s job is making sure all imaging techniques, including x-rays, CT scans, MRIs, and nuclear medicine, are administered properly and safely enough to treat young children.

Vascular and Interventional Radiology: Treating Vascular Conditions

Diagnostic radiologists have the option to subspecialize in vascular and interventional radiology. These physicians use a variety of medical imaging techniques to diagnose and treat disease, including:

  • CT scans
  • MRIs
  • Digital radiography
  • Fluoroscopies
  • Sonographies

Vascular and interventional radiology is used to treat conditions like cardiovascular disease, cancers, and even varicose veins therapies used by these subspecialists include:

  • Stent placement
  • Drainage
  • Angioplasty
  • Embolization

Benefits Offered by Medical Imaging Technology

Experts agree that medical imaging is one of the most widely beneficial and useful medical developments in recent history. The New England Journal of Medicine has even ranked medical imaging as one of the top medical developments of the past 1,000 years!

Below, you’ll find a list of some of the top benefits offered by medical imaging technology:

Early Detection of Diseases and Other Conditions

Medical imaging by radiologists has made it possible for doctors to detect diseases much earlier on in their progression. This is especially useful for asymptomatic conditions, or those that show no outward symptoms. When doctors are able to catch a harmful disease earlier, there’s more that can be done for the patient treatment-wise.

Most health issues are much easier and less expensive to treat in the earlier stages, while those caught late tend to require expensive, intense treatment or invasive surgeries.

One example of how early detection with medical imaging has saved countless lives is digital mammograms. Digital mammograms are used to detect breast cancer and can catch signs of it an average of two years before a tumor would even begin to form. This gives those affected less invasive and a greater number of options for their next step.

Quicker, More Reliable Diagnoses

Medical imaging procedures can render a faster and more accurate diagnosis, because the radiologist can actually see what’s causing a problem. It’s also far safer than having the patient undergo an unnecessary exploratory surgery and can help doctors better determine when surgery is actually needed.

Most medical imaging requires little to no special preparation. With CT scans, you may be asked not to eat anything less than four hours prior to the scan, and PET and SPECT scans will require you to either take a small dose of radiotracers orally or intravenously.

Barring special circumstances, these are the only preparative measures that need to be taken prior to a medical imaging procedure.

Better Monitoring of Known Conditions

Medical imaging can also help radiologists, and other types of physicians better monitor the progress of known conditions and how well these conditions are responding to ongoing or previous treatment.

Diagnostic imaging is painless and non-invasive, so patients who suffer from conditions that need to be monitored will be subjected to less invasive procedures, including exploratory surgeries. This can, in turn, reduce the length of time a patient spends in the hospital for their condition.

Imaging technologies can show if and how a condition is progressing, how it’s responding or not responding to treatment, and the severity of any internal injuries, like bone fractures.

Medical animation, biovisualization and medical illustration

The terms medical animation, biovisualization and medical illustration are sometimes confused with medical imaging.  Medical animation is the process or product of creating a 3D educational film about a physiological process or other medical topic, which often includes models built from scratch.  Biovisualization is the process of representing biological data visually and may include processing medical imaging data.  Medical illustration is the process or product of creating any  illustration including 2D and 3D visuals of biological and medical topics and may encompass medical animation.

Each of these may be based on or include data and images acquired through medical imaging technologies.

What are Radiologists’ Credentials

Becoming a radiologist will require medical degree, along with the proper licenses and certifications for your state. According to CME Science, you’ll need a Doctor of Medicine (M.D.) or Doctor of Osteopathic Medicine (D.O.) to become a radiologist.

After graduating with from medical school, many prospective radiologists, or radiology technicians as they’re sometimes called, choose to do a radiology residency at a hospital. This may or may not be required, depending on your state, but could be helpful in making connections and building your resume!

After all your training is complete, you’ll need to pass a state exam to become a licensed radiologist. This exam varies by state and may require you to complete a certification program with the American Registry of Radiologic Technologists.

Even if your state does not require this certification for licensing, it may be beneficial to do so anyway to increase job prospects.

Below is a useful introduction to medical imaging from the University of Buffalo:

 

 

Final Thoughts

While the terms medical imaging and radiology tend to be used interchangeably, they are far from the same thing. Radiology refers to the use of radiation technologies to diagnose and treat diseases and injuries, while medical imaging is a subset of these radiation technologies used by radiologists.

Radiologists may specialize in many different areas, but all radiologists use medical imaging to one degree or another.

Click on the following link to learn how to improve the quality of MRI images.

Maya vs. 3ds Max: Which is Better for Modeling?


Maya and 3ds Max are two of the most popular software options available for people interested in 3D modeling for medical animation.  Due to their extreme popularity and vast resources, it can be difficult to choose between the two for modeling purposes.

3d printed prosthetic model

Let me get into the topic of choosing a software package for modeling, define what the differences between the two programs are in this aspect, and offer some advice.

Both Maya and 3ds Max are incredible tools for 3D modeling. Both programs are just as capable as the other, and the main choice will come down to preferred workflow and additional needs. 3ds Max is easier to learn, while Maya offers expanded options through advanced scripting.

For the purposes of medical animation, both programs are capable of producing highly accurate and detailed models. 3ds Max is known to have a shorter learning curve, but exploring some of the specific pros and cons of each piece of software may help in coming to an informed decision.

Is Maya Good For Modeling?

Maya is certainly near the top of the list for most powerful 3d applications available. It is perfectly suited for a variety of modeling, animation, rendering, and simulation. Essentially any part of the 3d image creation process can be completed in Maya, making it a powerful suite in its own right.

Focusing on 3d creation as a whole, Maya is known to have a variety of tools introduced in recent builds that make modeling easier. Maya is powerful enough to successfully create any 3d model, but the tools available may make it more frustrating than other options for complex creations. While the capability is there, Maya’s workflow when it comes only to modeling can be confusing, especially for beginners.

However, this is a problem that Maya has been fixing ever since its 2014 release. Features such as remesh, sculpting, and polygon modeling are standard in the current version and allow for detail to be easily added. More information on the current modeling toolset can be found here, on Maya’s website.

Specific Tools For Modeling In Maya

There are many tools that have been directly integrated into Maya to make it a more powerful 3d modeling tool. While the focus of Maya is still firmly planted in animation and rendering, these extra features provide the program with enough power to serve as the 3d modeling software of choice for many medical animation needs.

Of the available tools, some of the most relevant ones for medical animation are:

  • Remesh
  • Retopologize Features
  • Sculpting Tools

Each of these specialized tools allow for additional detail or quicker access to technical changes that improve workflow and make modeling easier. With some creativity, everything can find a home in any workflow.

Remeshing

Remeshing in Maya is a quick way to select an area and break down its components into smaller triangles, allowing for more detail when working on the selected piece. For example, a human ear may consist of 50 or so surfaces; a remesh application will split these pieces further into triangles, creating an additional 50 or even more surfaces. As surfaces decrease in size and increase in number, more detail can be added and structured.  This is essential for creating models of intricate or small areas.

Retopologizing Features

The retopologizing feature is a quick way to clean up any unevenness or missing areas of any model to improve efficiency and ensure the conservation of detail. Cleaning up a model after painstakingly creating it can take an enormous amount of time but is essential to create accurate models, essential for medical animation. This tool takes out much of the pain of the procedure.

Sculpting Tools

Sculpting tools are now commonplace across almost every 3d modeling software, but some sets of tools are better than others. Sculpting tools take the process of digital 3d modeling and transform it into something more similar to working with clay or another physical object, allowing for some artistry to be injected into the workflow. Sculpting tools are incredibly useful for creating organic models.

sculpting tool options in maya

Pipeline Integration

One of the strongest reasons to choose Maya is for it’s incredible integration capabilities into other workflows. Depending on what other programs you may use for 3d animation, Maya has flexible tools that allow for easy file and data transfers. Even if the specific program you use is not inherently supported, Maya supports a small handful of scripting languages to allow for custom plug-ins that make exporting easier.

Thanks to Python and Maya Embedded Language (MEL) support, Maya can seamlessly fit into almost any existing workflow. There is also a large community of active Maya users who share plug-ins online and are willing to help newcomers become acquainted with the software at large as well as its advanced features.

Python is the most popular programming language in the world and is commonly praised for its flexibility and low barrier of entry. Learning Python expands Maya’s modeling capabilities almost directly, as some of the missing 3d modeling tools that users may want can be custom-coded in.

MEL is a proprietary scripting language that was designed for easy integration into the Maya software. This is the most popular scripting language for Maya, as it has been around for almost the entire lifetime of the program. Custom plug-ins supporting exporting into various programs, defining new modeling tools, or ease-of-life shortcuts can be found all over the web.

More information on the specifics of scripting in Maya and a glimpse into the power it provides can be found here.

Here is a useful video on Maya modeling:

 

Is 3ds Max Good For Modeling?

3ds Max is arguably the quintessential 3d modeling program, designed from the ground up with usability and modeling workflow in mind. While Maya excels at other aspects of the digital 3d creative space, 3ds Max undoubtedly has more tools and pipelines for pure modeling purposes.

3ds Max sees use in architecture, game development, historical recreations, and, of course, medical animation. The tools are explicitly robust enough to accommodate any 3d modeling needs. Thanks to the program’s extreme focus on modeling capability, even beginners should be able to quickly get into the swing of things and start creating.

3ds Max comes equipped with a variety of advanced tools that can speed up any pipeline and make modelers feel more confident in their workflow. Many tools found in Maya, such as sculpting and remeshing, are also standard. The main difference between Maya and 3ds Max when it comes to modeling is the existence of features which decrease wait time and allow for constant creation.

Advanced Modeling Features of 3ds Max

3ds Max has many features that make specific tasks in 3d modeling much easier. While many similar results can be achieved with Maya through its advanced scripting languages, there is something to be said for how easy 3ds Max makes the process in comparison.

To a beginner, some of these tools may seem needless or as if they barely save anytime at all; however, as you grow more accustomed to 3d modeling and venture into more advanced tasks, a little bit of creativity with some of these features can save an enormous amount of time.

Some of the modeling and texturing features that 3ds Max offers include:

  • Spline workflows
  • Baking to texture
  • Weighted normals modifier

Spline Workflow

Spline workflows can fundamentally change how 3d modeling occurs thanks to it’s intelligent design. Simply put, spline has a variety of functions that all center around cutting out  time spent on basic tasks. Things such as mirroring a design, morphing and blending between shapes, soft selecting and editing areas, and line smoothing are simple quality of life improvements that drastically improve how easy it is to create using 3d models. These even mesh seamlessly with sculpting tools and other aspects of 3ds Max to make modeling intuitive.

More information about the various functions that Spline workflows offer can be found here, alongside detailed documentation.

Baking To Texture

Baking to texture is a scripting-based function that creates a library of texture maps to apply to 3d models. This library can then be accessed quickly using scripts, allowing for textures to be approximated while modeling is happening.

This is extremely helpful while trying to line up objects, complete final edits, and generally get a good look at what the finished product may appear as. Under traditional workflows, textures would not be able to appear on the objects during edits – instead, lighting would have to be rebuilt, materials recompiled, etc. This cuts work time significantly and creates a great environment for quick edits.

Baking to texture can get even deeper than surface level textures, even including the ability to bake UV tiles while editing. However, for most people, this type of functionality will prove unnecessary.

Weighted Normals Modifier

Weighted normals are meant to improve the shading of models and the bouncing of light actively, as edits occur. This functionality is similar to the aforementioned baking to texture, but only touches upon lighting. It also smooths it out quickly so that less load time needs to occur.

With this functionality, lighting can be quickly edited, moved, deleted, or replaced and the effects will happen in close to real time. Lighting can also be blended at various intervals and edges can be detected.

This is most useful for creating complex scenes with lots of different light sources, as may happen when mapping out a complex medical model.

There are a variety of other tools and time-saving technologies built into 3ds Max that really make it a pleasant experience for almost anyone looking to 3d model. However, it does lack in some other areas where Maya takes the lead. Subjects like animation, rendering, and pipeline integration are all better suited for Maya.

Considering both are more than capable of tackling almost all 3d modeling needs, other factors should also be considered.

Below is a good video on 3ds Max modeling:

 

Community Support

3ds Max is the more popular choice for purely 3d modeling, meaning that more plug-ins, support, and tutorials are available online. Specifically, there are many downloadable plug-ins that are specifically meant to make modeling easier that can be found and applied to a variety of workflows.

Where many of Maya’s plug-ins focus on animation or rigging, 3ds Max plug-ins are meant to improve modeling even further. Taking advantage of the sleek and easy to parse UI, many users may also have an easier time getting used to 3ds Max plug-ins.

Animating in 3ds Max or Maya

Although I am focusing on modeling here, animation is an important thing to consider, especially since many models, even those for prototyping, are often animated in the end . Whether creating a video walkthrough or description of a part of the body, showing the layering of muscles and skin, or creating a walking or healing animation, the animation needs are endless.

While 3ds Max has the edge for modeling, Maya takes the lead when it comes to most aspects of animating 3d models. Thanks to a robust toolset that incorporates a variety of rigging and quick animation features, the workflow for animating in Maya can be much faster.

As with modeling, the truth is either program can achieve similar results. Instead, it is best to look at which program is easiest to use for the intended purpose and which has more tools available. In that regard, once again, Maya wins.

Applications of Animation For Scientific Purposes

There are plenty of areas where animation is useful. While exporting models to an alternative program for animation can be done, it’s often beneficial to be able to outline the basic movement of various 3d models in the same program before shipping out for additional effects.

One of the most common medical uses for animation is for education. Creating a 3d model of any part of the human body is hugely beneficial, but adding the ability to walk through and explore various parts in video format can be even more so.

Even without large animations, the ability to move various pieces of a 3d model and introduce transitions or motion graphics can elevate any 3d model and make it more visceral, professional, and useful.  Both 3ds Max and Maya can be used for this purpose and more.

Motion in either program can be broken down into two parts: rigging and animation. Rigging is often wrapped up into the larger category of animation as a whole, but both are equally important in adding some movement to any 3d model.

What Is Rigging?

Rigging is the process of attaching points of movement to 3d models where animation can occur. When applied to human models, it is often called a “skeleton”, where the various joints are placed as underlying moving elements. For instance, a pumping heart, a breaking bone, or a moving machine. Any area of a model where movement will occur receives a rigging element or joint.

The basics of rigging stay the same across almost any 3d modeling software, but some specific tools available in either Maya or 3ds Max can make the process easier.

Many modern advancements in rigging are meant to automatically find points by detecting the geometry of the model or organize nodes and connections to declutter rigging, as it can quickly get complicated.

What Is Animation?

Animation is the act of making 3d models move. This is done through the use of keyframes; the model is positioned one way using rigging and assigned a keyframe on a timeline. Then, the model is moved to the next position/pose  and assigned a later keyframe on the same timeline. For example, a walking animation is created by starting the person as still, then moving the hip, arms and legs and adding another keyframe.

Good animation requires setting enough rigging, moving the correct parts, and establishing a proper timing of keyframes. A walk where the person only moves their legs will look unnatural, and if it’s too slow people will notice something looks strange. This is applicable to every animation.

The animation program will detect the changes between keyframes and try to automatically fill the frames in-between with movement. If there are too few keyframes, this will look unnatural and the program is likely to make mistakes. Likewise, too many keyframes take up a significant amount of time and memory for little to no benefit.

3ds Max Animation

Animation in 3ds Max is highly capable of producing beautiful and effective work, but many nice tools are missing or require significant plugins to get working.

For basic animation, as is often common for medical technologies, this program is likely to serve more than well enough. However, those looking for more powerful animation or an easier workflow may wish to turn to Maya.

3ds Max focuses on providing the basics of animation and rigging in a simplistic and easy to parse way. Its features are largely limited to basic timelines and procedural animation tools, but occasionally, they slip in additional features that are worth taking a look at. One such feature is the 3ds Max Fluids technology, which allows for realistic liquid behavior that responds to gravity and collisions. More about this feature can be found here.

Many of the specific animation tools that 3ds Max provides are focused around character animating, which is not always used in medical animation.  However, with some ingenuity and a little bit more elbow grease, it will serve any necessary animation functions perfectly.

Some of the animation tools that 3ds Max provides include:

  • Motion paths
  • Particle flow effects
  • Animation layers

Motion Paths

Motion paths are a feature that let you preview the path of animated objects. For instance, if blood pumping through arteries is being animated, the path of the blood will appear and is editable to achieve the desired result. This is most useful when combined with the aforementioned spline capabilities of 3ds Max, so a path can be built directly into the model.

The majority of the time, a motion path is useful for working out details of motion when it requires a specific path or area to stay in. Animating the movement of a swallowed object through the throat is an example where motion paths may be useful. More information on motion paths and their use can be found here.

Particle Flow Effects

Particle flow effects are extremely powerful and can be used in a myriad of situations. The technology behind effective particle flow is fairly complicated, but the basics involve individual objects being defined by shape and speed.

particle flow options in maya

Once the thousands of individual objects have been generated and defined, they are moved and interact with each other and other models in the space to create effective movement.

The particles constantly interact with each other and react to the environment, creating a natural look for things such as smoke, liquids, or semi-solid substances. Essentially, anything that can flow can use particle flow effects to achieve a realistic movement animation.

Medically, this is applicable to a wide variety of uses, such as showing blood movement, displaying liquid medicine, the filling of the lungs, or other uses.

Animation Layers

3ds Max employs animation layers to overlay multiple tracks on top of each other, either for testing purposes or to combine animations into one, larger result.

This is most useful for iteration and the editing of animations; simply copy the existing animation into a new layer, hide it, and edit on the original. This way, if something goes wrong or you are unhappy with the results, you can quickly revert back to the first copy.

While not as intuitive as Maya’s nondestructive editing environment, it does offer many of the same benefits. Merging layers is also highly beneficial for working out any kinks in animation if you have multiple layers that look great at different points.

Maya Animation

Animation in Maya revolves largely around scripting in either Python or MEL, its proprietary language. Luckily, a deep knowledge of these languages is not required to achieve fantastic results and gain access to the incredible number of tools that Maya provides.

In spite of the need for scripting, Maya’s animation still holds the crown for ease of use when compared to 3ds Max. This is largely due to MEL being incredibly easy to customize and learn – a few hours in an afternoon are enough to set up almost anyone with enough knowledge to do most animations they desire.

What the language doesn’t immediately cover can be quickly found online, as there is an incredible rigging and animation community around Maya. Tutorials covering the various parts of Maya, custom plug-ins for specific types of animations, and additional resources for practice are all easy to find.

In addition to having every basic tool needed for animation, Maya takes the lead for the various tools it has to speed up workflow or introduce advanced techniques in an easy to parse way. Tools such as:

  • Cached Playback
  • Animation Bookmarks
  • Motion Library
  • Nondestructive Time Editor

All allow for quick edits and changes to animations that allow for easy iteration and speed.

Cached Playback

Cached playback is one of the important features of animating in Maya. This allows for you to see changes made to an animation immediately, rather than waiting on Maya to redraw and render everything out.

Especially with large animations, this rerendering could take significant time. It works by saving  the animation scene in multiple parts. When edits are made, Maya only needs to reload that specific slice instead of the whole thing. You can read more about it here.

Animation Bookmarks

Animation bookmarks allow for specific splits of time to be saved on the timeline for various animations for quick revisiting.

These bookmarks are not linked to any specific keyframes, but are instead linked to another function of Maya called the Time Slider, where animations can be scrubbed through like a video. This is highly useful while making quick edits to an animation and comparing the results.

Motion Library

Maya has recently introduced native support for a motion library plugin of various capture data of people moving and completing various daily tasks. This is a game changer for a variety of fields, as gaining access to natural movements and automatically rigged models is a common challenge.

While less relevant for medical animation, this quick library is a great example of what can be done with plugins for Maya, and the models can be used for details or background in a variety of cases.

Nondestructive Time Editor

Finally, Maya’s animation sequence editor is non-destructive, so edits can be made without losing parts of the animation that were previously created. This is similar to a video editor where, when a cut is made, the video that has been cut off still exists in case further edits need to be made.

Maya’s editor is a powerful tool for all parts of animation that is sure to see significant use for any required animation work. It is here on the timeline that important facets like timing, speed, length, and keyframes are defined. The fact that the timeline is non-destructive is a fantastic bonus for all professionals, but especially beginners who may make more mistakes than others.

Choosing Between The Two Programs

Choosing between the two programs for general modeling and animation needs can be difficult. Truthfully, it’s hard to make a wrong choice; they are both wonderful and capable pieces of software that can help any professional elevate their work. However, as a general rule, 3ds Max is better for modeling, and Maya is better for animating.

I hope you enjoyed this article.  Click the following link to learn if 3d modeling is hard to learn.

 

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