OMC News

July 2011:

New BSL2 microscopy facility at MRB.

Live Cell Confocal and TIRF Microscope.

OMC-TIRF

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Software:

Digital image analysis is an essential component of modern Optical Microscopy Imaging, the core is very well equipped in terms of image analysis software. The personnel of the core can provide technical support to the users in the form of training and assistance with the design and troubleshooting of image analysis strategies. Many of the software packages have the ability to write custom applications via scripting language. The core staff can assist users by writing custom applications as part of collaborative projects.

Metamorph (Molecular Devices):

The core has at least 7 seats for offline image analysis copies of this program, 3 at the MRB and 4 at the GNL. This software is the main tool used by the core for image processing and analysis of 2D and 3D image data sets as well as time series and spectral images. Metamorph has a wide range of built in functions ranging from  the most basic operations to more sophisticated applications such as automated morphometry analysis, automated cell counting, object tracking, movies and FRET analysis. In addition advanced custom applications can be developed using the journal scripting functions, including batch processing of large numbers of images. (software list)

Nikon Elements (Nikon Instruments):

This software is used to analyze our live cell and multidimensional experiments. Complex 2D and 3D time series with multiple locations can be easily visualized. This program has a great collection of features for advanced image processing and analysis with a friendly user interface. (software list)

Image J (open source):

This free software is very popular as it can be downloaded and installed in any personal computer. The core staff can provide basic technical support with the use of this software. Metamorph however is a more powerful tool and is the preferred option. (software list)

Imaris Suite (Bitplane):

This is one of the best software packages available for processing and analysis of 3D and 4D images. The core has two licenses for this program, one at the MRB and one at the GNL. This software can easily generate astonishing volume renderings of 3D data sets as well as dramatic animations of 3D rotations, however this software also provides a collection of advanced tools for image quantifications and analysis such as 3D colocalization analysis, 3D object tracking, Filament tracing,  3D image segmentation and automatic object measurements. (software list)

Huygens Essential (SVI):

This a true 3D deconvolution package for image restoration. Based on measured point spread function constrained iterative algorithms. 3D deconvolution uses a mathematical algorithm to correct the autofocus blur of 3D image datasets based on the known properties of the imaging system. The result are images in which the contrast and resolution are greatly enhanced. It can be used to improve confocal images or to generate 3D image reconstructions based on z-series of wide field images. The core has one license running in the MRB. (software list)

Volocity (Perkin Elmer):

Volocity 3D image analysis and Volocity image restoration (3D deconvolution). This is a 3D image analysis and rendering package of functionality similar to Imaris, the 3D image deconvolution module is similar to the functionality provided by Huygens. Several license seats are available to OMC users in the GNL image analysis core. (software list)

Acapella (Perkin Elmer):

High content image base citometry analysis. Acapella is used for cell based automated image analysis of large volumes of data, this is the software that powers Perkin Elmer's high content  imaging platforms such as the Opera and Operetta systems. Acapella is accesible to OMC users at the GNL image analysis core. (software list)

Columbus Conductor (Perkin Elmer):

This is a multifunctional system that include software and hardware components designed to handle, organize and analyze large quantities of images. This system is intended to handle the images generated by the GNL Imaging Cores. It provides storage and database organization of image files from almost just any format available. Also, provides image visualization and manipulation features for quick access and examination of datasets as well as advanced tools for image analysis. The advanced tools include: Acapella high content citometry analysis, Volocity 3D image analysis and Volocity image restoration (3D deconvolution). Columbus Conductor is available for all users of the GNL imaging cores. (software list)