SlideBook software carries biomedical imaging through the entire experimental process. By addressing everything from device control to image processing to automated data analysis, SlideBook allows users to focus on scientific investigation and novel methods rather than on core instrument functionality.

SlideBook comes standard with a wide variety of acquisition drivers to control over 100 devices from dozens of companies. Data can be acquired in 3D, over time, via many color channels and even measuring fluorescence lifetimes. Also standard are a wide variety of analytical tools for image processing, mathematical operations and full suite of statistics functions.
We are pleased to announce the release of SlideBook 5.5, available as of February 2013 to all customers and free to any customer under a current support contract. SlideBook 5.5 is only compatible with Windows 7. If you are not currently running your SlideBook system on Windows 7, please contact 3i for a consultation.

Click here to learn about what's new in the latest version, or use the list on the right to navigate to a specific section.


Exquisite control of a comprehensive range of microscopes, detectors, lasers, filters and over 100 peripheral devices for finding and marking any specimen.


Collect data through space, time, color, multiple positions and fluorescence lifetime. Capture data at extremely high rates in RAM or stream to disk for high content experiments. Manipulate specimens via photo-bleaching, photo-activation, or perfusion.


Correct raw data with intelligent processing via flatfield correction and filtering. Deconvolve 3D data via any of four algorithms to best match experimental conditions.


See and inspect specimen data through any numbers of portals, from single images to z-stacks, time lapse, color channels and 4D views.


Segment image data via intensity, gradient and watershed algorithms to non-destructively cull out areas of interest for statistical analysis.


Track objects in 2D and 3D via automatic or manual delineation for analysis based on time or pathway.


Analyze images and extract statistical data via a wide variety of algorithms while maintaining original data integrity. Data is directly portable to MATLAB® and adheres to Open Microscopy Environment standards.


Present and export data visually or textually via single images, 3D movies, graphs and Excel spreadsheets.

3D Deconvolution

Image restoration at very high speed through a constrained iterative algorithm using a measured point spread function.

CellNet™ Pattern Recognition

Neural network technology to train SlideBook in specific analysis and then automatically apply to large amounts of data.


Measure FRET via acceptor photobleaching, sensitized emission and fluorescence lifetime methods.

Super-Resolution Particle Tracking

Identify and track single molecules, reporting object statistics and path statistics.

Ratio Imaging

One or two ratiometric labels (such as Fura-2, BCECF, and cameleon) can be easily calibrated, acquired, graphed, and analyzed using SlideBook's ratio imaging module. Elaborate experiments which combine ratio acquisition with non-ratiometric labels, 3D and 4D imaging, or plate screening are all possible.

Photomanipulation/FRAP Imaging

Pinpoint control of laser illumination for photobleaching, photoactivation and photoablation.

Synchronization of TTL Devices

Complex sub-millisecond timing and synchronization of lasers, detectors, shutters and fine motion devices.

AutoQuant 3D Blind Deconvolution

When PSF measurement is not practical or s/n is low, this method produces robust and accurate deconvolved data.

6-Dimensional Multicapture

6D Multicapture can revolutionize how you run multiple location experiments and can save days of image acquisition time. This new set of tools allows you to design unique experiments to assign at distinct xy locations in a dish, chamber slide, or multiwell dish. Each location can have a customized z range, channel set, imaging mode, even binning and chip extent! For example, you can run a two channel TIRF experiment in one chamber, a 3D confocal experiment in the next chamber, and a binned montage in a third chamber. You can then set up capture to acquire images over 24 hours, accomplishing 3 days of experiments in 1!

Interactive Mask Segmentation

Interactive Mask Segmentation provides a single tool to create a complex mask based on segmentation of more than one channel, perform binary operations, remove small objects, and link directly to statistical analysis. It also adds novel operations, such as polygon selection in a two channel scatter plot. You may select up to three different channels to contribute to the mask generation: two individual channels as well as a gating channel. This tool may also be used for complex analysis of 3D and 4D data.


LaserStream is a critical tool for enabling a number of super resolution acquisition techniques. For example, you could quickly capture 1 image of channel A then 100 images of channel B and repeat this pattern many times. This laser macro editor may also have uses in centroid mapping super resolution methods.

Context Sensitive Help

A complete, interactive help system is accessible by pressing F1 or the  button at any time. The help page for the active window will automatically open. The new help system is indexed and searchable for ease of use. All module manuals are incorporated as well as complete explanations of every user interface window and tutorials for many applications.

Cell Tracking

Region based cell tracking has been added for use during image capture. Simply draw a region and set it for tracking. SlideBook will move the motorized xy stage to recenter the imaging field based on several user-defined parameters.

Montage Improvements

The montage auto align feature now has improved speed and accuracy; the ability to capture multiple montages in a single capture setup has also been added.

Automatic Cloud Backup of Configuration Files

By simply checking a box, you can direct SlideBook to send configuration backup files to a 3i cloud server any time the configuration is modified.

Live Preview Available in Capture Controls

A Live preview button has been added to the Capture user interface, allowing you to quickly adjust a sample before initiating capture without using the Focus Controls.

Slide Interface and Slide View

Images may now be renamed or deleted directly from the .sld view by right-clicking on the image name or simply selecting the image and pressing the Delete key.

SlideBook™ ReaderSlideBook Reader

SlideBook Reader Screenshot
SlideBook Reader Screenshot Thumbnail
A free version of SlideBook™! Review and share your .sld slide files in their native format from anywhere!

The SlideBook Reader includes a robust feature set to help you work together with lab members and collaborators:
  • Familiar user-interface of the SlideBook
  • Open proprietary .sld images
  • View data in XY, XZ and YZ projections
  • Full renormalization and lookup table options
  • Export 16 bit tiffs
  • View and edit regions of interest
  • Graph regions of interest
  • Export graph and graph data
  • Perform basic measurements in 2D and 3D
  • Display and edit annotations
  • Online help with step-by-step tutorials
  • Compatible with Windows XP, Vista and 7, Mac OSX not available at this time

Fill out the form here to download the free SlideBook Reader today.
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