ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software’s ability to handle the requirements of modern science. We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called “ImageJ2” in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ’s development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.

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ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. 
We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs.

The paper presents MeshLab, an open source, extensible, mesh processing system that has been developed at the Visual Computing Lab of the ISTI-CNR with the helps of tens of students. We will describe the MeshLab architecture, its main features and design objectives discussing what strategies have been used to support its development. Various examples of the practical uses of MeshLab in research and professional frameworks are reported to show the various capabilities of the presented system.

MeshLab: an Open-Source Mesh Processing Tool

In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes contain a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with Shared Information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different level of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems. This special issue aims at gathering the recent advances in learning with shared information methods and their applications in computer vision and multimedia analysis. Both state-of-the-art works, as well as literature reviews, are welcome for submission. Papers addressing interesting real-world computer vision and multimedia applications are especially encouraged. Topics of interest include, but are not limited to:  • Multi-task learning or transfer learning for large-scale computer vision and multimedia analysis • Deep learning for large-scale computer vision and multimedia analysis • Multi-modal approach for large-scale computer vision and multimedia analysis • Different sharing strategies, e.g., sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, • Real-world computer vision and multimedia applications based on learning with shared information, e.g., event detection, object recognition, object detection, action recognition, human head pose estimation, object tracking, location-based services, semantic indexing. • New datasets and metrics to evaluate the benefit of the proposed sharing ability for the specific computer vision or multimedia problem. • Survey papers regarding the topic of learning with shared information.  Authors who are unsure whether their planned submission is in scope may contact the guest editors prior to the submission deadline with an abstract, in order to receive feedback.

IEEE transactions on pattern analysis and machine intelligence

Deep learning has been transforming our ability to execute advanced inference tasks using computers. Here we introduce a physical mechanism to perform machine learning by demonstrating an all-optical diffractive deep neural network (D2NN) architecture that can implement various functions following the deep learning-based design of passive diffractive layers that work collectively. We created 3D-printed D2NNs that implement classification of images of handwritten digits and fashion products, as well as the function of an imaging lens at a terahertz spectrum. Our all-optical deep learning framework can perform, at the speed of light, various complex functions that computer-based neural networks can execute; will find applications in all-optical image analysis, feature detection, and object classification; and will also enable new camera designs and optical components that perform distinctive tasks using D2NNs.

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All-optical machine learning using diffractive deep neural networks

This paper describes an efficient technique for out-of-core rendering and management of large textured terrain surfaces. The technique, called Batched Dynamic Adaptive Meshes (BDAM) , is based on a paired tree structure: a tiled quadtree for texture data and a pair of bintrees of small triangular patches for the geometry. These small patches are TINs and are constructed and optimized off-line with high quality simplification and tristripping algorithms. Hierarchical view frustum culling and view-dependent texture and geometry refinement is performed at each frame through a stateless traversal algorithm. Thanks to the batched CPU/GPU communication model, the proposed technique is not processor intensive and fully harnesses the power of current graphics hardware. Both preprocessing and rendering exploit out-of-core techniques to be fully scalable and to manage large terrain datasets.

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BDAM — Batched Dynamic Adaptive Meshes for High Performance Terrain Visualization

We describe an efficient technique for out-of-core management and interactive rendering of planet sized textured terrain surfaces. The technique, called planet-sized batched dynamic adaptive meshes (P-BDAM), extends the BDAM approach by using as basic primitive a general triangulation of points on a displaced triangle. The proposed framework introduces several advances with respect to the state of the art: thanks to a batched host-to-graphics communication model, we outperform current adaptive tessellation solutions in terms of rendering speed; we guarantee overall geometric continuity, exploiting programmable graphics hardware to cope with the accuracy issues introduced by single precision floating points; we exploit a compressed out of core representation and speculative prefetching for hiding disk latency during rendering of out-of-core data; we efficiently construct high quality simplified representations with a novel distributed out of core simplification algorithm working on a standard PC network.

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Planet-sized batched dynamic adaptive meshes (P-BDAM)

We describe an efficient technique for out-of-core construction and accurate view-dependent visualization of very large surface models. The method uses a regular conformal hierarchy of tetrahedra to spatially partition the model. Each tetrahedral cell contains a precomputed simplified version of the original model, represented using cache coherent indexed strips for fast rendering. The representation is constructed during a fine-to-coarse simplification of the surface contained in diamonds (sets of tetrahedral cells sharing their longest edge). The construction preprocess operates out-of-core and parallelizes nicely. Appropriate boundary constraints are introduced in the simplification to ensure that all conforming selective subdivisions of the tetrahedron hierarchy lead to correctly matching surface patches. For each frame at runtime, the hierarchy is traversed coarse-to-fine to select diamonds of the appropriate resolution given the view parameters. The resulting system can interatively render high quality views of out-of-core models of hundreds of millions of triangles at over 40Hz (or 70M triangles/s) on current commodity graphics platforms.

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Adaptive tetrapuzzles: efficient out-of-core construction and visualization of gigantic multiresolution polygonal models

We describe a compressed multiresolution representation for supporting interactive rendering of very large planar and spherical terrain surfaces. The technique, called Compressed Batched Dynamic Adaptive Meshes (C-BDAM), is an extension of the BDAM and P-BDAM chunked level-of-detail hierarchy. In the C-BDAM approach, all patches share the same regular triangulation connectivity and incrementally encode their vertex attributes using a quantized representation of the difference with respect to values predicted from the coarser level. The structure provides a number of benefits: simplicity of data structures, overall geometric continuity for planar and spherical domains, support for variable resolution input data, management of multiple vertex attributes, efficient compression and fast construction times, ability to support maximum-error metrics, real-time decompression and shaded rendering with configurable variable level-of-detail extraction, and runtime detail synthesis. The efficiency of the approach and the achieved compression rates are demonstrated on a number of test cases, including the interactive visualization of a 29 gigasample reconstruction of the whole planet Earth created from high resolution SRTM data.

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Fabio Ganovelli

Papers

MeshLab: an Open-Source Mesh Processing Tool

BDAM — Batched Dynamic Adaptive Meshes for High Performance Terrain Visualization

Planet-sized batched dynamic adaptive meshes (P-BDAM)

Adaptive tetrapuzzles: efficient out-of-core construction and visualization of gigantic multiresolution polygonal models

C-BDAM - Compressed Batched Dynamic Adaptive Meshes for Terrain Rendering