BIOQUANT Topographer Add-on

BIOQUANT Life Science with the BIOQUANT Topographer add-on enables the following 2D Mapping and 3D Modeling features.

Atlas Modeler Workspace

Display Tools

Show models as smooth surfaces, polygon meshes, or points. 

Small Cells as Points or Spheres

Display neuron bodies or other cells as spheres or points when modelled. 

Export to PLY

Export edited model to PLY format for easy 3rd party rendering. 

Hide Portion of Contour 

Allows the user to designate a portion of the model's contour as "not rendered" so that inner structures are featured. 

Lighting, Color, Opacity Parameters 

Define Global Ambient Light, Surround Lighting, Color, and Opacity per Structure. 

Movement Tools 

Rotate with the mouse, scale, and pan your 3D model.

Atlas Shop and Viewer

Reconstruction Quantification

Measures, in microns, count per volume, area, count per area, and distance. 
Serial Section Alignment

Uses dual point alignment to automatically align serial sections. 

SVG Output

Export BMP files with SVG overlay for dynamic resizing of tracings without distortion. 

Object Selection and Manipulation Tools

Include select by color, select with polygon, select with rectangle, and select from data list. Rotate, resize, change Z height, change color, Z sort, change resolution, and open/close polygon. 

Object Editing Tools

Include split and join objects, straighten edge, redefine edge, delete objects.

Sample Application: Characterization of the Central Cell Groups Regulating the Kidney in the Rat

Dr. Mark Weiss, Jianhua Huang, & Julie Hix
Department of Anatomy and Physiology
Kansas State University


Retrograde, transneuronal viral tracing technique combined with neurotransmitter immunohistochemistry was used to identify the type of neurons in spinal cord and brain that project to the rat's kidney. Pseudorabies virus (PRV) injections were made into the left kidney. After an incubation of 4 days postinjection, PRV-infected neurons were located immunocytochemically in the ipsilateral intermediolateral (IML) cell column of the spinal cord and several brainstem cell groups: medullary raphe nuclei, ventromedial medulla (VMM), rostral ventrolateral medulla (RVLM), A5 cell group and the hypothalamic paraventricular nucleus (PVH). The study has confirmed the presence of segmental patterns and has also provided first evidence for intrasegmental patterns of renal sympathetic preganglionic neurons (SPN).

This reconstruction contains 93 sections. The white shell is the White Matter, and grey the Grey Matter. Green represents the central canal and the yellow dots indicate viral bodies.

BIOQUANT Life Science Topographer Add-On

Opaque White Matter

Opaque White Matter

Wire frame of the Gray Matter with the White Matter removed

Wire frame of the Gray Matter with the White Matter removed

The central canal with White and Grey Matter removed

The central canal with White and Grey Matter removed

The Topographer Add-On creates 3D Models like this one. The data required to build these models is stored automatically during the measurement of morphometric parameters such as area, length, shape, perimeter, and number. There are three workspaces that make up the Topographer Plug-in: Atlas Viewer, the Atlas Shop, and the Atlas Modeler. In the Atlas Viewer, using a quick preview of the model, structures and cell groups are selected and color coded for the final model. In the Atlas Shop, mistakes in the model data are corrected. This can include trasposing sections that were mounted upside-down, rotating sections into alignment with each other, or changing the Z height of a section. The Atlas Modeler then takes the data and color settings and makes the final model. In the Atlas Modeler, the model can be rotated and zoomed, structures can be made translucent, and movies can be recorded of the the rotating reconstruction.

Citation and Related Publications

Huang J, Weiss ML.
Characterization of the Central Cell Groups Regulating the Kidney in the Rat
Brain Res. 1999 Oct 16;845(1):77-91.
MID: 10529446; UI: 20002181 Weiss ML, Chowdhury SI.
The renal afferent pathways in the rat: a pseudorabies virus study
Brain Res. 1998 Nov 23;812(1-2):227-41.
PMID: 9813344; UI: 99032945