Visual perception strategies for 3D reconstruction

A sketch-based system for modeling 3D objects: Applications to taxonomy

Zootaxa ◽

10.11646/zootaxa.5039.4.5 ◽

2021 ◽

Vol 5039 (4) ◽

pp. 537-550

Author(s):

SAULO RAMOS ◽

CHARLES MORPHY D. SANTOS ◽

MARIO COSTA SOUSA ◽

JOÃO PAULO GOIS

Keyword(s):

Visual Perception ◽

3D Reconstruction ◽

Visual Effects ◽

Single View ◽

3D Objects ◽

Solid Objects ◽

The Subject ◽

Species Descriptions

We present a sketch-based system for modeling 3D objects with multiple contours as overlaid structures, allowing users to infer perceivable symmetries and occluded parts of the model prior to its automatic 3D reconstruction. Many approaches for sketch-based interfaces and modeling focus on the final drawing and 3D reconstruction of solid objects, exploring, as inputs, contours; however, when the subject consists of multiple drawings as overlaid structures, as usual in species descriptions, these approaches have to roughly infer or discard occluded parts. Unlike previous sketch-based techniques, we explore a set of 2D visual effects to enhance the visual perception of users while sketching multiple overlaid objects in single-view. The proposed system was applied to general simple zoological and botanical sketches as well as to published descriptions of species of Diptera, demonstrating its usefulness for taxonomy.

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Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100181026 ◽

1990 ◽

Vol 48 (1) ◽

pp. 454-455

Author(s):

Jose-Maria Carazo ◽

I. Benavides ◽

S. Marco ◽

J.L. Carrascosa ◽

E.L. Zapata

Keyword(s):

3D Reconstruction ◽

3D Structure ◽

Three Dimensional ◽

Software Tools ◽

Mapping Method ◽

Computer Architectures ◽

Parallel Computer ◽

Reconstruction Process ◽

Computing Power ◽

Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

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Structural Studies on the Eukaryotic Ribosome

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100180033 ◽

1990 ◽

Vol 48 (1) ◽

pp. 256-257

Author(s):

Adriana Verschoor ◽

Ronald Milligan ◽

Suman Srivastava ◽

Joachim Frank

Keyword(s):

Chick Embryo ◽

3D Reconstruction ◽

Single Particle ◽

Mass Density ◽

Particle Surface ◽

Uranyl Acetate ◽

Electron Microscopic ◽

Eukaryotic Ribosome ◽

Negative Stain ◽

Reconstruction Methods

We have studied the eukaryotic ribosome from two vertebrate species (rabbit reticulocyte and chick embryo ribosomes) in several different electron microscopic preparations (Fig. 1a-d), and we have applied image processing methods to two of the types of images. Reticulocyte ribosomes were examined in both negative stain (0.5% uranyl acetate, in a double-carbon preparation) and frozen hydrated preparation as single-particle specimens. In addition, chick embryo ribosomes in tetrameric and crystalline assemblies in frozen hydrated preparation have been examined. 2D averaging, multivariate statistical analysis, and classification methods have been applied to the negatively stained single-particle micrographs and the frozen hydrated tetramer micrographs to obtain statistically well defined projection images of the ribosome (Fig. 2a,c). 3D reconstruction methods, the random conical reconstruction scheme and weighted back projection, were applied to the negative-stain data, and several closely related reconstructions were obtained. The principal 3D reconstruction (Fig. 2b), which has a resolution of 3.7 nm according to the differential phase residual criterion, can be compared to the images of individual ribosomes in a 2D tetramer average (Fig. 2c) at a similar resolution, and a good agreement of the general morphology and of many of the characteristic features is seen.Both data sets show the ribosome in roughly the same ’view’ or orientation, with respect to the adsorptive surface in the electron microscopic preparation, as judged by the agreement in both the projected form and the distribution of characteristic density features. The negative-stain reconstruction reveals details of the ribosome morphology; the 2D frozen-hydrated average provides projection information on the native mass-density distribution within the structure. The 40S subunit appears to have an elongate core of higher density, while the 60S subunit shows a more complex pattern of dense features, comprising a rather globular core, locally extending close to the particle surface.

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