3D Analysis
Why 3D Cell Biology?
The full 3D information of a z-stack can be more accurate and conclusive than a 2D (projected) image. Also, in single-slice time-lapse microscopy (2D + Time), the shape of an object can change considerably over time, and the full spatio-temporal evolution should be described in a 3D X-Y-T coordinate (bacterial shape, actin dynamics, ...).
What to use?
Recent advances in computer hardware and software have facilitated 3D visualization dramatically and made it a common free tool. Interactive 3D visualization/analysis in a PDF file or with a web browser has been around for a few years. We use primarily the two programs of ImageJ and UCSF Chimera for processing raw 3D data and extraction of 3D surfaces out of 3D volume data.
These programs can do fast and also high-quality 3D visualization (with more accurate models of illumination). Furthermore, these programs can export data in a variety of standard 3D (surface) formats required for 3D printers, 3D PDF, and 3D visualization with web browsers (Web 3D).
We also use special tools such as X3DOM and Three.js to bypass most of the technical and programming details associated with Web 3D.
How to start?
We offer both courses and services (in 3D analysis) to cell biologists. 3D images are aesthetically appealing, yet non-trivial to interpret and potentially misleading. Our goal is to extract more reliable information out of microscopy datasets to obtain more accurate and conclusive biological results.
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