iVision‐Mac™: Imaging and Automation for Science

iVision‐Mac 4.0.9 under OS X 10.5 “Leopard”

Main Tools

The Main Tools provide easy access to the most common image operations in Life Science imaging: creation of new images; opening and saving image files; normalization; pseudocoloring; and creation of new color images from multiple images representing data in multiple colors, representing fluorescent signals and brightfield background, or representing fluorescent labels that may be colocalized.

Image Tools

The Image Tools allow one to scroll across an image that does not fit within its window, to adjust the magnification of the pixels in the image window, to measure lengths or angles, to rotate the color tables on indexed color images, and to set registration marks used for image registration.

Function Key Palette

Operations not available on other toolbars can be bound to keyboard function keys and listed in the Function Key Palette, providing easy access to facilities used every day. iVision‐Mac binds function keys to individual functions that it provides or to scripts recorded within iVision‐Mac. This provides easy access to the operations that one uses frequently.

Here is an example of a typical function key palette. The function keys run scripts for display of the camera's view of the specimen, capture of images using fluorescence microscopy or brightfield microscopy, enhancement of the image, cropping unneeded data, and saving the results to disk.

Device Toolbar

iVision‐Mac provides a point‐and‐click interface for control of imaging‐related hardware. The position of devices such as filter wheels, X-Y stages and Z-axis focus drives can be displayed and may be altered.

Region of Interest Tools

The Region of Interest tools allow the selection of the area within an image for processing, filtering or quantifying. The defined region of interest may be a rectangle, an oval, a polygon, a shape drawn freehand or a shape defined by the segments as defined by automated segmentation or by manual use of iVision‐Mac Segment Tools.

Segment Tools

The Segment tools define areas to be measured. iVision‐Mac allows the creation of as many as nine segments in each image window, and can measure the segments individually.

These tools define segments as rectangles, ovals, polygons, lines, or areas defined with a paintbrush. A Cut tool allows the separation of objects that are clumped together, allowing iVision‐Mac to count the objects as individuals.

Drawing Tools

The drawing tools add annotations, highlighting, and outlines to an image. Drawings exist within the drawing overlay, which is a layer independent of
the image data. Drawings do not affect the image data.

These tools define drawing objects as rectangles, ovals, polygons, lines, shapes drawn freehand, or text annotations. Each drawing on the drawing overlay is an individual object, and may be treated without affecting other drawing objects present.

3D Tools

The 3D Tools provide easy access to common operations on sequences of two‐dimensional data sets that are loaded into image windows:

Viewing a multi‐frame stack as a volume in 3‐D space, rotating it in any direction by grabbing it with the mouse;

Viewing one of the frames of the stack as an image;

Constructing a single‐image in-focus view of a stack of frames that were acquired at different positions along the Z‐axis;

Synthesis of a two‐dimensional image of the data in the entire stack;

Creation of a sequence of 3‐D projections through the data set, representing views from positions at regular intervals around the stack’s X‐axis or its Y‐axis;

Creation of a QuickTime™ movie from the frames in an an image window;

No Neighbor Deconvolution (“single‐image deconvolution”) and Nearest Neighbor Deconvolution (“three‐image deconvolution”);

No Neighbor deconvolution that is based on a theoretical point spread function;

Deconvolution, each resulting frame using information from data set planes as dictated by a theoretical point spread function or one sampled from the microscope that acquired the original data.