iVision

Tools

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.



QuickTime is a trademark of Apple, Inc., Cupertino, CA.

iVision‐Mac is a trademark of BioVision Technologies, Inc, Exton, PA.

System Requirements

iVision‐Mac 4.5 for Macintosh OS X

• Operating System: Mac OS X version 10.5, 10.6, 10.7; OS X 10.8, 10.9, 10.10;
• Any Power Mac;
  • Supported camera with an IEEE 1394 (FireWire) interface, a Conventional PCI interface or a PCI Express (PCIe) interface;
• Any Intel-based Macintosh;
  • iVision‐Mac 4.5 is a ‘Universal’ application: it runs native Intel code on Intel-based Macs;
  • Devices must have Intel-native drivers;
  • Supported camera with an IEEE 1394 (FireWire) interface or a PCI Express (PCIe) interface;
• At least 512 MB RAM, 1 GB recommended;
• A CD-ROM drive or Internet access, for installation;
• A hard disk or solid state drive for the application and data;
• A display card and monitor set to ‘Millions of Colors’ (24-bit or greater) is best.

PCI boards, PCI Express boards, Power Mac G5s and Mac Pros

The Mac Pro (Late 2013)

This Mac has no expansion slots built in. Any interface board must be plugged into an external card cage that attaches to one of the Mac’s Thunderbolt ports, and the manufacturer must provide drivers tested for use when connected via Thunderbolt.

Apple sells a Thunderbolt to FireWire Adapter through which one can attach a FireWire-based (IEEE 1394) camera.

Contact BioVision regarding use of this computer for image acquisition.

Other models of Mac Pro

Mac Pros are equipped with ‘PCI Express’ expansion slots which are not compatible with ‘PCI’ interface boards. They include FireWire ports and can control FireWire-based (IEEE 1394) cameras and PCI Express interface cards;.

Hamamatsu Photonics offers PCI Express interface cards.

Contact BioVision Technologies regarding use of a Mac Pro computer for image acquisition.

The Power Mac G5 (Late 2005)

This Mac is equipped with ‘PCI Express’ expansion slots which are not compatible with ‘PCI’ interface boards. It includes FireWire ports and can control FireWire-based (IEEE 1394) cameras.

Hamamatsu Photonics offers PCI Express interface cards.

Contact BioVision Technologies regarding use of this computer for image acquisition.

Other models of Power Mac G5

These Macs require PCI cards that operate at 3.3 Volts. Most camera cards made prior to 2004 operate at 5 Volts and can not be plugged into a Power Mac G5. ‘Universal PCI’ cards that work with both 3.3 and 5 volt slots are available from the following manufacturers for use in these G5 Macs and older machines:

• Diagnostic Instruments
• Hamamatsu Photonics
• Photometrics

Further information

For more information on specific Apple computers visit Apple's website.
Contact us for help determining if your computer can run iVision-Mac

Software Features

Image Capture

Camera Control	Capture images using popular scientific grade CCD cameras.
Time Lapse	Capture images at specified time intervals. Measure and plot intensities over time.
Control Microscopes	Control motorized microscope stands and confocal imagers from popular manufacturers.
Control Devices	Control third-party devices: shutters, filter wheels, stages, light sources.
Z-Stacks	Capture through-focus series using Z-axis focus drives.
Multi-Fluorescence	Capture images from multiple wavelengths, overlay colors, and quantify intensities.

Image Processing

Batch File Processing	Create a list of files to process all at once. Indexed files provide automatic file naming and numbering.
Split Color Channels	Split any 24- or 48-bit color image into the separate components. View the separated images in their corresponding colors. Operate on the color component images as you would any grayscale image.
Merge Color Channels	Build a 24- or 48-bit color image out of three separate image files or sequences. Blend a fluorescent image or sequence with a DIC or other grayscale image.
Image Arithmetic	Combine and compare two images on a pixel-by-pixel basis. Perform background subtraction and image averaging to reduce noise. Mask certain frequencies in the Fourier domain.
Point Functions	Choose from an extensive list of built-in mathematical operations to apply to each pixel for analysis and enhancement.
Geometric Transforms	Arbitrary rotation, scale and translation with sub-pixel accuracy. Choose nearest neighbor or bilinear interpolation methods. Also transpose and flip images to view them differently.
Complex Arithmetic	Complex multiplication of Fourier spectrum real and imaginary components. Convert between real-imaginary and magnitude-phase.
FFT and Cosine Transformations	Forward and inverse 1-D and 2-D Fast Fourier transform with results in either real-imaginary or magnitude-phase. Forward and inverse cosine transform. All transformations are done with floating-point values for best accuracy.
Cut, Copy, Paste	Exchange image data with other programs through cut-and-paste.

Image Adjustment and Enhancement

Normalization	Enhance brightness and contrast, and apply a gamma curve to the displayed image data.
Background/Shading Correction	Easily perform flat-fielding to correct for lighting and sensor non-uniformities.
Enhance	Choose from built-in sharpening, smoothing, and median filters; pseudocolor tables, contrast enhancements and tools for geometric re-sizing.
Custom Filters	Define your own linear filter kernels.
Image Registration	Add registration marks to several images and let iVision‒Mac automatically rotate, scale and shift the images to bring them into alignment.
Image Size and Orientation	Rotate, Scale, Flip.
Transfer Attributes	Easily transfer information from one image to another, including the ROI and object definitions, color table, overlays and units.
Edit Color Table	Complete control over the color lookup table to pseudo-color images, equalize histograms and stretch the image contrast.

Image Analysis

Measurements	iVision‒Mac has a long list of measurements you can perform, for measuring density, shape, position and intensity moments. Limit measurements to specific regions and/or value ranges.
Quantify	Count objects and measure density, shape, position, and intensity moments for individual objects and for groups. Limit measurements to specific regions and/or value ranges. Automatically label measured items. Export results to spreadsheets.
Densitometry	Integrated and mean densities, RMS and standard deviation, max and min values.
Histogram	Plot image data using color histograms. Customizable or automatic binning.
Scripts and Macros	Record your own macros to automate your experiments. Run reproducible protocols as if they were a single command. Assign your most common scripts to keyboard function keys. Turn complex procedures into a sequence of labeled key-presses. There is no scripting language to learn; just point and click.
Image Ratios	Compute optical density, perform accurate ratios of images taken at different wavelengths.
Graphs and Plots	Our integrated graphing functions produce publication-quality graphs of your data and analysis results.
Calibrate Units	Calibrate measurements in units of your choice – microns, mm, cm, inches, etc.
Slices and Object Boundaries	Plot data values along a slice through the image, or list the (x,y) coordinates and data values at each point along the boundary of an object.
Interactive Measurement	Click the mouse to quickly measure lengths and angles. Automatically creates table of measurements and marks the measured lines and angles on the image within a nondestructive overlay.
Segmentation / Thresholding	Interactively select thresholds to separate objects from their background.
Segment Morphology	Erosion, dilation, opening and closing filter operations, with user-definable kernels.
Row/Column Averages	Plot the average value or the sum of all the pixels along a row or column of a rectangular or polygonal region.
Custom Extensions	Customize iVision‒Mac further by programming your own algorithms. The manual gives complete instructions and examples for including your own code and dialogs written using CodeWarrior for Macintosh and Microsoft Visual C++TM.
Set Pattern	Add or replace values to the region of interest: horizontal and vertical ramps, Gaussian and uniform random noise.

Data Display and Export

Image Annotation	Non-destructive overlays let you draw text and graphics on top of your images without altering the underlying data values. iVision‒Mac saves both the overlay and image data.
Opening and Saving Images	Read and write files in a number of formats: TIFF, Text, and our own iVision‒Mac format. iVision‒Mac also handles IPLab/Windows IPLs, PICTs, FITS, and EPR (*.raw and *.psf) formats. iVision‒Mac’s powerful Open As command imports foreign files in almost any file format.
Animation	Create a movie loop from your time lapse and 3D images. Play it in iVision‒Mac or export it as a QuickTime movie files.
View As Text	Switch easily between a text view and a standard image view of your data.
Export to Excel	Easily export results to Microsoft Excel spreadsheet software. Save your data as text and easily open it in Excel® or any other spreadsheet program.
Mosaic	Capture multiple images and place them together in one large montage.
Print	Print images as halftones to any PostScript printer or QuickDraw compatible printer. Make a PostScript file of your image data.

Supported Cameras

Manufacturers of Supported Cameras

• Cooke-PCO
• Diagnostic Instruments
• Hamamatsu
• JenOPTIK AG
• Photometrics
• QImaging
• Scion

Cooke-PCO	Interface	PowerPC	Intel
Sensicam	PCI	Yes	No
Sensicam EM	PCI	Yes	No
Sensicam QE	PCI	Yes	No
Diagnostic Instruments	Interface	PowerPC	Intel
SPOT Flex	IEEE 1394	Contact BioVision5	Contact BioVision5
SPOT Insight Firewire (Color and Monochrome)	IEEE 1394	Yes	Yes
SPOT Insight and Insight QE (Color and Monochrome)	PCI	Yes	No
SPOT Pursuit	PCI or PCI Express	Contact BioVision5	No
SPOT RT series	PCI	Yes	No
SPOT RT3 series	IEEE 1394	Yes	Yes
SPOT RT-KE series	PCI	Yes	No
SPOT RT-SE series	PCI	Yes	No
SPOT Xpress	PCI or PCI Express	Contact BioVision5	No
Hamamatsu	Interface	PowerPC	Intel
Orca-Flash 4.0 LT (C11440-42U)	USB 3.0	No	No
Orca-Flash 4.0 V2 (C11440-22CU)	USB 3.0 or Phoenix ‘CamLink’ PCI Express	No	No
Orca-Flash 4.0(C11440-22C)	Phoenix ‘CamLink’ PCI Express	No	No
Orca-Flash 2.8 (C11440-10C)	Phoenix ‘CamLink’ PCI Express	No	No
C8484-03G, C8484-05G, C8484-xxG01, C8484-xxG02	IEEE 13942	Yes2	Yes1, 2, 10
Orca-285G (C4742-95-12G04), (C4742-96-12G04)	IEEE 1394	Yes	Yes1, 10
Orca-AG (C4742-80-12AG)	IEEE 1394	Yes	Yes1, 10
Orca-ERG (C4742-95-12ERG)	IEEE 1394	Yes	Yes1, 10
Orca-NRG (C4742-95-12NRG)	IEEE 1394	Yes	Yes1, 10
Orca-II ERG (C4742-98-24ERG)	IEEE 1394	Yes	Yes1, 10
Orca-R2 (C10600-10B)	IEEE 1394b (800 Mbps)	Yes	Yes10
C9100-01, C9100-02, C9100-11, C9100-12	Phoenix ‘CamLink’ PCI or Phoenix ‘CamLink’ PCI Express	Yes	Yes6, 10
ImageEM X2 (C9100-23B)	IEEE 1394b (800 Mbps)	Yes	Yes9, 10
ImageEM (C9100-13)	Phoenix ‘CamLink’ PCI or Phoenix ‘CamLink’ PCI Express	Yes	Yes6, 10
ImageEM-1K (C9100-14)	Phoenix ‘CamLink’ PCI or Phoenix ‘CamLink’ PCI Express	Yes	Yes6, 10
C4880-40	Phoenix DIG36 PCI	Yes	No
C4880-40	Snapper DIG16 PCI	With interface replaced3	With interface replaced3, 10
Orca 100 (C4742-95)	Phoenix ‘LVDS/RS‐422’, PCI or PCI Express	Yes	Yes10
Orca 100 (C4742-95)	Snapper DIG16 PCI	With interface replaced3	With interface replaced3, 10
Orca II (C4742-98)	Phoenix ‘LVDS/RS‐422’, PCI or PCI Express	Yes	Yes10
Orca II (C4742-98)	Snapper DIG16 PCI	With interface replaced3	With interface replaced3, 10
Orca-ER (C4742-95-12ER)	Phoenix ‘LVDS/RS‐422’, PCI or PCI Express	Yes	Yes10
Orca-ER (C4742-95-12ER)	Snapper DIG16 PCI	With interface replaced3	With interface replaced3, 10
Orca-NR (C4742-95-12NR)	Phoenix ‘LVDS/RS‐422’, PCI or PCI Express	Yes	Yes10
Orca-NRB (C4742-95-12NRB)	Phoenix ‘LVDS/RS‐422’, PCI or PCI Express	Yes	Yes10
JenOPTIK AG	Interface	PowerPC	Intel
ProgRes MFscan	IEEE 1394	Yes	Yes
ProgRes MFcool	IEEE 1394	Yes	Yes
ProgRes MF	IEEE 1394	Yes	Yes
Photometrics	Interface	PowerPC	Intel
CoolSNAP CF2, ES2, EZ, HQ2	IEEE 1394	Yes	Yes1
Cascade	PCI 3.3/5-volt	Yes	No
Cascade 128, 128+, 1K, 512B, 512F, 650, II:512	PCI 3.3/5-volt	Yes	No
CoolSNAP CF Color, CF Mono, CF2, EZ, FX, HQ, HQ2, K4	PCI 3.3/5-volt	Yes	No
QuantEM:512SC	IEEE 1394	Contact BioVision5	Contact BioVision5
Sensys, Quantix, PXL, and Series 300	PCI 3.3/5-volt	Yes	No
Sensys, Quantix, PXL, and Series 300	Snapper DIG16 PCI	With interface replaced4	No
QImaging	Interface	PowerPC	Intel
MicroImager	IEEE 1394	Yes	No
MicroPublisher, all models	IEEE 1394	Yes	Yes
QICam, all models	IEEE 1394	Yes	Yes
Retiga, all models	IEEE 1394	Yes	Yes
Rolera-XR	IEEE 1394	Yes	Yes
Scion	Interface	PowerPC	Intel
CFW-1310C (Color)	IEEE 1394	Yes	Yes
CFW-1310M (Monochrome)	IEEE 1394	Yes	Yes

Supported Microscopes

Manufacturers of Supported Microscopes

iVision‐Mac, with the optional Motion Control software module, provides computer control of automated microscopes.

Automated Microscopes

• Leica Microsystems
• Nikon
• Olympus
• Zeiss

Spinning Disc Confocal Systems

• BD Biosciences
• Crisel Electrooptical Sciences & Technology
• Olympus
• Yokogawa Electric

Supported Automation Hardware

iVision‐Mac, with the optional Motion Control software module, provides computer control of XY stages, Z-axis focus drives, shutters, filter wheels, serial port (RS-232) hardware, and other devices. The Shutters & Filters module controls shutters, filter wheels, and serial port (RS-232) hardware.

Recommendations for adding RS-232 serial ports to a Mac are available.

Adding RS-232 Serial Ports to a Macintosh

Most Macs lack a built-in serial port, so you will need a USB–to–RS‐232 adapter to add a port with a DB‐9 or DE‐9 connector. We recommend adapters based on chips manufactured by Future Technology Devices International (also known as “FTDI”). Such adapters are widely used and are available from multiple manufacturers; please contact BioVision Technologies for specifics.

The iVision‐Mac 4.5 Upgrade from BD™ IPLab on MacOS 9

A Path to Current Macs

iVision‐Mac 4.5 offers a path to current Macs running OS X for users running Version 3.6 of BD IPLab imaging software under MacOS 9. It is a Carbon application that can control all supported cameras that have OS X drivers. It can also control supported motorized microscopes and microscopy hardware.

It requires Mac OS X 10.5 (Leopard), 10.6 (Snow Leopard), 10.7 (Lion), or OS X 10.8 (Mountain Lion) operating system software. More information on the requirements is available.

New Facilities

Upgrading to iVision‐Mac 4.5 will provide access to a number of improvements and additions made since the release of IPLab 3.6.

Multi-D Acquire Command

This command makes it easy to capture multi-mode images in 3‐D. You may select from multiple filter positions and two shutters to grab fluorescence and brightfield sequences.

Within the live preview window, you can now change camera settings such as offset, gain, and electronic gain. You can also set the normalization (display contrast) parameters during the preview to match your preferences.

Camera Preview Dialog with Improved Controls

Within the live preview window, you can now change camera settings such as offset, gain, and electronic gain. You can also set the normalization (display contrast) parameters during the preview to match your preferences.

“File Sets” for Automated File Input/Output

iVision‐Mac can now store multiple file sets for “indexed files” and “file lists” used in more demanding automated applications. There are two kinds of file sets:

• Folder Sets, which let you work with every image in a folder;
• Indexed Sets, which let you open numbered files in order or according to their index.

File Set commands have been significantly updated to provide more functionality. Dialogs with File Set menus in them also have a “Show” button that will open the current File Set’s folder in the OS X Finder.

Data Logging Enhancements

iVision‐Mac logs to text files in “CSV” format for easy import into Microsoft® Excel® and Apple® Numbers®.

The Export Measurements to File command writes a text file and opens it in the application specified via the iVision‐Mac Preferences command.

Microsoft Excel reopens an open text file when iVision‐Mac updates it via Export Measurements to File.

Scripting

To complement the new file handling commands, new loop control commands have been added to the script window. These allow you to loop (and exit from the loop) on conditions other than just a count.

Almost all commands that reference image windows now include a window name field. Fields for image window names can select “relative” image window names (“Front Window,” “Second Window,” “Back Window.”)

Variables can now contain string values.

• The Set Variables command accepts string values typed at the keyboard as the script runs. From an image window it can retrieve non-numeric acquisition parameters such as the filter name or a date. It can retrieve the name of an image window.
• The iVision‐Mac 4.5 Enter Variable command can produce string values:
  • it accepts string values typed at the keyboard as the script runs;
  • the user can select a filter by name from a pop‐up list;
  • the user can select an image window by name from a pop‐up list of image windows that is generated as the script runs.

Variables may appear in window name fields of commands, in the Draw Text command’s text, and in fields within the dialogs Enter Variables, Script Query, and Script Alert.

Animation Player

A movie player control dialog appears when you play back sequences of data. Multiple sequences can be animated at once. Animations now run continuously once started (even while you go on to do other things).

Multiple Users

The iVision‐Mac 4.5 User Folder stores scripts, images, and preferences. Each OS X user on the machine has such a folder, which is located within the user's Home folder. No longer will you have to worry about other users changing your preferences, macros (scripts), or settings. Your data and your setup are now your own.

Cameras

Supported cameras include models from QImaging, Hamamatsu Photonics, JenOPTIK AG, Cooke Corporation/PCO AG, Diagnostic Instruments, Photometrics, and Scion. More information is available under Requirements and Supported Cameras, and from BioVision Technologies.

Access to Existing Data

Your Images

iVision–Mac 4.5 reads image files from IPLab/Mac and from IPLab/Windows.

Your Scripts

iVision–Mac 4.0 opens and converts scripts from versions 3.5 and 3.6 of IPLab/Mac, but some editing may be necessary: a number of old file-related commands cannot be converted.

Other Stored Information

iVision–Mac 4.0 imports stored information from your existing IPLab/Mac 3.6 application, such as your X‐Y calibrations, linear filters and pseudocolor tables. Place a copy of your Command Data file from IPLab/Mac 3.6 in the iVision Preferences folder (within your iVision 4.0 User Folder), and launch iVision‐Mac to convert it.