Microscope to AMIRA

A series of optical sections is collected using laser scanning confocal microscopy.  The data  is then passed to AMIRA where it is rendered in 3D.  The data is segmented using a variety of thresholding tools.  The segmented data is transformed into an iso-surface (mesh) which can be exported as a .obj file.

AMIRA to Instant Meshes

The iso-surface mesh created by AMIRA is generally far too large to be used  by animation and games engine software. Therefore, the mesh needs to be reduced to fewer geometric faces.  Where possible the mesh should also be converted from triangles to quads.  This can be done in the animation packages.  However, Instant Meshes is an excellent application for mesh reduction and quad transformation.


This professional animation package from Autodesk is one of the most powerful systems.  Once a mesh is imported it can be transformed in an infitinte number of ways.  The mesh can be animated, textured and lit.  Additional components (characters) can be added to the animation.  Various physics engines and particle flows can be used to enhance the animations.


Maya files can be exported directly to UNITY.  This games engine provides interactivity , meaning that players (students) can interact and manipulate the objects in a scene.  Unity scenes can be rendered out as games that will run on virtually all platforms (PC, tablet, mobile etc.).  A range of opperating systems are also supported.

Virtual Reality

UNITY and STEAM VR work extremely well together.  This enables quick visualisation of UNITY scenes in 3D.  This completes the microscope to VR workflow.

3D Printing

Having created 3D-mesh representations of biological samples and proteins, we can then send them to a 3D printer.  Here we see the oestrogen receptor printed as a backbone structure

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