What's new

• Update to offline software licensing. Due to updates to the Stereo Investigator activation process, systems that that do not have access to the internet or have intermittent/unreliable internet access require reactivation. View instructions for offline software activation.

• Automated assistance with hardware alignment and calibration; use the new Auto-calibrate button to automatically:

  • Calibrate lenses to determine the number of pixels per micrometer

  • Compensate for micro-misalignment of camera and stage and avoid the tedious process of very fine manual adjustment

• New Scan Repair for continuing incomplete slide scans and replacing problematic image tiles without having to re-acquire the entire slide scan

• Added the ability to Live Zoom or zoom in on the live-camera feed for viewing finer details without having to change to a higher power objective

• Slide scanning workflow now includes the option to employ “Stitching” for improved alignment of adjacent images

• Added the ability to conduct Parcentric Parfocal calibration of just a single objective saving time if only one is out of calibration

• Slide Scanning added a new filter for background subtraction for removing non-specific background staining from fluorescent images

• New ability to set the rotation angle in 3D view making it easier to create figures for presentations and publications

• Added support for the new MBF Bioscience Vesalius Spinning disk confocal structured illumination device

• Added support for Aura Light source and the 89 North LDI

• Can now save a file containing a single color channel from a multi-color channel image

• Added support for 12-bit OME-TIFF files

• Biolucida integration

  • New image browser

  • Improved Biolucida connection interface

See the current Release Notes or all Release Notes for Stereo Investigator.

Recent improvements

• Added support for Leica K5 and K3C cameras

• Decimal points can now be entered during setup in the Slide Scanning workflow

• The Smart optimization feature is off by default. Find the setting in File > Preferences > Images.

• New Batch Pipeline enables easy-to-use batch processing for image filtering

• New Pipelines ribbon now houses features previously located in the Automatic section of the Trace Ribbon

• Improved & expanded image support

• New automatic, smart image-optimization preference for low-signal images available

• The Subvolume tool is now restricted by the bounds of the image

• Image montage can now assemble images of varying x/y sizes

• Faster image acquisition and image/data handling: Stereo Investigator software includes new image acquisition and image/data display technologies that maximize efficiency and speed, and improve overall software function and performance. Acquire, compile, save, load, display, and process your files faster than before thanks to new imaging and data-handling engines that employ intelligent image loading, concurrent usage of CPU cores, and multiple levels of data caching for efficient use of RAM and GPU resources. Overall software function and performance is improved, highlights include:

  • Acquire much, much larger images than was previously possible—in the multiple terabyte range

  • Capture and assemble images in significantly less time—minutes, rather than hours

  • Image- and data-files load noticeably faster than in previous releases

  • You'll notice that Stereo Investigator software responds more quickly as you work; it handles hundreds of thousands of data points simultaneously.

  • Image adjustments are immediately displayed in both the 2D and 3D windows—without clicking any buttons.

• Improved slide scanning workflow: The new imaging engine dramatically increases the size of images that can be acquired and the speed of image acquisition and assembly in the slide scanning workflow. Benefits include:

  • Create larger slide-scans—at higher magnification and/or from larger specimens than possible in previous releases

  • Preview image-compilation before finalizing your large-image acquisition settings

  • Include optional XY stitching for better image-tile alignment and cleaner compiled images

  • Mitigate uneven illumination artifacts in fluorescence imaging using (optional) intelligent, image-data based flatfield correction

• Simpler software authorization: Stereo Investigator autofills the online Authorization Request Form with information about your computer system. Just fill in your name and contact information, plus the name of your PI to submit the form.

• Floating licenses are now available—share one Stereo Investigator license on more than one computer

• More options for opening images:

  • Open all images in container files such as Leica .lif and Zeiss .czi formats.

  • Choose to display images in a grid, stack images, or display on top of each other without stacking.

  • Drag and drop to open files—the new Image Opener window makes it easier and more powerful than before

• Probe-workflow improvements include the following:

• Optional second counting frame in the Optical Fractionator Workflow makes it easier to count two sets of objects in a single pass—ideal for structures that are very different in size and/or population density.

• Significantly easier method to launch the Optical Fractionator Workflow using images that were acquired on other (non-MBF Bioscience) microscope systems— choose to Start a new subject from image stacks:Load image stacks acquired in a systematic random sampling (SRS) manner using another microscope system (i.e., not an MBF Bioscience system). See Using Optical Fractionator with external image sources . .

• Use the new Select Acquired SRS Image Series button to streamline the use of some stereology probes by incorporating information from the settings used to acquire the systematic random-sampling (SRS) image-series.

• New Freehand Selection tools provide more options for selecting markers or contours

• Improvements to the 3D Visualization window include:

  • A new subvolume function that enables you to easily and systematically focus on portions of images/image stacks.

  • Color channel selection via a new Channel panel enables you to select one or more color channels to view and hide.

  • New tool that clips tracings to a partial projection view

• Updates to the Image Montage tool that support automatic z-alignment and the option to consider image names in the 2D image-alignment process.

• Updated the Illumination Correction tool.

• You can now clip tracings to partial projection view in the 3D environment. In addition, tracing with partial projection will automove the image in the Z orientation.

• The default image-save format is now .xml.

• New hardware support for the Zeiss Apotome 3, Luminera CMOS camera, and Basler cameras

• New support for Big tiff and Hdf5 image formats