There are currently four avenues for image analysis for Microscopy users.

For confocal images, LSM510 confocal microscope computer has the Zen software by Zeiss which is suited to such measures as intensity profiling, intensity integration, area calculations, co-localization, image filtering, linear measurements and changes in the LUT profile. At this point there is no charge for offline use of the Zen software, however such time to use the LSM510 computer must be booked in advance using Schedulebook. The Zen software comes in a free or “Light” version for the PC for basic image organization, projection and formatting. Download instructions for this software may be obtained by contacting Microscopy staff. On account of the heavy use of the confocal microscope, users are encouraged instead to use one of three other alternative image analysis options described below.

A second avenue for image analysis is the Metamorph offline image analysis software package. This is a comprehensive image analysis package suited for 2D image analysis for which specialized training will be provided on an application-specific basis. The software includes application modules which include morphology filters, binary and arithmetic operations, motion analysis particle tracking, colocalization, correlation measurements, 4D viewer/3D measurements, angiogenesis, neurite outgrowth, count nuclei, cell scoring, multi-wavelength cell scoring and cell cycle. This software is presently located on the Axio Observer A1 imaging workstation on the 5th floor of CNY 149.

A third resource is Imaris software from Bitplane. This advanced 2D, 3D and 4D image analysis software will be added to as the needs of Microscopy grows. The present package consists of the core confocal image analysis software along with Measurement Pro, Imaris Track, Imaris Coloc, and Imaris InPress. Imaris is well suited to more advanced segmentation for identification of individual cells in tissue. Imaris Measurement Pro enables the calculation and display of many statistical measurements from both voxel data and segmented objects. It permits interactive 3D distance and line intensity measurements, and a means to construct 3D surface objects from 2D drawn contours. ImarisTrack permits automatic and manual tracking of the movement over time of individually labeled particles, including cells, molecules, nucleic acids, lipids and many others that can be segmented in Imaris. Tracking is possible on both surface objects and spot objects created with Imaris. ImarisColoc enables one to quantify and document co-distribution or colocalization of multiply-stained biological components. Imaris InPress provides a tool to create figures of all Imaris views including titles, captions, labels, and other annotations for presentations or publications, and can do so in 2D, 3D or 4D. Such files can also be exported as html files. The Imaris PC workstation is located on the 6th floor of CNY 149.

A fourth resource is the freely available ImageJ software, which is a Java-based image processing program with a significant number of public domain plug-ins for different imaging applications, and which is available for use on PC (Windows), Mac, and Linux-based operating systems. Images from the MIRAX MIDI must be converted to individual images from the full stitched image for export to be analyzed on Metamorph or ImageJ. Consultation on the use of ImageJ is also provided for basic image analysis.

At the present time users are not charged for image analysis training or consultation, although depending on the amount of time spent with a user, this policy may be subject to change. Any use of image analysis workstations must be done with prior consultation and training by Microscopy staff, and users will then be provided with Schedulebook access so they can then reserve time online.