CISMM Microscope Simulator 1.2.1 Instructions

Introduction
The Microscope Simulator enables a scientist to simulate what a given 3D scene should look like under a fluorescence microscope or an atomic force microscope (AFM). 3D scenes can be constructed from primitives or imported files in VTK, OBJ, or PLY format. Once a 3D model has been created, you can provide the point spread function (PSF) for a given fluorescence microscope and view simulated fluorescence images. In addition, you can specify the parameters of a simple AFM tip model and quicky generate a simulated AFM surface scan.

The fluorescence image simulation algorithm takes advantage of recent advances in graphics hardware for accelerating the simulation. The algorithm for generating a simulated AFM surface uses graphics hardware-accelerated grayscale image dilation to achieve interactive update rates.

The simulator also includes an optimization algorithm to fit model objects to fluorescence microscope images. Given a hypothesized specimen model, a 3D image from a fluorescence microscope, and a PSF from the microscope, the optimization algorithm finds the model parameters that best explain the 3D image.

The application relies on the following software libraries:

• Java Runtime Environment
• VTK
• ImageJ
• TetGen
• Xalan-Java

See the Quick Start Guide to AFM Simulation for screen shots and instructions.

Acknowledgements

The Center for Integrated Systems for Microscopy and Manipulation is a National Institute of Biomedical Imaging and Bioengineering Resource. Sponsor award number P41-EB002025-21A1.

Release Notes for Version 1.2.1

Changes from previous release

• PLY files may now be imported.
• Added x-y-z reference axes widget to the rendering window that may be turned on or off.
• Added volume labeling capability for fluorescence microscope simulation. Geometry imported from OBJ, PLY, or VTK files must form a closed volume for volume labeling to work, i.e., the geometry must be water-tight.
• The Flexible Tube model now features smooth curves.
• Fixed some problems that would occasionally make the program crash.

Known issues in release 1.2.1

• Same as v. 1.1.0.

Release Notes for Version 1.2.0

Changes from previous release

• Added exhaustive-search fluorescence model optimization that minimizes the mean squared error between simulated images and experimental images.
• Fluorescence simulation is now approximately pixel-accurate among all simulator types.
• The object representing the focal plane in the model object window will now display the fluorescence image at that focal plane if the fluorescence renderer window is open. If that window is not open, a semi-opaque plane is shown instead.

Known issues in release 1.2.0

• Same as v. 1.1.0.

Release Notes for Version 1.1.0

Changes from previous release

• Extensive GUI interface changes. Almost all windows have been reduced to a single window with controls on either side of the main model object window.
• Added visualization option for comparing simulated and experimental AFM scans.
• Added visualization modes for comparing simulated and experimental fluorescence stacks.
• Fixed some off-by-one pixel errors in fluorescence simulators.
• Added UNCA file export.
• Added OBJ file export.
• Improved geometric quality of simulated AFM scan as it appears in the model object window.

Known issues in release 1.1.0

• On some systems, if the resolution in the AFM simulator settings is lower than 115 pixels, there will be errors in the resulting scan.
• AFM comparison visualization can take excessive time to compute if the resolution of the simulated scan or resolution of the imported experimental AFM scan is too high (greater than 100 samples on a side).
• When changing among fluorescence simulator types, the program may crash.

Release Notes for Version 1.0.8

Changes from previous release

• Added 32-bit hardware-accelerated fluorescence microscopy simulator that is faster than the 64-bit software simulator and more accurate than the 16-bit hardware simulator.
• Changed AFM simulator behavior so that objects are scanned if and only if they are designated as scannable. This lets you make selected model objects hidden, but the simulator still dilates them.

Known issues in release 1.0.8

• The program may crash when switching from the 32-bit fluorescence simulator to another simulator.

Release Notes for Version 1.0.7

Changes from previous release

• Added accurate (but slow) software fluorescence microscopy simulator for computers lacking graphics hardware with floating-point blending.
• Added controls for rescaling image values to those of the display.
• Fixed some bugs in the AFM simulator, mostly related to non-square simulation regions.

Known issues in release 1.0.7

• After changing the size of the simulated region, the current AFM scan may appear corrupted. To work around this, update "Scan Resolution" settings in the AFM control panel, and the AFM will be recomputed.

Release Notes for Version 1.0.6

Changes from previous release

• Added ability to import sequences of 16-bit tiff images. Isosurfaces from these stacks can be used to help position model objects.
• The simulated region can now be set to the boundaries of the model object.

Known issues in release 1.0.6

• See "Known issues in release 1.0.5" below

Release Notes for Version 1.0.5

Changes from previous release

• Added multi-channel fluorescence rendering. Model objects can now be rendered to red, green, or blue channels, or all three.

Known issues in release 1.0.5

• See "Known issues in release 1.0.4" below

Release Notes for Version 1.0.4

Changes from previous release

• New plugin interface for model objects.
• Numerous user-interface bug fixes.
• Re-enabled fluorescence microscope simulation feature.
• Added improved fluorophore point sampling strategy.
• Implemented a 16-bit floating-point renderer for fluorescence rendering.

Known issues in release 1.0.4

• Program may hang when a new object is created while the fluorescence window is open. Make sure to close the window before adding a model object.
• AFM scans may have unusual artifacts.
• The PSF bounding box in the model object window may not update immediately.
• Program may crash occassionally when adding a model object.