HyperStackView

HyperStackView is an application that allows interactive rendering of 3-dimensional projection of voxel bitmap or time series of such bitmaps. It uses OpenGL API to process data. Real-time rendering of animations is also possible (tested with 1024×1024 output image, and 1000 z-samples).

The application allows for simultaneous preview of one image in the maximum-intensity projection and of the other one that contains (possibly labeled) objects to be rendered with shading and diffuse lighting.

The former is used for maximum- or average-intensity projection with adjustable brightness, contrast and gamma. It can contain floating-point or integer values. The latter can contain boolean values, where true denotes object presence and false background, or integer values where zeroes represent background whereas positive values represent the object. If an image with integer values is used, the preview can be limited to voxels with user-specified value (use File→Object Selector, Ctrl-Shift-O).

The view can be rotated and zoomed using the mouse and keyboard controls. When time series are being viewed, keyboard shortcuts or Next/Prev buttons (on a five-button mouse) can be used to change the currently viewed frame.

It is possible to render animations of rotating 3D bitmap or to play time-series in real time on consumer hardware.

Rendering quality (and hence its speed) can be adjusted using two controls: the Z-axis sample count control allows to decrease sample count on the axis perpendicular to the projection plane, the Intermediate buffer resolution menu can be used to decrease resolution of the preview.

Overview of rendering pipeline

This package has been developed within in the frame of my internship in the Institute of Information Theory and Automation (ÚTIA), under the supervision of Dr. Jan Schier.

The internship has been supported by the “Open Science” project (linked page in Czech) of the Academy of Sciences of the Czech Republic, which provides support for the scientific internships of the Czech secondary-school students.