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IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images. PLoS One 2022; 17:e0279825. [PMID: 36584152 PMCID: PMC9803232 DOI: 10.1371/journal.pone.0279825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/14/2022] [Indexed: 12/31/2022] Open
Abstract
Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since "seeing is believing", it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital workflows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer.
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Singh NM, Harrod JB, Subramanian S, Robinson M, Chang K, Cetin-Karayumak S, Dalca AV, Eickhoff S, Fox M, Franke L, Golland P, Haehn D, Iglesias JE, O'Donnell LJ, Ou Y, Rathi Y, Siddiqi SH, Sun H, Westover MB, Whitfield-Gabrieli S, Gollub RL. How Machine Learning is Powering Neuroimaging to Improve Brain Health. Neuroinformatics 2022; 20:943-964. [PMID: 35347570 PMCID: PMC9515245 DOI: 10.1007/s12021-022-09572-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2022] [Indexed: 12/31/2022]
Abstract
This report presents an overview of how machine learning is rapidly advancing clinical translational imaging in ways that will aid in the early detection, prediction, and treatment of diseases that threaten brain health. Towards this goal, we aresharing the information presented at a symposium, "Neuroimaging Indicators of Brain Structure and Function - Closing the Gap Between Research and Clinical Application", co-hosted by the McCance Center for Brain Health at Mass General Hospital and the MIT HST Neuroimaging Training Program on February 12, 2021. The symposium focused on the potential for machine learning approaches, applied to increasingly large-scale neuroimaging datasets, to transform healthcare delivery and change the trajectory of brain health by addressing brain care earlier in the lifespan. While not exhaustive, this overview uniquely addresses many of the technical challenges from image formation, to analysis and visualization, to synthesis and incorporation into the clinical workflow. Some of the ethical challenges inherent to this work are also explored, as are some of the regulatory requirements for implementation. We seek to educate, motivate, and inspire graduate students, postdoctoral fellows, and early career investigators to contribute to a future where neuroimaging meaningfully contributes to the maintenance of brain health.
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Affiliation(s)
- Nalini M Singh
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jordan B Harrod
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sandya Subramanian
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mitchell Robinson
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ken Chang
- Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Suheyla Cetin-Karayumak
- Department of Psychiatry, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, USA
| | | | - Simon Eickhoff
- Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7) Research Centre Jülich, Jülich, Germany
| | - Michael Fox
- Center for Brain Circuit Therapeutics, Department of Neurology, Psychiatry, and Radiology, Brigham and Women's Hospital and Harvard Medical School, 02115, Boston, USA
| | - Loraine Franke
- University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Polina Golland
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Daniel Haehn
- University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Juan Eugenio Iglesias
- Centre for Medical Image Computing, University College London, London, UK
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, MA, 02115, Boston, USA
| | - Yangming Ou
- Department of Radiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Yogesh Rathi
- Department of Psychiatry, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, USA
| | - Shan H Siddiqi
- Department of Psychiatry, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, USA
| | - Haoqi Sun
- Department of Neurology and McCance Center for Brain Health / Harvard Medical School, Massachusetts General Hospital, Boston, 02114, USA
| | - M Brandon Westover
- Department of Neurology and McCance Center for Brain Health / Harvard Medical School, Massachusetts General Hospital, Boston, 02114, USA
| | | | - Randy L Gollub
- Department of Psychiatry and Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, 02114, USA.
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Burkhardt J, Sharma A, Tan J, Franke L, Leburu J, Jeschke J, Devore S, Friedman D, Chen J, Haehn D. N-Tools-Browser: Web-Based Visualization of Electrocorticography Data for Epilepsy Surgery. FRONTIERS IN BIOINFORMATICS 2022; 2:857577. [PMID: 36304315 PMCID: PMC9580919 DOI: 10.3389/fbinf.2022.857577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Epilepsy affects more than three million people in the United States. In approximately one-third of this population, anti-seizure medications do not control seizures. Many patients pursue surgical treatment that can include a procedure involving the implantation of electrodes for intracranial monitoring of seizure activity. For these cases, accurate mapping of the implanted electrodes on a patient’s brain is crucial in planning the ultimate surgical treatment. Traditionally, electrode mapping results are presented in static figures that do not allow for dynamic interactions and visualizations. In collaboration with a clinical research team at a Level 4 Epilepsy Center, we developed N-Tools-Browser, a web-based software using WebGL and the X-Toolkit (XTK), to help clinicians interactively visualize the location and functional properties of implanted intracranial electrodes in 3D. Our software allows the user to visualize the seizure focus location accurately and simultaneously display functional characteristics (e.g., results from electrical stimulation mapping). Different visualization modes enable the analysis of multiple electrode groups or individual anatomical locations. We deployed a prototype of N-Tools-Browser for our collaborators at the New York University Grossman School of Medicine Comprehensive Epilepsy Center. Then, we evaluated its usefulness with domain experts on clinical cases.
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Affiliation(s)
- Jay Burkhardt
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
| | - Aaryaman Sharma
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
| | - Jack Tan
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
| | - Loraine Franke
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
| | - Jahnavi Leburu
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
| | - Jay Jeschke
- Department of Neurology, New York University, Grossman School of Medicine, New York, NY, United States
| | - Sasha Devore
- Department of Neurology, New York University, Grossman School of Medicine, New York, NY, United States
| | - Daniel Friedman
- Department of Neurology, New York University, Grossman School of Medicine, New York, NY, United States
| | - Jingyun Chen
- Department of Neurology, New York University, Grossman School of Medicine, New York, NY, United States
- *Correspondence: Jingyun Chen,
| | - Daniel Haehn
- Machine Psychology Lab, Department of Computer Science, University of Massachusetts Boston, Boston, MA, United States
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Puhar EG, Korat L, Erič M, Jaklič A, Solina F. Microtomographic Analysis of a Palaeolithic Wooden Point from the Ljubljanica River. SENSORS 2022; 22:s22062369. [PMID: 35336540 PMCID: PMC8951160 DOI: 10.3390/s22062369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/05/2022]
Abstract
A rare and valuable Palaeolithic wooden point, presumably belonging to a hunting weapon, was found in the Ljubljanica River in Slovenia in 2008. In order to prevent complete decay, the waterlogged wooden artefact had to undergo conservation treatment, which usually involves some expected deformations of structure and shape. To investigate these changes, a series of surface-based 3D models of the artefact were created before, during and after the conservation process. Unfortunately, the surface-based 3D models were not sufficient to understand the internal processes inside the wooden artefact (cracks, cavities, fractures). Since some of the surface-based 3D models were taken with a microtomographic scanner, we decided to create a volumetric 3D model from the available 2D tomographic images. In order to have complete control and greater flexibility in creating the volumetric 3D model than is the case with commercial software, we decided to implement our own algorithm. In fact, two algorithms were implemented for the construction of surface-based 3D models and for the construction of volumetric 3D models, using (1) unsegmented 2D images CT and (2) segmented 2D images CT. The results were positive in comparison with commercial software and new information was obtained about the actual state and causes of the deformation of the artefact. Such models could be a valuable aid in the selection of appropriate conservation and restoration methods and techniques in cultural heritage research.
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Affiliation(s)
- Enej Guček Puhar
- Computer Vision Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia;
- Correspondence: (E.G.P.); (F.S.)
| | - Lidija Korat
- The Laboratory for Cements, Mortars and Ceramics, Slovenian National Building and Civil Engineering Institute, Dimičeva Ulica 12, SI-1000 Ljubljana, Slovenia;
| | - Miran Erič
- Institute for the Protection of Cultural Heritage of Slovenia, Poljanska 40, SI-1000 Ljubljana, Slovenia;
| | - Aleš Jaklič
- Computer Vision Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia;
| | - Franc Solina
- Computer Vision Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia;
- Correspondence: (E.G.P.); (F.S.)
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