Feature Chronology

Following is a list of new features and enhancements added to BIOQUANT OSTEO from BIOQUANT OSTEO 2014, v 14.2.6, to BIOQUANT OSTEO 2019, v 19.6.6. For complete release notes, see Version History.

BIOQUANT OSTEO Version 19.6.6

New Features


Jenoptik equips the JENOPTIK GRYPHAX® PROKYON microscope cameras with the latest CMOS technology. Short exposure times and high image refresh rates make the system time-saving and convenient to use. This means you can position and focus fast and easily.

BIOQUANT is currently offering a 20% discount on the JENOPTIK GRYPHAX® PROKYON camera for the trade in of your existing camera.



The Threshold Sliders box allows the user to refine the threshold values for red, green, and blue, by moving slider bars in single digit increments from 255 to 0.

BIOQUANT OSTEO Version 19.2.6

New Features

Imaging Extensions are now part of BIOQUANT OSTEO

Tools which were previously part of the BIOQUANT Imaging Extensions add-on have been integrated into all versions of BIOQUANT.

BIOQUANT SCAN remains a separate add-on. BIOQUANT SCAN is responsible for the automated control of motorized stages, the automatic focus correction of images, and the whole slide scanning of sections.

Data Region New Features & Enhancements

The Selected List region has been renamed to the Data region. The Arrays menu, the Edit menu, and parts of the File menu have been moved into the data region. Now, all the functions related to data are now found in the Data region.

Editing Region New Features & Enhancements

The Editing region has changed quite a bit in this version. The number of tools has increased substantially. Note in particular that there are now 4 kinds of Draw tools, 4 kinds of Erase tools, 2 new Separate tools, and 2 Clean tools. Many of these new tools help with separating touching cells and are useful with the Measure Cells and Myofibers Measurement Types.

In addition, there are new hotkeys to swap between Editing buttons while you are editing in the Image window. Even better, the “U” key will undo the last threshold edit made while the cursor is still editing in the Image window.


Threshold Enhancements

The threshold color can now be assigned the array. Then, whenever the array is selected in the Selected box on the Data region, the assigned threshold color is retrieved


Density - Avg Fluorescence - Immunofluorescent Staining

  • This template collects stain intensity data for fluorescing samples. Data are collected for each of 3 color channels: red, green, and blue. Data units are “grayscale” and are reported on a scale from 0 to 255 where 0 is black and 255 is the maximum intensity for that color.

Density - Integrated Optical - Immunohistochemical Staining

  • This data set is used in the quantitative analysis of immunohistochemistry data.

  • Integrated Optical Density is the sum of all the absorbance values for the pixels in an object. The absorbance data comes from Beer’s Law: A = -log(I/Io) where I is the intensity of the light coming through the sample and Io is the intensity of the background light.

  • IOD data has also been used in the analysis of genome size by feulgen staining as IOD values correlate well with picograms of DNA in nuclei.

Measure Cells - 1 Cell Type

  • This is a good template to start learning the Measure Cells Measurement Type. It uses the Measure Cells measurement type. Using this template, it’s possible to (a) count cells only within a specified boundary and (b) to avoid double counting cells even when they reappear in adjacent and overlapping fields of view.

Measure Cells - 2 Cell Types

  • This template is similar to the 1 cell type template, but is expanded to account for two classes of cells. It reports the total number of each class of cell, the numeric density of the cell populations, and proportion of each cell type to the total.

Density Wand Type - Cells

  • This template is used with the Density Want measurement type. Using the density wand, circular or rectangular regions are marked on the image and the intensity of the stain is measured in those regions. Data are in units of “grayscale” and are reported on a scale of 0 to 255 where 0 is black and 255 is white. This is a handy way to analyze the stain intensity of cells when they are difficult to threshold individually.

Density - Avg Brightfield

  • This template collects stain intensity data from brightfield stains. Data units are “grayscale” and are reported on a scale from 0 to 255 where 0 is black and 255 is white. This is most commonly used in conjunction with immunohistochemistry data so that both the area of the positively stained tissue and the intensity of the stain can be reported.

Trace Type - Specimen Area

  • This specialized template is used for system which have either a motorized or encoded stage. It allows a very large area to be traced at high magnification when the whole area doesn’t fit in one field of view. It is preferred that you scan your section over using the Trace Type. This template is provided for compatibility for older BIOQUANT users who have upgraded.

Improvements to Tutorials

The OSTEO 2019 Tutorial Volume has new and improved Tutorial Sets. Each Tutorial Set has an associated guide and sample image(s). Follow the Guide steps to learn the protocol.

The Tutorials also often have procedures in the BIOQUANT OSTEO manual, which provide images or videos to help learn the protocol.

To see if the tutorial has an associated video, in the Measurement region, click the > button to open the OSTEO 2019 Video Handbook.

BIOQUANT OSTEO Version 18.2.6

New Features

Myofibers Measurement Type

There is a new Measurement Type called the Myofibers Measurement Type. The Myofibers Measurement Type simultaneously measures myofiber area, central nuclei number/myofiber, and myofiber diameter. This protocol replaces the Muscle Phenotyping protocol from previous versions of BIOQUANT.

Support for QImaging BIOQUANT PV1 Camera

Developed in cooperation with QIMAGING, the BIOQUANT PV1 camera is built specifically for the imaging requirement of musculoskeletal research. This ensures high sensitivity in color imaging of real-time multi-channel fluorescence.

Convert Sequence to BIF

BIOQUANT now support the batch conversion of TIF, JPG, or BMP images into the BIF format. This is helpful for converting images captured with slide scanners or other digital cameras.



A new Myofibers Template has been added.

This template replaces the Muscle Phenotyping template found in BIOQUANT OSTEO 2017.

BIOQUANT OSTEO Version 17.2.6

New Features

Video Help

BIOQUANT OSTEO 2017 still has integrated video within the BIOQUANT OSTEO 2017 Manual. These videos have also been pulled out into a second manual that consists only of videos. There are several ways to quickly open video help:

  • Each region of the Ribbon has a new video tutorial buttons. Clicking this button opens the video help PDF to the relevant page.

  • On the Help menu, the “Tutorial Videos...” has been added. This opens the front page of the Tutorial Videos manual.

  • On the Desktop, Double Click the OSTEO Video Tutorials Manual

Referent Data

There is a new Measurement Type called the “Referent Data” Measurement Type. It is used to simultaneously measure Tissue Volume, Bone Volume, and Bone Surface. It replaces the “Bone Referent Array Set” used in previous versions.

Pyramid TIF Export

Users can save up to 4 GB TIF images as Pyramid TIF images.

Pyramid TIF files are compatible with a wide range of digital pathology software applications. These include both desktop applications and web server applications, like IIP server.

Pyramid TIF Export is only used to export TIF images for third party software. We do not recommend saving Pyramid TIF images for analysis in BIOQUANT. However, BIOQUANT can open Pyramid TIF images it has saved.

Auto All in Threshold

The new Auto All button in the Threshold region automatically sets the Red, Green, and Blue threshold ranges to 0 to 255, which thresholds everything in the Image window. This is particularly useful if you want to measure the area of a region of interest.

Sample datasets are now Tutorial Sets

In BIOQUANT OSTEO 2017, the Sample Datasets have been replaced with Tutorial Sets that are opened directly using the Open a Tutorial Set box.

In the previous version of BIOQUANT OSTEO we included Sample Datasets that installed into a BQDATA\BQ2016 folder. The user could open these Sample Datasets and follow their guides to learn how to use BIOQUANT.

All BIOQUANT OSTEO 2017 Tutorial Sets have been updated to use the new Referent Data Measurement Type, if applicable.



The “Sarcopenia Template” has been renamed “Muscle Phenotyping” to better reflect the range of applications that it can support.

SCAN - Set by Edges

The scan area can now be set by marking the various edges of the area to be scanned. BIOQUANT will compute the necessary size and shape of the scan area. Scanning multiple slides at once is not supported with “Set by Edges.”

In previous versions, the only way to set the scan area for a section was to mark the center of the scan area and then tell BIOQUANT how big of an area to scan around the center.

Welcome Screen - Open a Tutorial Set

On the Welcome splash screen that comes up when you open BIOQUANT OSTEO, a new “Open a Tutorial Data Set” button has been added.

This button opens the Open Tutorial Set box, which lists all the Tutorial Data Sets included with BIOQUANT OSTEO. Once a Tutorial Data Set is selected, you can follow its Guide to learn the protocol. The Tutorial Data Sets use Sample Images that were installed when you installed BIOQUANT OSTEO 2017.

LIN - Crop Image

The Large Image Navigator has a new feature that lets you crop a Scan to the region you are actually interested in measuring. This is also useful because the Shrink To Fit zoom level will now be able to show the measurement region at a higher resolution since there will be less extra tissue to fit in the Image window.

You can crop a BIF, BMP, or TIF image. The system will crop the image to the same file type that it was before the crop, i.e., BIF to BIF, BMP to BMP, and TIF to TIF.

LIN - Pan box snaps to ROI

The Large Image Navigator now shows the current Tissue Volume/Sampling Area ROI tracing.

If the Pan box is moved outside the Tissue Volume/Sampling Area ROI tracing, it now snaps to the closest ROI tracing border.

This prevents you from measuring a field outside of the Tissue Volume/Sampling Aea ROI tracing.

It also allows the Coarse Move Pan Box button to sequence field to field without leaving the Tissue Volume/Sampling Area. When the Pan box reaches the ROI tracing edge, it loops back around to the next row of the ROI tracing.

Color Palette Changes

The Color palette has changed to offer brighter colors.

BIOQUANT OSTEO Version 16.2.6

New Features

Windows 10 Support

BIOQUANT OSTEO now supports Windows 10 and Windows 7.

We do not officially support Windows 8. BIOQUANT will probably work, but we haven’t tested under Windows 8, and we haven’t created a BIOQUANT profile for the interface, so it will look crowded. We recommend you upgrade to Windows 10.

The installation program auto detects your version of Windows and installs the correct BIOQUANT profile for the operating system.

Multi-Band Threshold

A new Multi-Band Threshold feature has been added. This feature is in beta stage. We look forward to your feedback. Currently Multi-Band Threshold works independently of traditional thresholding, however, the two methods will be integrated in future versions.



The Muscle Isoform Analysis template and sample data set, as well as protocol, have been changed to use the new Measure Cells type to measure Myocyte positive and negative cells.

The Osseointegration template and protocol has been changed so that the user can identify and measure Contact Surface at higher magnification using Auto Surface and Auto ROI.

dLS - Max Width Length Added

To avoid issues with C and S shapes, a new dLS Setting has been added called “Max Width Length.” The default is 50. If the width lines on C and S shapes are darting to the wrong surface, lengths above this value will be excluded. They will be marked with a square, but no line will extend from the square and no data value will be recorded.

To set the Max Width Length, in the Measurement region (dLS Type), click the Settings button. Then on the Settings box, change the Max Width Length and click OK.

Imaging Toolkit - Increase montage max to 4GB

The Imaging Toolkit can now create a montage up to 4 GB, as long as the system has enough resources.

BIOQUANT OSTEO Version 15.2.6

New Features

Welcome Screen

When you double click the BIOQUANT OSTEO icon, the “Welcome to BIOQUANT! How would like to proceed?” splash screen now opens. This box offers several options for deciding which data volume and data set should be open in BIOQUANT.

On the Welcome to BIOQUANT screen, the Current Data Volume and Current Data Set is listed above the horizontal line on the Welcome screen. If no data set has been opened in the past or if this is the first time you’ve opened BIOQUANT, this region will be empty.

Measure Cells Measurement Type

The new Measure Cells measurement type is used to quickly measure cells from field to field. This tool enables quick cell measurement by ensuring that only cells within the measurement area counted, automatically filtering out partial cell profiles cells cut by the region of interest, and preventing duplicate measurements on overlapping fields of view. The Measure Cells Type replaces Auto Exclusion and Edge Rejection from BIOQUANT OSTEO 2014.

Add/Remove to Threshold using Scroll Wheel

The easiest way to define a threshold now is to use the scroll wheel when using Select and Add. Once the starting color has been chosen, scrolling the mouse wheel up adds similar colors automatically to the threshold. Scrolling the wheel down removes the least similar colors from the threshold.

Disable Threshold Button

The threshold can be disabled by clicking the Disable button so that it is DOWN to quickly turn off all three of the color channels. Clicking the Disable button so that it is UP will turn back on all three color channels.

When the stain is hard to threshold, disabling the threshold is useful because it allows the user to manually paint in the threshold using the Draw Threshold tool. Once the threshold is manually painted in, it can be automatically measured using the Measurement region.

Zoom and Draw/Erase Threshold

The Draw Threshold and Erase Threshold brush size circle now updates automatically when using the Z key to zoom in and out on the image.

Increase/decrease brush size using scroll wheel while drawing/erasing

When drawing or erasing threshold the user may now increase or decrease the brush size by using the scroll wheel on their mouse.

Camera Presets

Camera Presets have been added for supported QImaging digital cameras. Camera presets store exposure time, master gain, and white balance (red gain, green gain, and blue gain) values to a file in the Camera Presets folder on the hard drive. The camera preset file can be loaded later to retrieve the camera settings.



The Chondrocyte Proliferation template and protocol have changed to use the new Measure Cells type to measure PCNA+ and PCNA- cells.

Multi select Osteoid Type

The Osteoid measurement type has been enhanced so that multiple osteoid seams can be measured at a time. In addition, the Osteoid Measurement Type now automatically finds the ends of the osteoid seams. Also, the symbols used to represent parts of the osteoid measurements are now more visible.

SCAN - Back button to recapture blurry images

A “Back” button has been added.

When the stage pauses to allow for refocusing, clicking the back button moves the stage to preceding image capture positions. This is helpful if the stage is set to only stop every 3 fields of view to adjust focus. The stage can be backed up to the 1st or 2nd field to adjust the focus and recapture the images. Clicking the Continue button resumes automated image capture.

SCAN - Photobleach safe Spot

When scanning a large fluorescent section, the technician may not always be on hand to swap the slides when the scan is finished. To avoid photobleaching the section, two new features have been added: Automatically close the PhotoFluor II excitation Shutter, and Move to a Blank Location on the Slide.

BIOQUANT OSTEO Version 14.2.6

New Features

Assign to Data Set

You may now assign the selected order of measurement arrays and the calculation list to the data set. This is automatically load the lists when the set is opened.

Auto ROI

BIOQUANT will now automatically keep the user within a Region of Interest that was defined at a lower magnification.

Auto Surface

A New measurement type, Auto Surface allows the user to define a line using threshold. The system will then determine the length.

SCAN to more than one image file type: BIF, BMP, TIF, JPG

Previously SCAN only create BIF (BIOQUANT Image Format) files. Now you may collect images in BMP, TIF, and JPG for external montaging programs.



The Guide Editor box has been redesigned with an improved user interface.


The Batch Script dialog box has been redesigned. The buttons now have text labels. Functionality is the same.