My new textbook and job

So many things have happened in the last few months and I have not had time to add new entries to my blog. The first is the textbook that I co-authored with Sridevi Pudipeddi which was released at the end of February.  It was marathon run to complete and get the book ready for publishing.  I also moved to a new job in California in April.


During my work as image processing consultant at the Minnesota Supercomputing Institute, I have worked with students in various disciplines of science.  In all these cases, images were acquired using x-ray, CT, MRI, Electron microscope and Optical microscope.  It is important that the students have knowledge of both the physical methods of obtaining images and the analytical processing methods to understand the science behind the images. Thus, a course in image acquisition and processing has broad appeal across the STEM disciplines and is useful for transforming undergraduate and graduate curriculum to better prepare students for their future.

There are books that discusses image acquisition alone and there are books on image processing alone.  The image processing algorithms depend on the image acquisition method. We wrote a book that discusses both, so that students can learn from one source. You can check out sample chapter of the book at reedwith.us. You can buy the book at Amazon by clicking on the image below.

I also changed job.  I started working as Senior Engineer at Elekta in Sunnyvale, CA. I will be focussing mostly on x-ray and CT during my tenure at Elekta.

Comparing different DICOM viewers

Digital Imaging and Communication in Medicine (DICOM) is a standard format for encoding and transmitting medical CT and MRI data. This format stores the image information along with other data like patient details, acquisition parameters etc. Since DICOM standards have become popular, many image processing readers and viewers have been created to read, process and write images. There are so many such software and its details can be seen here.

Since the details of the various software can be obtained using the previous website, in this blog we will classify some of these softwares based on the user requirement and discuss accordingly.

The users might need
1. A simple viewer with limited manipulation like ezDICOM
2. A viewer with ability to manipulate images and perform rendering like Osirix
3. A viewer with image manipulation capability and also extensible with plugins like ImageJ
4. A command line reader and viewer that allows batch processing like ImageMagick

There are more softwares that can be classified under the four categories but we will limit to these software for this blog. This does not limit the number of software available for viewing and manipulating dicom image, rather helps users choose the software right for them.

ezDICOM
It is a viewer that provides sufficient functionality that allows users to view and save dicom files without installing any software in their system. It is available only for Windows OS. It can read dicom files and save them in other file formats. It can also convert image files to Analyze format.

Osirix
It is a viewer with functionality that you might generally find in expensive workstation. It works great and it is free! But unfortunately, it is available only in MacOSX.
Like other dicom viewer, it can read and store files in different file formats and as movies. It can performs Multi-planar Reconstruction (MPR), 3D surface rendering, 3D volume rendering, endoscopy. It can also view 4D dicom data. The surface rendered data can also be stored as VRML, STL files etc. In short, I would highly recommend it if you have a Mac system.

ImageJ
ImageJ was funded by National Institute of Health (NIH) and is available as open source. It was written in Java and users can add their own Java class or plugins. It is available in all major operating system like Windows, Linux, UNIX, Mac etc. It can read all dicom formats and can store the data in various common file formats and also as movies. The plugins allow various image processing operation. Since the plugins can be easily added, the complexity of the image processing operation is just limited by the users knowledge of Java.

ImageMagick
If the various operations in image processing can be classified in to input, processing and output, ImageMagick provides functionalities that perform all these three operations. ImageMagick can be used in command line in almost all the common operating systems like Windows, Linux, UNIX, Mac etc by combining the read, write and image processing operations. Since ImageMagick is a command line tool, it can be used in any scripting language like perl, PHP, shell script etc. For users who are more adventurous, ImageMagick also provides APIs that allow programming low level image processing operation.

If you want to be even more adventurous and would like to program in C and C++, check out dicom toolkit.