BIOQUANT OSTEO 2016 Key Features

BIOQUANT OSTEO 2016 16.1.6 was released on January 31, 2016. BIOQUANT strives to provide annual upgrades to users with Technical Service Plans. If you have an active, Technical Services Plan, request your copy below.



  • Upgrade? Request an Upgrade Quote
  • Potential User? To request a customized quotation, the Pricing Request Forms on the BIOQUANT OSTEO site.

To read the full Release Notes: BIOQUANT OSTEO 2016, 16.1.6, Release Notes

Windows 10 Support

BIOQUANT OSTEO now supports Windows 10, as well as Windows 7.

Template Changes


BIOQUANT OSTEO 2016 now has a standard template for the analysis of sarcopenia, the loss of muscle tissue associated with aging.

This data set is designed for use with sections that have undergone some form of muscle specific staining. Analysis of muscle tissue by H&E staining can be exceptionally tedious. Common staining methods include myosin ATPase staining, dystrophin immunohistochemistry, and dystrophin immunofluorescence. A nuclear counterstain can also be applied to identify “satellite cells” associated with the myocytes.

New abbreviations have been added as needed to the BIOQUANT Terminology dictionary.


The Osseointegration template, Osseointegration sample data set, and Osseointegration protocol have been changed so that the user identifies and measure Contact Surface at higher magnification using Auto Surface and Auto ROI.


The Stereology templates support the Stereology Tools box, which is part of the optional BIOQUANT Imaging Extensions. These templates have been updated to count Bone Hits and Bone Surface Hits on the Merz grid at high magnification instead of at the low magnification where the entire sample fits in the Image window.

Multi-Band Threshold

We are introducing a new Thresholding tool in OSTEO 2016. Our goal is to make is simpler and faster for the software to identify structures by stain color. We’re calling it Multi-band Threshold.

Thresholding marks the part of the image that is to be measured by a particular automatic measurement type. For example, before using the osteoid tool, the osteoid in the image must be thresholded. This can be done either automatically based on the color of the osteoid or manually by drawing with the Threshold Draw tool.

Previously, a threshold was limited to a particular color and its lighter and darker shades. We noticed that when one stain transitions to another the mixed colors at the borders are difficult to threshold at the same time. Multi-band threshold means that it’s now possible to create one threshold from multiple colors and therefore more accurately detect objects to measure.

Multi-band Threshold is in the beta stage. This means is works well in our lab, but that it needs feedback from labs working with diverse samples in the real world. We look forward to and will be asking for your feedback. Currently Multi-Band Threshold works independently of traditional thresholding, however, the two methods will be integrated in future versions. 

Threshold by Scroll Wheel Improvements

Since OSTEO 2015 the threshold could be adjusted by scrolling the mouse wheel up or down. Scrolling it up added similar colors and scrolling it down removed the least similar colors.


  • Click Select or Add and then click once on the structure that should be thresholded. This will give BIOQUANT the color of the stain that identifies the structure.
  • Scroll up and BIOQUANT will expand the threshold automatically to include other similar colors.
  • Scroll down and BIOQUANT will contract the threshold by removing the least similar colors.


  • Automatically Choose the Starting Stain Color
    When you click the Select button and scroll up, BIOQUANT will examine the image and choose the strongest stain color automatically and continue to expand the threshold to include similar colors.
    This works best for tissues stained with a single stain such as TRAP staining or Calcein labeling.
  • Add Specific Colors by Clicking
    To add a specific color to the threshold, you can now just click on it. The threshold will be expanded to include that color. You can continue scrolling up and down to adjust the newly expanded threshold.
  • Better Undo Support for Very Light and Dark Colors
    Now when the threshold is very dark (near 0) or very light (near 255) the scroll up and scroll down behavior works symmetrically as expected. Previously, the 0 and 255 limits could skew the color ranges when trying scrolling down to remove less similar colors.

Large Image Navigator has more Step Sizes

Pan Box Size Options: 1:2, 1:4, 1:8, 1:16, Shrink/Expand Image

Pan Box Size Options: 1:2, 1:4, 1:8, 1:16, Shrink/Expand Image

The Large Imaging Navigator loads very large digital image scans and enables you to pan around and load portions of the image at different magnifications into the Image window for measurement. 


  • Two New Pan Box Sizes: 1:8 and 1:16. For very high resolution images, in addition to Shrink image, you now can view the image with 1:2, 1:4, 1:8, and 1:16 Pan Box sizes.
  • Only Supported Pan Box Sizes are Visible If the images does not support a particular step size, its icon will not be on the Large Image Navigator.

Assign to Data Set now supports Measurement Filters

Once objects are thresholded, Measurement Filters allow the software to select objects based on their shape, specifically cross-sectional area, circumference, and roundness.

For example, Measurement Filters can help the software accurately identify adipocytes even though they are often the same white color as tears or gaps in the marrow. Adipocytes are often round whereas tears are often irregular. Similarly, it’s possible to use size to differentiate between multinucleated TRAP positive osteoclasts and TRAP positive monocytes. Finally, it is helpful to know that Measurement Filters use calibrated units so they work across magnifications without adjustment.

Measurement Filter files can now be assigned to data sets using Assign to Data Set. Individual filters
are also assigned to specific arrays.

This saves time as you no longer have to load the Measurement Filter file when you come into BIOQUANT OSTEO. Also, if you use the data set as a template for another data set, you won’t have to load the Measurement Filter file with the new data set.

In fact, if you haven’t checked out assigning Selected Lists, Guides, Calculation Lists, and Measurement Filters to the data set, you really should. They save time and keep you organized!

Open Current Guide Step

Guides are custom protocols visible in the BIOQUANT OSTEO ribbon that walk you through step-by-step the steps in your procedure. All BIOQUANT Templates come with default guides, which you can customize to match your specific needs. 

The Guide region has a new feature called Open Current Guide, which opens the current guide in the Guide Editor and highlights the current step. This really speeds up customizing guides on the fly. 

Imaging Extensions Add-on: Imaging Toolkit 4 GB montages

The Imaging Toolkit can now create a montage from individual image files of up to 4 GB, as long as the system has enough resources. Previously, only BIOQUANT SCAN could create montages up to 4 GB.

With the BIOQUANT Imaging Extensions add-on, the Large Image Navigator could already open uncompressed TIF, BMP, and BIF files of up to 4 GB. 

Read About Even More Features

This is just a sample of the new features. To read all the features read the Release Notes.