The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes

Excellent - as research into connectomes increases, it will be cool to have an open source platform for sharing findings and images. Anyone can download the viewer software and look at the images - more importantly, to me, it creates an open access and open source platform for the sharing of brain science information. Other fields of science might learn something from this project.

Before the sharing the article, a brief definition of a connectome might be useful for those who do not follow brain science in all its geeky depth.

A connectome is a synapse-resolution mapping of connections between all neurons in a model organism's brain. In other words, a synapse-resolution circuit diagram of the brain. Current approaches to mapping the connectomes of model organisms employ serial block face scanning electron microscopy (SBF-SEM) and transmission electron microscopy (TEM). The only connectome that has been mapped out to date has been from the flatworm, C. elegans, which has only around 300 neurons. Candidate future connectomes include the fly, with around 10,000 neurons, and the mouse brain, with 100 million neurons.

A projectome is more modest than a connectome, and is defined as a mapping of all inter-areal connections, at the single axon level, within an individual brain.

Source: Kasthuri N, Lichtman JW. The Rise of the Projectome. Nat Methods. 2007 Apr;4(4):307-8.

Here is the introduction to the article, from the open access Frontiers in Neuroinformatics, which explains some of the technology and features of the tool kit that has been developed.

The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes

Stephan Gerhard¹*, Alessandro Daducci¹, Alia Lemkaddem¹, Reto Meuli², Jean-Philippe Thiran¹ and Patric Hagmann²

• ¹ Signal Processing Laboratory 5, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
• ² Department of Radiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer’s plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

1 Introduction

What nervous systems do – essentially – is to connect. Investigations into the connectivity properties of nervous systems have a long history (Douglas and Martin, 2007; Fishman, 2007). Despite many efforts, contemporary knowledge about the specificity of structural and functional connectivity is still poor. The new field of connectomics is emerging to tackle the challenge of mapping complete neural circuitry, or connectomes.

Connectomes represent the fundamental pathways on which complex spatiotemporal activity patterns evolve. In turn, these activity patterns modify underlying structural pathways. For an understanding of how activity patterns arise (physiology) and what they are able to produce and mean (behavior), it is indispensable to have connectome data (neuroanatomy) on all spatial descriptive levels.

On the cellular level of description, light, and electron microscopy are the main imaging tools for mapping neuronal circuitry. Partial and complete connectomes have been mapped in a variety of organisms and structures such as the nematode Caenorhabditis elegans (Ward et al., 1975; White et al., 1976), the crustacean Daphnia’s optic lobe (Macagno et al., 1979), cat visual cortex (Binzegger et al., 2004), macaque (Felleman and Van Essen, 1991; Markov et al., 2010), the rabbit retina (Anderson et al., 2011), the mouse interscutularis muscle (Lu et al., 2009), hippocampus (Ascoli, 2010), or Drosophila melanogaster (Cardona et al., 2010; Chklovskii et al., 2010; Hampel et al., 2011).

On the macroscale level of description, diffusion-weighted magnetic resonance imaging (MRI) is the main imaging technology employed for mapping the structural connectivity of the human connectome (Hagmann, 2005; Sporns et al., 2005; Sporns, 2011). Magnetic resonance connectomics (Hagmann et al., 2010) is increasingly recognized as a tool for basic and clinical neuroscience. Several methodological advances in image acquisition, reconstruction, and tractography (Wedeen et al., 2008; Johansen-Berg and Behrens, 2009) suggest that automated processing pipelines will make it possible to generate comprehensive in vivo whole brain statistical connectomes.

Despite the big differences in spatial scale and data size, both levels of connectome mapping consist of similar stages. Connectome mapping workflows involve image acquisition, registration and segmentation, data organization and sharing, high-throughput pipelining, analysis, and visualization. Advanced neuroinformatics tools will be required to meet challenges that each stage presents. In this article, we will focus on the development of neuroinformatics tools in the emerging field of macroscale connectomics.

The efficiency of sharing data and source code would benefit if a transdisciplinary lingua franca for programming was available. Especially in the neurosciences, where researchers with varying degrees of scientific knowledge and programming skills meet, a common programming language helps to bridge gaps between theoretical and experimental worlds of investigation. Moreover, the programming language must be high-level, cross-platform, easy-to-learn, and have a large number of scientific libraries available. In recent years, Python¹ has become a viable alternative to Matlab, Java, or C++. More and more, Python is becoming the language of choice in scientific computing communities (Oliphant, 2007; Langtangen, 2009). Python is a free, open source, cross-platform programming language with a rapidly growing number of high-quality scientific libraries and interfaces to legacy code. A special-topic issue on “Python in neuroscience” in Frontiers in Neuroinformatics, and a number of publications (Kinser, 2008; Spacek et al., 2008; Davison et al., 2009) give an indication of the significance of the Python programming language.

Due to improved data acquisition methods, it is now possible to acquire large multi-modal datasets in projects involving thousands of subjects. For instance, the Human Connectome Project² is currently underway and collects Diffusion MRI, fMRI, EEG, MEG, behavioral, and genetic data in a cohort of 1200 healthy subjects. In such large-scale projects, the neuroinformatics challenges of data handling, sharing, and analysis become unnecessarily difficult without common infrastructure and data format standards. Due to their longer tradition, in the fields of volume-based and surface-based analysis in neuroimaging, standardized data formats have already been established such as NIFTI³ for volume-based data and GIFTI⁴ for surface-based data. Importantly for MR connectomics, no common format for network-based data yet exists. To approach the task of specifying such a format for connectivity-related neuroimaging data, the Connectivity InFormatics Technology Initiative (CIFTI) was launched. Furthermore, a dedicated program of the International Neuroinformatics Coordinating Facility (INCF⁵) on standards for data and metadata sharing was established.

For data management and sharing of large and multi-faceted datasets, a flexible data format is necessary. The key requirements of such a flexible data format under the macroscale connectomics perspective are severalfold:

⊳ A standardized container format for raw and processed multi-modal datasets that is based on common neuroimaging data formats, extended by a standard format for network-based datasets.

⊳ A minimal set of required metadata that can be extended flexibly by user-defined metadata, and that allow easy sharing of data and metadata across collaborating groups.

⊳ The possibility of relating different data modalities to each other.

⊳ An interface to database infrastructures.

⊳ A mapping to an object model in common programming languages.

⊳ To enable the storage of behavioral data.

⊳ To enable the storage of provenance information such as processing scripts and runtime environment

⊳ The ability to link data and concepts to semantic frameworks.

⊳ To enable easier data visualization (Benger, 2009) and analysis.

To establish a novel data format, it must come with appropriate libraries for reading and writing. Only when it is possible to easily read, modify, and save data in the new format, does it benefit the researcher who wants to focus on analysis and visualization. There exist many standard formats for the different data modalities, but no one has yet tried to combine these multi-modal datatypes into a single format.

Complementary to common data formats, investigators in the field of macroscale connectomics will require interactive research and development environments for data analysis and visualization. An optimal solution would be an integrated neuroinformatics environment based on Python. It would need to provide a graphical user interface (GUI) with extensive libraries, an interactive scripting shell and built-in script editors with code-highlighting and debugging functionality. Graph analysis libraries are required to unravel the complex brain network organization of structural and functional systems (Bullmore and Sporns, 2009). Furthermore, such a macroscale connectomics research environment needs to support an interactive mode of analysis and visualization of multi-modal datasets. Scripting interfaces provide the required flexibility to allow the implementation of a variety of multi-modal data exploration and data mining strategies in an interactive way (Akil et al., 2011). The environment needs not only to provide a methodology to automatically perform elementary functionality, but also guidance for the performance of more complex analysis and visualization tasks. Moreover, a modular software architecture fosters contributions by the open source research community. Open interfaces facilitate the reuse of a diversity of tools and external libraries that the connectome researcher can draw from.

We used the Python programming language to develop the free and open source Connectome Viewer Toolkit. We specify the Connectome File Format (CFF) as a container data format for multi-modal neuroimaging datasets, specifying a connectome file. We present the Python-based Connectome File Format Library (cfflib) for data manipulation and data sharing of connectome files. The Connectome Viewer provides a framework for interactive visualization and analysis of connectomes and multi-modal datasets. We will illustrate the application of the Connectome Viewer Toolkit on Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Mapper is a Python-based tool that currently implements structural connectome mapping. Figure 1 summarizes the general connectome processing workflow for structural and functional data. It highlights the use of the Connectome Viewer tools presented in this article.

FIGURE 1

Figure 1. General processing stages of a connectome workflow. The Connectome Viewer Toolkit currently supports the workflow highlighted in yellow. Mapping streams for structural data, such as the Connectome Mapper, or functional data may converge to a connectome file and can be further managed, analyzed, and visualized with the Connectome Viewer. Connectome files may be reused in other frameworks for analysis and visualization tasks.

Citation: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P. (2011, June 6). The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes. Frontiers in Neuroinformatics, 5:3. doi: 10.3389/fninf.2011.00003

Tags: The Connectome Viewer Toolkit, open source, framework, manage, analyze, visualize, connectomes, connectomics, connectome, neuroimaging, python, multi-modal data, data management, network analysis, visualization, brain, mapping, imaging, neuroscience, neuroinformatics

Michio Kaku - Mapping the Brain (The Human Connectome)

Michio Kaku, writing for Big Think last month, offers come insights on efforts to map the human brain - cool project, but I suspect it might take more than five years. This sounds like an awesome thing to do, but I wonder if it will provide any more answers that got from mapping human DNA, which Craig Venter says has been fruitless so far (emphasis added):

While genetics influence every aspect of our existence, including behavior and personalities, there's no way to truly tell right now what's caused by our genes and what comes from the environment. Even with seemingly simple things like eye color, you can't tell from my genetic code whether I have blue eyes or not. So it's naive to think that complex human behaviors, like risk-seeking, are driven by changes in one or two genes. We need to know the full array of our genome (plus the environment) to try and understand these things.

Ah, yes, that pesky environment thing - seems likely to pose some serious issues to the Connectome project as well.

Mapping the Brain (The Human Connectome)

Michio Kaku on October 19, 2010

We have long wanted to create a neuron-by-neuron map of the brain's circuitry to give us a 3-D glimpse into its connections are, how they work and how the different parts of the brain talk to one another. This is called "reverse engineering the brain" and is one of the Holy Grails of artificial intelligence and brain research. Unfortunately, we are many decades from being able to understand the entire brain at the neural level. With all our medical advances, it is proving difficult to understand all the neural hook-ups of a fruit fly brain, let alone a human brain. But recently, a new promising step is being taken, compliments of MRI research.

A new project, dubbed "The Human Connectome," will take five years and cost $30 Million, will map out approximately 100 billion neurons and 150 trillion synapses. The study will include the work of 33 experts and 1,200 study participants at nine different institutions.

This massive and complex undertaking will finally give us the first (rough) map of the brain's neural network which computational neuroscientist H. Sebastian Seung says is one of the most technological and computational challenges of all time. With this (rough) map, we will be able to further determine what goes on in the brain of someone that is affected by autism, Alzheimer's disease or even psychological disorders like schizophrenia. We will finally be able to view misfires, bad or missing connections or even a bad-rewire after the brain has been damaged.

We have of course been able to study various chemical levels in the brain and determine abnormal or increased levels which we are then able to treat with drugs. Advancements in brain scanning technology including EEG (Electroencephalograph), CAT (Computerized Axial Tomography) Scans, MRI (Magnetic Resonance Imaging), fMRI (Functional Magnetic Resonance Imaging), MEG (Magnetoencephalography) have allowed us to gain a much larger insight in both neuroscience and psychiatry. The main problem however is that we have never been able to have a full understanding of the connections in the brain. The answer to this may lie with the new upcoming circuitry map.

One of the leaders of the project, Dr. David Van Essen, PhD, chief of the Department of Anatomy and Neurobiology, Washington University, St Louis, Missouri has gone on the record stating that "The Human Connectome Project seems, at times, daunting and overwhelming but will provide us a critical baseline for understanding not only what typical brain connectivity is but what the nature of the variability in brain circuits are and how that relates to normal differences in behavior."

The National Institutes of Health is the organization that is putting up money for the study which will look at 1,200 participants—all twins—to start collecting the overwhelming amount of data needed. Before researchers even start the process of creating the first 3-D map of the brain's connections, they need to test a specially modified 3-tesla magnet which they say will take about two years to make efficient and ensure that it's in perfect working order. Some of the twins will be scanned with this magnet and about 200 of them will be scanned with one about twice as powerful to give us a wider data set as an end result. The scanning of the brains should be the easy part. The more difficult element of the project will be organizing, assembling, compiling, producing and sorting of all of the data (about 1 quadrillion bytes, or 1 petabyte) into something that is widely available and usable in the future on some type of an open-source platform for qualified researchers to examine and build upon.

What we are doing in a sense is developing a key that we have hopes will unlock some of the secrets of the human brain and give us a much better understanding of exactly how it works, what makes it work and why.

Tags: National Institutes of Health, mapping the human brain, Human Connectome Project, H. Sebastian Seung, Michio Kaku, Big Think, neuron-by-neuron map, brain circuitry, neuroscience, Psychology, brain, mapping, research, consciousness, mind, Craig Venter