BioVis3D is a software application for three-dimensional visualization and analysis, specifically designed for biologists who work with serial sections.

Typically, a BioVis3D user obtains a set of digital images of serial sections of the object to be studied using any appropriate acquisition devise such as optical or electronic microscopes and magnifying glasses. For example, it has been applied to histological sections of several kinds of cells and serial sections of insects. BioVis3D aligns images spatially and detect contours of the objects of interest with a simple semi-automatic procedure. From this information, BioVis3D builds three-dimensional models that can be visualized, sectioned or made semitransparent and moved to appreciate all the morphological details. It is also possible to create clouds of points in the space to represent punctual objects whose shapes are not relevant.


All three-dimensional scenes are exportable to standard formats that can be included as pictures or videos in publications, congress presentations and web pages. BioVis3D is also capable of calculating volumes, areas, and distances.


When the acquisition device does not capture the full image of a section in one shot, it is necessary to take several overlapped pictures of the same slice. In this case, BioVis3d rebuilds the image of the section from that set of pictures. This process is performed using a set of tools to rotate and translate a single or several images that can be made semi-transparent to help with the aligning process. The images that comprise a section may be taken with different resolutions. BioVis3d handles multi-resolution images and shows a consistent view of the full section to the end user.

Contour Detection
The objects of interest can be detected with a simple semi-automatic procedure. The object is roughly delimited by the user and BioVis3D detects the exact contour applying a refinement algorithm. The resulting contour can always be edited by the user if the final result must be adjusted. Both the automatic detection and the manual contour edition tools work with any zoom factor to adjust to the appropriate level of detail.






Punctual Objects
When the morphology of an object is not relevant but its spatial localization is important, it can be marked as a sphere with a certain diameter and color. This way, the spatial distribution of several objects can be appreciated using different colors to categorize them.


Slices Alignment
In general, due to the acquisition process, it may be necessary to correct small displacements among slices. BioVis3D offers the necessary tools to align sections spatially. Slices can be translated, rotated and made semi-transparent to help with this registration process. Object contours may remain visible during slice movement to make this task easier and, once again, all these tools can be used with an appropriate zoom factor. The images of the sequence may be taken with different resolutions. BioVis3D handles multi-resolution images and shows a consistent view of the slices to the end user.

Once the slices are aligned and the object contours are detected, the object of interest is ready to be built and visualized. These objects are presented in a 3D scene where objects can be shown and hidden individually or by categories. All morphological details can be appreciated moving objects spatially, making some objects semi-transparent, and cutting a whole scene. All scenes are exportable to standard formats that can be included as pictures or videos in publications, congress presentations and web pages.

Extracting Measures
Apart from morphological information, it is also possible to measure volumes and surface areas of three-dimensional objects, areas and perimeters in slices, and distances between any two points. All these measures are presented in the unit of measure selected by the user.








Find valuable information on the product and how it works at Documentation