Software resources for the Caltech community In addition to microscopes, the BIF also provides software resources for processing and analyzing imaging data. This is consists of commercial programs running on powerful Windows or Linux workstations. We also provide off-line versions of the Zeiss Zen Black and Blue software packages controlling our Zeiss confocal and light sheet microscopes for basic image processing of Zeiss files.

Imaris software from Bitplane, an Oxford Instruments Company The BIF has two Windows computer workstations running the Imaris 3D/4D image processing and visualization software from Bitplane: (1) Puget systems workstation running Windows 10, (2) Dell Workstation running Windows 7. Imaris is Bitplane’s core scientific software module that delivers all the necessary functionality for data management, visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size. We are one of their North American Advanced Imaging Centers, so users are invited to present challenging problems to Bitplane through us.

Huygens software from Scientific Volume Imaging (SVI) The BIF has a Linux computer workstation running the Huygens software from Scientific Volume Imaging (SVI), a powerful program for image deconvolution that benefits from GPU acceleration. Functionalities include deconvolution, restoration, Fusion of SPIM data, interactive analysis, and volume visualization of 2D-3D multi-channel and time series images from fluorescence microscopes such as wide-field, confocal, multi-photon, spinning disk, STED and SPIM.

Arivis Vision 4D software from Arivis AG This software was purchased and installed on one of the Windows 7 computer workstations that came with our Zeiss Z.1 light sheet fluorescence microscope. Arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints

Other Software FIJI: Fiji is just imageJ, open source software for Image processing.

MATLAB software from Mathworks. The MATLAB platform is optimized for solving engineering and scientific problems. The matrix-based MATLAB language is the world’s most natural way to express computational mathematics. Built-in graphics make it easy to visualize and gain insights from data. A vast library of prebuilt toolboxes lets you get started right away with algorithms essential to your domain. MATLAB scripts can be run in Imaris.