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Digital Confocal Microscopy Suite (DCMS) is now available for free!

For more information click here.

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Digital Confocal Microscopy Suite (DCMS)


DCMS is a 3D Confocal Microscope simulator, with the goal of performing several types of virtual experiments on diffusive fluorescent markers in arbitrary cell geometries. This software contains a comprehensive list of relevant scanning confocal parameters that allow the user to generate xyt image stacks of FRAP experiments along with fluorescence recovery curves. It allows the user to explore how cell shape, confocal imaging, and confocal photobleaching all can influence fluorescence recovery curves for diffusing particles. To download click here.

DCMS-screenshot


Why DCMS?


In vivo microscopy experiments are often difficult, expensive, and have many uncontrolled factors. This makes them non-ideal for testing potential ideas, or for making controlled comparison experiments. DCMS provides an easy, inexpensive method for trying experiments under controlled conditions.

DCMS is for researchers

DCMS allows experimentalists to test the feasibility of an experiment before performing it, or to set up a controlled comparison experiment, to determine if diffusive behavior can replicate what is seen experimentally.

DCMS is for educators

DCMS allows educators to demonstrate how various properties of a microscope affect the resulting images. Using a virtual platform, parameters can be changed in isolation, and physical limits can be broken, in order to show students how microscopy systems work.

DCMS is for students

DCMS allows students to test out their ideas, and to try fluorescence microscopy experiments for free on their own computer.
This allows them to experiment with potential ideas, without having to gain access to contested physical instruments.

Credits



This software was developed in collaboration between two groups at Worcester Polytechnic Institute lead by


Contributing graduate students:

  • James Kingsley (Physics)
  • Iman Mousavi (Physics)
  • Jeffrey Bibeau (Biology)

Contributing undergraduate students:

  • Cem Unsal (Physics, Computer Science)

This software is based upon work supported by the National Science Foundation under Grant No. CBET 1309933, and NSF-MCB 1253444.

References

  • A GPU Accelerated Virtual Scanning Confocal Microscope, J. Kingsley, Z. Chen, J. Bibeau, L. Vidali, X. Huang, E. Tüzel, IEEE High Performance Extreme Computing Conference (HPEC), September 2014.


Get DCMS


This software is currently in beta state. Files for download:

Latest version of DCMS
DCMS documentation
Samples used in the documentation
Additional sample meshes and configuration files

System Requirements

Minimum Requirements
• Java 1.7 or higher*
• Graphics card supporting OpenGL ES 2.1 or higher

Additional Recommended Requirements
64-bit JRE
• Dedicated GPU with OpenCL 1.2 support (for GPU accelerated simulation)
• Windows** (7) , Mac OS X (10.9 or newer), or Linux (Ubuntu 10.04, RHEL 5.4 or newer)

Due to the computational demands of our software, we recommend a modern dedicated GPU. Less powerful machines, such as laptops can run the software, but need to be used with caution for large numbers of particles. Please refer to the documentation for more information on performance.

* In 64-bit Windows machines, make sure you are running 64-bit Java Runtime Environment (JRE). Some machines may not have this installed by default, and instead have a 32-bit or mixed mode version of the Java HotSpot Client. You can download the correct version
here.

** Due to driver issues, the software may not run with GPU acceleration on some Windows 10 machines. In addition, OpenGL may not display the mesh when connecting to a machine via Remote Desktop.