EIT-MESHER – Segmented FEM Mesh Generation and Refinement

EIT-MESHER (https://github.com/EIT-team/Mesher) is C++ software, based on the CGAL library, which generates high quality Finite Element Model tetrahedral meshes from binary masks of 3D volume segmentations. Originally developed for biomedical applications in Electrical Impedance Tomography (EIT) to address the need for custom, non-linear refinement in certain areas (e.g. around electrodes), EIT-MESHER can also be used in other fields where custom FEM refinement is required, such as Diffuse Optical Tomography (DOT)

Feasibility of imaging evoked activity throughout the rat brain using electrical impedance tomography

Electrical Impedance Tomography (EIT) is an emerging technique which has been used to image evoked activity during whisker displacement in the cortex of an anaesthetised rat with a spatiotemporal resolution of 200 μm and 2 ms. The aim of this work was to extend EIT to image not only from the cortex but also from deeper structures active in somatosensory processing, specifically the ventral posterolateral (VPL) nucleus of the thalamus. The direct response in the cortex and VPL following 2 Hz forepaw stimulation were quantified using a 57-channel epicortical electrode array and a 16-channel depth electrode. Impedance changes of -0.16 ± 0.08% at 12.9 ± 1.4 ms and -0.41 ± 0.14% at 8.8±1.9 ms were recorded from the cortex and VPL respectively. For imaging purposes, two 57-channel epicortical electrode arrays were used with one placed on each hemisphere of the rat brain. Despite using parameters optimised toward measuring thalamic activity and undertaking extensive averaging, reconstructed activity was constrained to the cortical somatosensory forepaw region and no significant activity at a depth greater than 1.6 mm below the surface of the cortex could be reconstructed. An evaluation of the depth sensitivity of EIT was investigated in simulations using estimates of the conductivity change and noise levels derived from experiments. These indicate that EIT imaging with epicortical electrodes is limited to activity occurring 2.5 mm below the surface of the cortex. This depth includes the hippocampus and so EIT has the potential to image activity, such as epilepsy, originating from this structure. To image deeper activity, however, alternative methods such as the additional implementation of depth electrodes will be required to gain the necessary depth resolution

Imaging fast electrical activity in the brain during ictal epileptiform discharges with electrical impedance tomography

Electrical Impedance Tomography (EIT) is an emerging medical imaging technique which can produce tomographic images of internal impedance changes within an object using non-penetrating surface electrodes. It has previously been used to image impedance changes due to neuronal depolarisation during evoked potentials in the rat somatosensory cortex with a resolution of 2 ms and <200 μm, using an epicortical electrode array. The purpose of this work was to use this technique to elucidate the intracortical spatiotemporal trajectory of ictal spike-and-wave discharges (SWDs), induced by electrical stimulation in an acute rat model of epilepsy, throughout the cerebral cortex. Seizures lasting 16.5 ± 5.3 s with repetitive 2-5 Hz SWDs were induced in five rats anaesthetised with fentanyl-isoflurane. Transfer impedance measurements were obtained during each seizure with a 57-electrode epicortical array by applying 50 μA current at 1.7 kHz to two electrodes and recording voltages from all remaining electrodes. Images were reconstructed from averaged SWD-related impedance traces obtained from EIT measurements in successive seizures. We report the occurrence of reproducible impedance changes during the initial spike phase, which had an early onset in the whisker barrel cortex and spread posteriorly, laterally and ventrally over 20 ms (p < 0.03125, N = 5). These findings, which confirm and extend knowledge of SWD initiation and expression, suggest that EIT is a valuable neuroimaging tool for improving understanding of neural circuits implicated in epileptic phenomena

Tutorial: A guide to techniques for analysing recordings from the peripheral nervous system

The nervous system, through a combination of conscious and automatic processes, enables the regulation of the body and its interactions with the environment. The peripheral nervous system is an excellent target for technologies that seek to modulate, restore or enhance these abilities as it carries sensory and motor information that most directly relates to a target organ or function. However, many applications require a combination of both an effective peripheral nerve interface and effective signal processing techniques to provide selective and stable recordings. While there are many reviews on the design of peripheral nerve interfaces, reviews of data analysis techniques and translational considerations are limited. Thus, this tutorial aims to support new and existing researchers in the understanding of the general guiding principles, and introduces a taxonomy for electrode configurations, techniques and translational models to consider

Imaging physiological brain activity and epilepsy with Electrical Impedance Tomography

Electrical Impedance Tomography (EIT) allows reconstructing conductivity changes into images. EIT detects fast impedance changes occurring over milliseconds, due to ion channel opening, and slow impedance changes, appearing in seconds, due to cell swelling/increased blood flow. The purpose of this work was to examine the feasibility of using EIT for imaging a gyrencephalic brain with implanted depth electrodes during seizures. Chapter 1 summarises the principles of EIT. In Chapter 2, it is investigated whether recent technical improvements could enable EIT to image slow impedance changes upon visual stimulation non-invasively. This was unsuccessful so the remaining studies were undertaken on intracranial recordings. Chapter 3 presents a computer modelling study using data from patients, for whom the detection of simulated seizure-onset perturbations for both, fast and slow impedance changes, were improved with EIT compared to stereotactic electroencephalography (SEEG) detection or EEG inverse-source modelling. Chapter 4 describes the development of a portable EIT system that could be used on patients. The system does not require averaging and post-hoc signal processing to remove switching artefacts, which was the case previously. Chapter 5 describes the use of the optimised method in chemically-induced focal epilepsy in anaesthetised pigs implanted with depth electrodes. This shows for the first time EIT was capable of producing reproducible images of the onset and spread of seizure-related slow impedance changes in real-time. Chapter 6 presents a study on imaging ictal/interictal-related fast impedance changes. The feasibility of reconstructing ictal-related impedance changes is demonstrated for one pig and interictal-related impedance changes were recorded for the first time in humans. Chapter 7 summarises all work and future directions. Overall, this work suggests EIT in combination with SEEG has a potential to improve the diagnostic yield in epilepsy and demonstrates EIT can be performed safely and ethically creating a foundation for further clinical trials

Feasibility of imaging epileptic seizure onset with EIT and depth electrodes

Imaging ictal and interictal activity with Electrical Impedance Tomography (EIT) using intracranial electrode mats has been demonstrated in animal models of epilepsy. In human epilepsy subjects undergoing presurgical evaluation, depth electrodes are often preferred. The purpose of this work was to evaluate the feasibility of using EIT to localise epileptogenic areas with intracranial electrodes in humans. The accuracy of localisation of the ictal onset zone was evaluated in computer simulations using 9M element FEM models derived from three subjects. 5 mm radius perturbations imitating a single seizure onset event were placed in several locations forming two groups: under depth electrode coverage and in the contralateral hemisphere. Simulations were made for impedance changes of 1% expected for neuronal depolarisation over milliseconds and 10% for cell swelling over seconds. Reconstructions were compared with EEG source modelling for a radially orientated dipole with respect to the closest EEG recording contact. The best accuracy of EIT was obtained using all depth and 32 scalp electrodes, greater than the equivalent accuracy with EEG inverse source modelling. The localisation error was 5.2 ± 1.8, 4.3 ± 0 and 46.2 ± 25.8 mm for perturbations within the volume enclosed by depth electrodes and 29.6 ± 38.7, 26.1 ± 36.2, 54.0 ± 26.2 mm for those without (EIT 1%, 10% change, EEG source modelling, n = 15 in 3 subjects, p < 0.01). As EIT was insensitive to source dipole orientation, all 15 perturbations within the volume enclosed by depth electrodes were localised, whereas the standard clinical method of visual inspection of EEG voltages, only localised 8 out of 15 cases. This suggests that adding EIT to SEEG measurements could be beneficial in localising the onset of seizures

Imaging fast neural activity in the brain during epilepsy with electrical impedance tomography

Electrical impedance tomography (EIT) is a medical imaging technique which reconstructs images of the internal conductivity of an object using boundary measurements obtained by applying current through pairs of non-penetrating surface electrodes. EIT is able to image impedance changes which arise during neural activity at a high spatiotemporal resolution through the rat cerebral cortex and therefore represents a novel method for understanding neuronal network dynamics in epilepsy. Additionally, it holds therapeutic potential for improving the presurgical localisation of epileptogenic foci in individuals with drug-resistant epilepsy. This thesis was aimed at developing EIT for imaging epileptiform activity in vivo and assessing its potential for clinical use. Chapter 1 is a review of existing functional neuroimaging modalities, the principles of EIT and previous studies that have used EIT for imaging epileptic events. In Chapter 2, the safety of continuous current application to the rat cortical surface at 10-100 μA and 1725 Hz, parameters that are representative of fast neural EIT protocols, was verified by histological evaluation. Chapter 3 details the development of two acute rat models of focal epilepsy, the cortical and hippocampal epileptic afterdischarges models, for assessing the feasibility of imaging epileptiform activity with fast neural EIT using epicortical electrode arrays. In Chapter 4, EIT was used to image the propagation of ictal spike-and-wave activity through the cerebral cortex at a resolution of 2 ms and ≤300 µm. In order to enable imaging of epileptiform discharges in deeper subcortical structures, the optimal carrier frequency for current application was determined in Chapter 5. Results demonstrated that the maximal signal-to-noise ratio of fast neural impedance changes during ictal discharges is obtained at 1355 Hz. Finally, in Chapter 6, epileptiform activity in the hippocampus was imaged, with a localisation accuracy of ≤400 µm, using epicortical impedance measurements obtained at this optimised carrier frequency

Imaging fascicular organisation in mammalian vagus nerve for selective VNS

Nerves contain a large number of nerve fibres, or axons, organised into bundles known as fascicles. Despite the somatic nervous system being well understood, the organisation of the fascicles within the nerves of the autonomic nervous system remains almost completely unknown. The new field of bioelectronics medicine, Electroceuticals, involves the electrical stimulation of nerves to treat diseases instead of administering drugs or performing complex surgical procedures. Of particular interest is the vagus nerve, a prime target for intervention due to its afferent and efferent innervation to the heart, lungs and majority of the visceral organs. Vagus nerve stimulation (VNS) is a promising therapy for treatment of various conditions resistant to standard therapeutics. However, due to the unknown anatomy, the whole nerve is stimulated which leads to unwanted off-target effects. Electrical Impedance Tomography (EIT) is a non-invasive medical imaging technique in which the impedance of a part of the body is inferred from electrode measurements and used to form a tomographic image of that part. Micro-computed tomography (microCT) is an ex vivo method that has the potential to allow for imaging and tracing of fascicles within experimental models and facilitate the development of a fascicular map. Additionally, it could validate the in vivo technique of EIT. The aim of this thesis was to develop and optimise the microCT imaging method for imaging the fascicles within the nerve and to determine the fascicular organisation of the vagus nerve, ultimately allowing for selective VNS. Understanding and imaging the fascicular anatomy of nerves will not only allow for selective VNS and the improvement of its therapeutic efficacy but could also be integrated into the study on all peripheral nerves for peripheral nerve repair, microsurgery and improving the implementation of nerve guidance conduits. Chapter 1 provides an introduction to vagus nerve anatomy and the principles of microCT, neuronal tracing and EIT. Chapter 2 describes the optimisation of microCT for imaging the fascicular anatomy of peripheral nerves in the experimental rat sciatic and pig vagus nerve models, including the development of pre-processing methods and scanning parameters. Cross-validation of this optimised microCT method, neuronal tracing and EIT in the rat sciatic nerve was detailed in Chapter 3. Chapter 4 describes the study with microCT with tracing, EIT and selective stimulation in pigs, a model for human nerves. The microCT tracing approach was then extended into the subdiaphragmatic branches of the vagus nerves, detailed in Chapter 5. The ultimate goal of human vagus nerve tracing was preliminarily performed and described in Chapter 6. Chapter 7 concludes the work and describes future work. Lastly, Appendix 1 (Chapter 8) is a mini review on the application of selective vagus nerve stimulation to treat acute respiratory distress syndrome and Appendix 2 is morphological data corresponding to Chapter 4