The Manipulation Toolkit

History

  • 2019-2021: Observing certain similarity between the orientation distribution function used to determine the direction of fibers and the extraction of prominant spikes among intensity distribution of an image, Xavier asked himself whether he could apply the same idea to identify the most plausible direction of a fiber of interest along its tracking, in order to improve the reconstructed streamlines. In his Mestrado's thesis he investigated his conjecture by comparing the extracted directions with the expected neuroanatomical directions. His projest is supported by CNPq financial support (Grant 132790/2019-0).
  • 2018-: Because of the interest in biomedical engineering, Felippe Trigueiro Angelo joined to our research group aiming at integrating the feature of a customized neuroanatomy atlas into VMTK-Neuro for the purpose of neuroanatomy teaching. In his Mestrado's thesis he developed an interactive atlas of gross neuroanatomy per individual. Instead of segmenting a human bran into neuroanatomical gross structures, he proposed to consider that MNI152 average brain is fully aligned with the Talairach atlas. This reduced the segmentation problem to a deformable registration problem of the anatomical T1-weighted MR scan and the standard MNI 152 average brain, such that each deformed brain may be individually labeled by the Talairch atlas. His projest was supported by CAPES.
  • 2017-: Because of his interest in mobile communication, Voltoline proposed to investigate a way to make VMTK-Neuro accessible from mobile devices in his Doutorado's dissertation. The aimed application for this mobile VMTK-Neuro is collaborative neurosurgery planning. Under co-supervision of Prof. Dr. Enrico Ghizoni, Voltoline also concluded a GPU-based tractography from the DTI map he estimated in his Mestrado's thesis which is useful for nerusurgical planning. He receives CNPq financial support (Grant 141068/2017-5).
  • 2016-: After a period of hesitation and frustrating attempts to "teach a machine" a procedure to reconstruct cerebral fiber tracts, Benites decided to join the Voltoline's project. He developed in his Mestrado's thesis an interface that coupled through a CPU the human coginition and the number crunching power of a GPU for more reliable expert-guided reconstruction. He aimed at providing better analysis of cerebral connections, and hence safer neurosurgical planning. His projest was supported by CAPES.
  • 2016-: The results of Rubianes's Mestrado work called attention of the NIRS research team headed by Prof. Mesquita. They conjectured that the neuronavigation procedure developed by Rubianes is promising for improving the accuracy of diffuse optical measurements, because of its ability in providing relative location of invisible target tissue with respect to the visible scalp. Rubianes decided to deepen his knowledge about NIRS and to apply what he learned in his Mestrado's thesis to this new challenge in his Doutorado research. He receives CNPq financial support (Grant 142018/2017-1).
  • 2014-2018: Attracting by the power and the mystery of 3D image processing, Loos begins his Doutorado's dissertation aiming at developing a tool that detects subtle lesions of focal cortical dysplasia automatically. The co-supervision of Prof. Dr. Clarissa L. Yasuda is crucial in providing medical data and the state-of-the-art of medical knowledge about this kind of abnormalities. Meanwhile, we have a very encouraging feedback from the neurosurgeon Prof. Dr. Enrico Ghizoni. He thinks that the curvilinear reformatting tool developed by Loos during his Mestrado's thesis could be very helpful in neurosurgery planning. This is because of its potential in revealing the spatial relationship of the vascular and the cortical brain structures. We decide to shift the focus of the work to the visualization of cortical structures for both diagnosis and pre-operative planning. Together with Rubianes they upgraded VMTK-Neuro to VMTK-Neuro v3.2. The work was supported by CNPq (Grant 165777/2014).
  • 2014-2017: In addition to clinical anamnesis and 3D neuroimaging studies, the recording of cerebral activities along the scalp may play an important role in the localization of the epileptogenic focus. This is because that the epilepsy causes abnormalities in cerebral signals and both the optodes and the eletrodes can capture them in millisecond-range temporal resolution. Rubianes investigated in the context of his Mestrado's thesis a method for accurate placement of cerebral activity sensors on the suspicious areas of an patient's scalp. The work receives CAPES financial support.
  • 2017: At the iniciative of Loos, the VMTKBeta received an improved curvilinear reformatting and a new site. It was VMTK-Neuro-3.1.
  • 2014-2016: Successful co-registration of anatomical and functional volumes motivates us to pursue another challenging goal: to integrate the neural tracts in our interactive visualization environment. According to our medical colleagues of FCM/Unicamp, it could be very useful in neurosurgical planning. Voltoline accepts to face the challenge and researches into the multimodal visualization of DWI (diffusion-weighted imaging) and RMI (resonance magnetic imaging) modalities in the context of his Mestrado's thesis. The work receives CNPq financial support (Grant 153389/2014-1).
  • 2015: Loos, Voltoline and Rubianes questioned the extensility of the current version of VMTK. Not only because that some issues raised by the medical staff are not easily implemented with wxWidgets, but also due to the concept of its code architecture. They decided to face a challenge before continuing their own works: to reimplement a cross-platform VMTK with use of Qt and the well-established project patterns. VMTKBeta (VMTK-Neuro-3.0) is born after six-month intense work.
  • 2013: Wu, together with Dr. Yasuda, prepared a lecture about the practical results obtained so far.
  • 2012-2015: As a lecturer of Mauá Institute of Technology Prof. Scalco identified in his Engineering students difficulties for grasping abstract scientific concepts. This motivates him to develop in the context of his Mestrado's thesis a playful learning environment for Physics class in which an inexpensive game controller Wii remote is applied for tangible interactions.
  • 2011-2014: Our research on interactive visualization leads us to the idea of applying the boundary representation to bridge the gestalt perception (entirety) and digital representation (pixel or voxelwise). In his Mestrado's thesis, Loos investigates an implementation for the brep model that is useful for interactive visualization of 3D medical images. He gets CNPq grants (135100/2011-9 and 144174/2012-0).
  • 2011-: In most cases, 3D image registration is required as pre-processing for multimodal visualiztion. Valente studies and implements in the context of his Mestrado's thesis the Maximilization of Mutual Information technique for multimodal medical image registration. His work is supported by CNPq (135199/2011-5). To avoid convergence to an incorrect local maximum, we further propose an interactive tool to segment valid samples and to use the obtained subsets for pre-aligning the volumes before registration. We used the Vanderbilt Database of the Retrospective Image Registration Evaluation Project to evaluate our proposed rigid registration technique.
  • 2010-: In his Doutorado's thesis Watanabe investigated solutions for problems related with multimodal visualizaiton of 3D neuro-images. The equipments necessary for conducting the project were acquired with Fapesp funds (2011/02351-0). He integrated the co-registration programs developed by Valente and the interaction tools designed by Elias, as shows this video presented in the First BRAINN Congress.
  • 2010-2012: The experiences adquired in the implementation of a new version of VMTK motivated Vidalón to improve the transfer functions for RMI neuro-images in his Mestrado's thesis. His work is supported by CAPES. Strong demand on multiplanar reformatting in arbitrary angulation motivates us to further develop an interactive tool (VMTK-Neuro-2.1) that performs such reformatting.
  • 2009-2010: At the beginning of 2009 it is started the development of a specific application for the interaction framework proposed by Batagelo: curvilinear reformatting. The prototype is named VMTK. Not the way that the interaction data is organized but also the way that large volume data is packed as texture data should be studied, as reported here (VMTK-Neuro-1.0). A novel cropping algorithm has been designed. Watanabe and Vidalón implemented a new version of VMTK (VMTK-Neuro-2.0) centered in this algorithm.
  • 2008-2009: During his Pós-doutorado, Batagelo investigated a way to narrow the gulf between the images generated from direct rendering on GPU and the underlying volume data, also available on GPU. His objective is to provide an application-independent framework for direct manipulations with volume data. This research received financial support from Fapesp under Grant Agreement Number 2008/51041-0.
  • 2003-2007: In his Doutorado's thesis Batagelo focused his attention on the performance of the interaction commands devised for MTK. He explored the hardware capabilities of different GPUs and proposed a software interaction architecture. CNPq provided the scholarship assistance to Batagelo (141685/2002-6) and the equipments used during his research were purchased with Fapesp grant funds (2003/13090-6).
  • 2004: Tost integrated the new functionalities of MTK in the CoMo developed by Gonzaga for his Doutorado's thesis. Gonzaga extends conceptually the architecture of MTK, which is a toolkit for mono-user graphics interface, to a toolkit that can support collaborative interactions. The netMTK was born. Gonzaga's research was supported financially by CAPES.
  • 2002-2003: Abrantes and Tost extended the functionalities of 3D cursor in the context of a undergraduate project. They implemented 3D picking and snapping facilities for the 3D cursor controlled by both the 2D (mouse) and the 3D input devices (Spaceball 3003). Besides, they reorganized the source of MTK, documented all available functions and designed this Web site. They received scholarship assistance from Fapesp under Grant Agreement Number 02/01161-3 (Abrantes) and 02/01162-0 (Tost).
  • 2000-2002: Mesquita developed in his undergraduate project the concept of 3D cursor for specifying a 3D point with use of a mouse. Differently from the approach adopted by Velásquez, that estimates the 3D position of a 2D cursor on the screen on the basis of its displacement relative to the projection of coordinate system axes, Mesquita considered that, instead of 2D, there is a 3D cursor whose movements in the 3D "world"are constrained either on xy- or on xz-planes. To visually feedback its positions, its image is rendered at each interaction. For handling input events, some windowing system routines are added in MTK to extend it for supporting 3D cursor. He named the extended version of MTK as MTKx. For this work he received scholarship assistance from Fapesp under Grant Agreement Number 00/09619-3
    Aiming at improving the rendering time, Batagelo proposed in his Mestrado's thesis a 3D regular grid for efficiently handling occluded objects in a dynamic scene. He received a sholarship sponsored by CAPES.
  • 1999-2002: Aiming at integrating 3D interactive functionalities in e-learning systems, Fisch developed in his Mestrado's thesis an architecture that integrates graphics and networking communication facilities. Some interaction concepts of MTK have been applied in his project. This project counted with the participation of Bostjan Kolar, a slovenian undergraduate student who spent his summer holidays at Unicamp in the context of the international exchange program of International Association for the Exchange of Students for Technical Experience (IAESTE).
  • 1995-1999: On top of Mesa3D, a 3D graphics library with an API which is very similar to that of OpenGL, Navarro and Malheiros have designed an object-oriented toolkit named MTK for providing both visualization and manipulation facilities. Two principles have guided our design: reuse of the existing software programs (Graphics Gems and STL) and reuse of the design patterns. Effectively, we did our first experiment in separating the interaction control flow and the application-dependent manipulation by including in MTK two classes of objects: draggers and constraints.
    In parallel, Gonzaga started his Doutorado's thesis aiming at developing a synchronous collaborative interactive geometric modeler with use of MTK. Navarro and Gonzaga received sholarship sponsored by CNPq.
  • 1993-1994: We developed on top of X system a toolkit for visualizing and interacting with the 3D wireframe objects on the canvas area of the Sun XView. The interaction is restricted to the 2D picking and, on the basis of the region partition principle presented by Nielson and Olsen, Velásquez have implemented a triad mouse for specifying a 3D point with use of a 2D mouse in her Mestrado's thesis. The programs are written in C language. Simultaneously, Bernardes investigated in his Mestrado's thesis the applicability of artificial intelligence techniques in modeling some vague geometric concepts, more specifically the fairness concept, in order to make the computer-human interface closer to the user's "world". Fapesp sponsored his scholarship under Grant Agreement Number 94/1650-6. The equipments necessary for conducting the project were acquired with Fapesp funds (96/00962-0).