Himar Fabelo

HELICoiD project: a new use of hyperspectral imaging for brain cancer detection in real-time during neurosurgical operations

Hyperspectral images allow obtaining large amounts of information about the surface of the scene that is captured by the sensor. Using this information and a set of complex classification algorithms is possible to determine which material or substance is located in each pixel. The HELICoiD (HypErspectraL Imaging Cancer Detection) project is a European FET project that has the goal to develop a demonstrator capable to discriminate, with high precision, between normal and tumour tissues, operating in real-time, during neurosurgical operations. This demonstrator could help the neurosurgeons in the process of brain tumour resection, avoiding the excessive extraction of normal tissue and unintentionally leaving small remnants of tumour. Such precise delimitation of the tumour boundaries will improve the results of the surgery. The HELICoiD demonstrator is composed of two hyperspectral cameras obtained from Headwall. The first one in the spectral range from 400 to 1000 nm (visible and near infrared) and the second one in the spectral range from 900 to 1700 nm (near infrared). The demonstrator also includes an illumination system that covers the spectral range from 400 nm to 2200 nm. A data processing unit is in charge of managing all the parts of the demonstrator, and a high performance platform aims to accelerate the hyperspectral image classification process. Each one of these elements is installed in a customized structure specially designed for surgical environments. Preliminary results of the classification algorithms offer high accuracy (over 95%) in the discrimination between normal and tumour tissues.

A Novel Use of Hyperspectral Images for Human Brain Cancer Detection using in-Vivo Samples

Hyperspectral Imaging is an emerging technology for medical diagnosis issues due to the fact that it is a non-contact, non-ionizing and non-invasive sensing technique. The work presented in this paper tries to establish a novel way in the use of hyperspectral images to help neurosurgeons to accurately determine the tumour boundaries in the process of brain tumour resection, avoiding excessive extraction of healthy tissue and the accidental leaving of un-resected small tumour tissues. So as to do that, a hyperspectral database of in-vivo human brain samples has been created and a procedure to label the pixels diagnosed by the pathologists has been described. A total of 24646 samples from normal and tumour tissues from 13 different patients have been obtained. A pre-processing chain to homogenize the spectral signatures has been developed, obtaining 3 types of datasets (using different pre-processing chain) in order to determine which one provides the best classification results using a Random Forest classifier. The experimental results of this supervised classification algorithm to distinguish between normal and tumour tissues have achieved more than 99% of accuracy.

Porting a PCA-based Hyperspectral Image Dimensionality Reduction Algorithm for Brain Cancer Detection on a Manycore Architecture

This paper presents a study of the parallelism of a Principal Component Analysis (PCA) algorithm and its adaptation to a manycore MPPA (Massively Parallel Processor Array) architecture, which gathers 256 cores distributed among 16 clusters. This study focuses on porting hyperspectral image processing into many core platforms by optimizing their processing to fulfill real-time constraints, fixed by the image capture rate of the hyperspectral sensor. Real-time is a challenging objective for hyperspectral image processing, as hyperspectral images consist of extremely large volumes of data and this problem is often solved by reducing image size before starting the processing itself. To tackle the challenge, this paper proposes an analysis of the intrinsic parallelism of the different stages of the PCA algorithm with the objective of exploiting the parallelization possibilities offered by an MPPA manycore architecture. Furthermore, the impact on internal communication when increasing the level of parallelism, is also analyzed. Experimenting with medical images obtained from two different surgical use cases, an average speedup of 20 is achieved. Internal communications are shown to rapidly become the bottleneck that reduces the achievable speedup offered by the PCA parallelization. As a result of this study, PCA processing time is reduced to less than 6 s, a time compatible with the targeted brain surgery application requiring 1 frame-per-minute.

Manifold Embedding and Semantic Segmentation for Intraoperative Guidance With Hyperspectral Brain Imaging

Recent advances in hyperspectral imaging have made it a promising solution for intra-operative tissue characterization, with the advantages of being non-contact, non-ionizing, and non-invasive. Working with hyperspectral images in vivo, however, is not straightforward as the high dimensionality of the data makes real-time processing challenging. In this paper, a novel dimensionality reduction scheme and a new processing pipeline are introduced to obtain a detailed tumor classification map for intra-operative margin definition during brain surgery. However, existing approaches to dimensionality reduction based on manifold embedding can be time consuming and may not guarantee a consistent result, thus hindering final tissue classification. The proposed framework aims to overcome these problems through a process divided into two steps: dimensionality reduction based on an extension of the T-distributed stochastic neighbor approach is first performed and then a semantic segmentation technique is applied to the embedded results by using a Semantic Texton Forest for tissue classification. Detailed in vivo validation of the proposed method has been performed to demonstrate the potential clinical value of the system.

An Intraoperative Visualization System Using Hyperspectral Imaging to Aid in Brain Tumor Delineation

Hyperspectral imaging (HSI) allows for the acquisition of large numbers of spectral bands throughout the electromagnetic spectrum (within and beyond the visual range) with respect to the surface of scenes captured by sensors. Using this information and a set of complex classification algorithms, it is possible to determine which material or substance is located in each pixel. The work presented in this paper aims to exploit the characteristics of HSI to develop a demonstrator capable of delineating tumor tissue from brain tissue during neurosurgical operations. Improved delineation of tumor boundaries is expected to improve the results of surgery. The developed demonstrator is composed of two hyperspectral cameras covering a spectral range of 400–1700 nm. Furthermore, a hardware accelerator connected to a control unit is used to speed up the hyperspectral brain cancer detection algorithm to achieve processing during the time of surgery. A labeled dataset comprised of more than 300,000 spectral signatures is used as the training dataset for the supervised stage of the classification algorithm. In this preliminary study, thematic maps obtained from a validation database of seven hyperspectral images of in vivo brain tissue captured and processed during neurosurgical operations demonstrate that the system is able to discriminate between normal and tumor tissue in the brain. The results can be provided during the surgical procedure (~1 min), making it a practical system for neurosurgeons to use in the near future to improve excision and potentially improve patient outcomes.

Hyperspectral database of pathological in-vitro human brain samples to detect carcinogenic tissues

Hyperspectral imaging is an emerging technology for medical diagnosis. Some previous studies have used this type of images to detect cancer diseases. In this research work, a multidisciplinary team conformed by pathologists and engineers has created a diagnosed hyperspectral database of in-vitro human brain tissues. In order to capture the hyperspectral information from histological slides, an acquisition system based on a microscope coupled with a hyperspectral camera has been developed. Preliminary results of applying two different supervised classification algorithms (Support Vector Machines and Artificial Neural Networks) to the hyperspectral database show that an automatic discrimination between healthy and tumour brain tissues from in-vitro samples is possible using exclusively their spectral information. The sensitivity and the specificity are over 92% in all the cases.

Spatio-spectral classification of hyperspectral images for brain cancer detection during surgical operations

Surgery for brain cancer is a major problem in neurosurgery. The diffuse infiltration into the surrounding normal brain by these tumors makes their accurate identification by the naked eye difficult. Since surgery is the common treatment for brain cancer, an accurate radical resection of the tumor leads to improved survival rates for patients. However, the identification of the tumor boundaries during surgery is challenging. Hyperspectral imaging is a non-contact, non-ionizing and non-invasive technique suitable for medical diagnosis. This study presents the development of a novel classification method taking into account the spatial and spectral characteristics of the hyperspectral images to help neurosurgeons to accurately determine the tumor boundaries in surgical-time during the resection, avoiding excessive excision of normal tissue or unintentionally leaving residual tumor. The algorithm proposed in this study to approach an efficient solution consists of a hybrid framework that combines both supervised and unsupervised machine learning methods. Firstly, a supervised pixel-wise classification using a Support Vector Machine classifier is performed. The generated classification map is spatially homogenized using a one-band representation of the HS cube, employing the Fixed Reference t-Stochastic Neighbors Embedding dimensional reduction algorithm, and performing a K-Nearest Neighbors filtering. The information generated by the supervised stage is combined with a segmentation map obtained via unsupervised clustering employing a Hierarchical K-Means algorithm. The fusion is performed using a majority voting approach that associates each cluster with a certain class. To evaluate the proposed approach, five hyperspectral images of surface of the brain affected by glioblastoma tumor in vivo from five different patients have been used. The final classification maps obtained have been analyzed and validated by specialists. These preliminary results are promising, obtaining an accurate delineation of the tumor area.

Demo: HELICoiD tool demonstrator for real-time brain cancer detection

In this paper, a demonstrator of three different elements of the EU FET HELICoiD project is introduced. The goal of this demonstration is to show how the combination of hyperspectral imaging and machine learning can be a potential solution to precise real-time detection of tumor tissues during surgical operations. The HELICoiD setup consists of two hyperspectral cameras, a scanning unit, an illumination system, a data processing system and an EMB01 accelerator platform, which hosts an MPPA-256 manycore chip. All the components are mounted fulfilling restrictions from surgical environments, as shown in the accompanying video recorded at the operating room. An in-vivo human brain hyperspectral image data base, obtained at the University Hospital Doctor Negrin in Las Palmas de Gran Canaria, has been employed as input to different supervised classification algorithms (SVM, RF, NN) and to a spatial-spectral filtering stage (SVM-KNN). The resulting classification maps are shown in this demo. In addition, the implementation of the SVM-KNN classification algorithm on the MPPA EMB01 platform is demonstrated in the live demo.

A low-cost control system for BLDC motors applied to teaching

In this paper, the process carried out to design and manufacture the hardware of a low-cost control system for brushless direct current motors based on a ATmega64M1 is described. The proposed control system, applied to teaching, consists of the controller presented in this paper and a C library specially created for this project. Three types of different control systems are detailed. The first is the basic system, which can be used for teaching microcontroller programming within the scope of brushless motors. The second system presented is used to monitor and manage electric vehicles powered by a 6-phase brushless motor. This system offers the possibility to be used as a practice teaching module for electromechanical students. Finally, we detail a system that enables the control of remotely operated vehicles. This configuration can also be oriented to the control of any type of robotic vehicle powered by brushless motors. These three systems use the controller proposed in this article. The difference between them is the number of controllers that are required for their operation and how the system components are interconnected.

Acceleration of brain cancer detection algorithms during surgery procedures using GPUs

Abstract The HypErspectraL Imaging Cancer Detection (HELICoiD) European project aims at developing a methodology for tumor tissue classification through hyperspectral imaging (HSI) techniques. This paper describes the development of a parallel implementation of the Support Vector Machines (SVMs) algorithm employed for the classification of hyperspectral (HS) images of in vivo human brain tissue. SVM has demonstrated high accuracy in the supervised classification of biological tissues, and especially in the classification of human brain tumor. In this work, both the training and the classification stages of the SVMs were accelerated using Graphics Processing Units (GPUs). The acceleration of the training stage allows incorporating new samples during the surgical procedures to create new mathematical models of the classifier. Results show that the developed system is capable to perform efficient training and real-time compliant classification.