Feature Chronology

Following is a list of new features and enhancements added to BIOQUANT OSTEO between BIOQUANT OSTEO 2013 v13.2.6 and BIOQUANT OSTEO 2023 v23.5.6.

Labs with active Technical Services have received each of these upgrade at not cost. If your lab does not have an active Technical Services Plan, you still may qualify for an upgrade discount.

BIOQUANT OSTEO 2023: Version 23.5

BIOQUANT OSTEO 2023 v 23.5.6 for Windows 10/11 was released on May 31st, 2023. If your system was covered by an active Technical Services Plan on May 31st, 2023, your lab can receive this upgrade free of charge. Download the complete release notes.

BIOQUANT OSTEO 2023 SUPPORTS WINDOWS 11 & WINDOWS 10

BIOQUANT OSTEO 2023 now supports Windows 11 64-bit. Windows 10 64-bit is also supported. As of 2020, BIOQUANT OSTEO no longer supports Windows 7.

Virtual Stage Controller

With the Virtual Stage Controller, BIOQUANT uses software features to simulate the movement of a motorized stage when measuring or imaging at high magnification.

The Virtual Stage Controller can also be used to scan sections with your microscope into the calibrated BIF format for faster analysis. The Virtual Stage Controller also allows you to measure directly on a live image without overlap.

The Virtual Stage Controller requires one of the three new high-speed, high-resolution, high-sensitivity Jenoptik cameras.

Save Navigator BIF Image Plus Stamp

Previously, calibration scale bars could be saved only on images from the Image Window. This was done through Save Image > Save Image Window plus Graphics.

Now, calibration scale bars can be saved on the entire BIF scan, regardless of size. This makes it possible to annotate whole slide scans so the micron per pixel calibration factor is easy to determine when exporting scans to TIF, an uncalibrated format.

To save the stamp on the BIF image in the Image Navigator, a new Save Image is available, “Save Image Navigator BIF plus Stamp.”

Editing Tool: Fill (ALL)

Previously, there were two kinds of fill: fill one hole and fill all the holes in a single object. In some contexts, this was inefficient.

A new fill tool has been added: Fill All Holes. This tool can quickly fill small holes in bone when measuring osteclast surface with TRAP stain. Additionally, this tool is especially helpful for unstained or partially stained tissue where the bone surface must be drawn by hand.

The Fill (All) tool is used to fill all holes in the thresholding that are smaller than the Fill All Operator minimum size specified on the Editing Setup box.

Use Stamp Tools to Help You Draw the ROI

Previously, there were two methods to standardize the shape of the tissue volume referent value: (1) Create a rectangle of know height and width that is a known distance from a point on the tissue section (2) Create a polygon shape that is a known distance from surfaces in the tissue section. These two tools are not flexible enough.

Now, all the annotations in the Stamp tools can used on the image prior to drawing the region of interest. These annotations help lay out the precise boundaries of the Tissue Volume region of interest.

One common example is to create a histology Tissue Volume shape that exactly matches the microCT Tissue Volume. For example: the Tissue Volume shape starts 150 microns below the lowest point of the growth plate, follows the shape of the cortical walls, maintaining a 150 micron offset, and descends exactly 1500 microns down the cortical shaft.

Another example is the analysis of osseointegration. The bone to implant contact surface can be measured within 150 microns of the screw shaft, starting 1000 microns below the periosteal surface and ending 150 microns from the screw tip.

Scan: New “Cancel Focus” Button Lets You Override Auto Focus

Currently, automatic focus correction is either enabled to disabled in the beginning setup for a series of scans.

Normally, it is on. However, it’s not always easy to predict if a tissue section is going to be compatible with the automatic focus correction. Some very wavy sections or some very thick sections don’t work well with autofocus.

To help address this situation, a “Cancel Focus” button has been added that is available while the scan is running. Now, if the auto focus controls are not working well with a scan, you can click the “Cancel Focus” button to revert the scan to Manual Focus Correction without interrupting the scan. The scan will continue as configured, now pausing periodically for manual focus correction.

Small Quality of Life Enhancements

Data Export Improvements

Data are always exported to 6 decimal places. Previously, some export tools defaulted to 2 decimal places.

Exported projects with data sets that have identical names are now properly formatted. Previously, the second data set didn’t have a name label.

Bulk add and remove for arrays on the Export Individual Arrays box is now supported. Previously, there was no support for bulk remove.

Exporting more than 21 arrays using Export Individual Arrays box is now supported.

TIF Import Improvements

BIOQUANT now supports importing TIFs in the tiled format. To speed up loading these images, a reformatted version of tiled TIFs are saved in the strip format.

BIOQUANT OSTEO 2022: Version 22.5

BIOQUANT OSTEO 2022 v 22.5.6 for Windows 10 was released on May 31st, 2022. If your system was covered by an active Technical Services Plan on May 31st, 2022, your lab can receive this upgrade free of charge. Download the complete release notes.

Live Background Correction - Jenoptik Cameras

A new background correction algorithm has been implemented to correct for uneven lighting and imperfections in the optics like dust. The background correction is done on the live image so the live image and held image are identical. Previously, the live image was uncorrected and the correction was applied retroactively after the image was captured.

One Click Brightfield Setup - Jenoptik Cameras

A new automatic setup algorithm for brightfield imaging has been implemented. Clicking a single “Brightfield Setup” button adjusts both image brightness and color accuracy. From there, turning on the live background correction gets you a near-perfect image with two simple clicks.

Black Fluorescent background - Jenoptik Cameras

A new algorithm called fluorescence black balance has been implemented to correct for for autofluorescence. Dim background fluorescence is now suppressed to black. This makes it easier to see strongly labeled mineralizing surfaces.

Enhanced Camera Presets - Jenoptik Cameras

BIOQUANT now loads a standardized camera preset file when started. This allows labs to customize their startup settings to match their specific microscope. Additionally, all new camera settings like fluorescent black balance can be stored in camera presets.

Enhanced manual setup - Jenoptik cameras

The Manual Setup dialog box has been simplified and enhanced. Color skew has been moved to the main region. Camera Frame Rate has been added to the advanced region.

Simplified Background Setup for IOD Data

The background correction and background storage user interface has been simplified to menu items in the Image region. This allowed the Background Correction dialog box to be removed. This is true for Jenoptik cameras, QImaging cameras, and image files.

BIOQUANT SCAN - Custom Names for set by topo

Each of the 8 possible scan areas can now be named individually.

BIOQUANT OSTEO 2021: Version 21.5

BIOQUANT OSTEO 2021 v 21.5.6 for Windows 10 was released on May 31st, 2021. If your system was covered by an active Technical Services Plan on May 31st, 2021, your lab can receive this upgrade free of charge.
Download the complete release notes.

NEw Expanded OME-TIFF Support

BIOQUANT has expanded support for multi-dimensional image data from confocal and light sheet microscopes. BIOQUANT 2021 now supports both single file and multiple file OME-TIFs.

BIOQUANT OSTEO now supports both single file and multiple file OME-TIFs. The previous version of BIOQUANT only supported single file OME-TIFs.

New Redraw/Overview Support for Z Offset

New Redraw menu items and Overview window menus make it easier to navigate 5D image data by only showing the measurement tracings for the current Z position. The current Z position is shown in the Parameters region, in the Z Offset field.

This feature can also be used to redraw at different Z positions in physical sections, as well as to redraw at different Z Positions in the Dicom Navigator.

Scan Multiple Areas and Skip Empty Fields

A new method, “Scan by Topo” has been introduced. This method allows scan areas to be quickly marked out using the lowest power objective on the microscope, then automatically scanned with you preferred imaging objective, usually 20X or 40X.

Up to 8 different scan areas can be scanned in one session.

This also means that BIOQUANT SCAN now skips all fields of view that are not in the scan area, significantly speeding up scan times. Previously, BIOQUANT SCAN collected an image of each field of view in a rectangle that contained the scan area. Since tissue sections are rarely rectangular, a lot of those fields of view were blank.

Control for Coolled Fluorescence Illuminator

BIOQUANT SCAN can now control the CoolLED pE-300 White fluorescence light source.

The pE-300 is a multi-channel LED fluorescence excitation light source. Since it is an LED light source, it has an extremely long life. Since it a multi-channel light source, the excitation strength of each fluorochrome can be adjusted individually.

This means that when working with multi-label mineralizing surfaces, you can turn down the brightness of the calcein label and turn up the brightness of the alizarine red label at the light source. This helps preserve the sample and simplifies camera settings. There no need now to use camera settings to adjust the relative brightness of labels in the image.

Motorized Stage “M” Toolbar Enhanced

The Motorized Stage “M” Toolbar is larger, making the icons easier to click.

The Coarse Move, Fine Move, and “Move Stage by Clicking Two Points” tools (the first 9 buttons) on the M Toolbar now automatically redraw the Topo data after the stage finishes moving.

BIOQUANT Scan: Background Correction Indicator

For bright field scans, the Scan Multiple Slides and Scan Well Plate boxes now have a Background Correction indicator that reminds you to save a background image and turn on Activate Capture Correction on the Background box.

BIOQUANT OSTEO 2020: Version 20.8

BIOQUANT OSTEO 2020 v 20.8.6 for Windows 10 was released on August 31st, 2020. If your system was covered by an active Technical Services Plan on May 1st, 2020, your lab can receive this upgrade free of charge.

This update contains several issue resolutions since the BIOQUANT OSTEO 2020 v 20.5.6 Release. If you request OSTEO 2020 on the menu to the left, this is the version you get! Download the complete release notes.

BIOQUANT OSTEO 2020: Version 20.5

BIOQUANT OSTEO 2020 v 20.5.6 for Windows 10 was released on May 31st, 2020. If your system was covered by an active Technical Services Plan on May 1st, 2020, your lab can receive this upgrade free of charge. Download the complete release notes.

WINDOWS 10 REQUIRED. WINDOWS 7 NOT SUPPORTED

Microsoft discontinued support of Windows 7 on January 14, 2020. BIOQUANT OSTEO 2020 no longer supports Windows 7.

JENOPTIK prokyon camera: new capture sizes

The PROKYON camera model adds additional capture sizes of 3840 x 2400 and 5760 x 3600.

In September 2019, BIOQUANT OSTEO added support for the biggest camera technology upgrade since the introduction of the first high resolution digital cameras.

BIOQUANT now supports the PROKYON, KAPELLA, and SUBRA cameras from Jenotpik. These Jenoptik cameras all use a next generation scientific CMOS sensor that eliminate the compromises inherent to all the prior CCD sensor cameras.

These cameras can deliver a full 1920x1200 resolution image at between 30 and 60 frames per second. This is 2X to 4X faster than current cameras at 4X the resolution. In BIOQUANT, supported Jenoptik cameras provide a live image at 1280x960 to the Image Window with optional 1920x1200 image capture.

5D IMAGE NAVIGATOR: Confocal and Lightsheet data

BIOQUANT is pleased to announce support for a new dimension in musculoskeletal research. BIOQUANT OSTEO now supports multi-dimensional image data from confocal and lightsheet microscopes.

Multi-dimensional image data in the OME-TIFF format is loaded into the 5D Navigator using with the new “Open OME TIF File to 5D Image Navigator” menu item on the Sequence button in the Image region

If your confocal or lightsheet software cannot save to OME-TIFF, the BIO-FORMATS plug-in to ImageJ can be used to convert it to the OME-TIFF format. We have a procedure that walk you through using ImageJ to covert to OME-TIFF, contact us!

Currently BIOQUANT opens single OME-TIFF files up to 4 GB. If future versions, BIOQUANT will support sequences of multiple OME-TIFF files which will allow the maximum image data size to expand beyond 4GB. If you are interested in beta testing this feature, contact BIOQUANT Support.

Export BIF Images as TIf

The Convert BIF Sequence to TIF feature is used to convert a collection of BIF images to the TIF format. This is useful if BIOQUANT SCAN or the Imaging Toolkit has been used to save a series of calibrated BIF images that the end user would like to also have in a format that other programs can use. To find this feature, in the Image region, click the Sequence button and choose “Convert BIF Sequence to TIF” from the pop-up menu to open the “Convert Sequence to TIF” box.

QUICKLY SAVE MULTIPLE REGIONS FROM A SCAN

Navigator Setup has new options for Crop. The crop tool can now save part of a scan without reloading the saved image by unchecking the new “Reload Image After Save” box.

CROP AUTOMATICALLY TO 4:3 RECTANGLE

A new “Crop 4:3 ratio” check box has been added to the Navigator Setup box. If this box is checked, then when you draw the crop box, it will be forced to a 4:3 ratio. This is the same ratio as the Image window and the Image Navigator Pan box. This makes it easy to use the Coarse Move Pan Box tool to navigate in a comb pattern through the Image Navigator at high zoom level.

SUPPORT FOR LZW COMPRESSED TIF IMAGES

Open Single and the Open Image Sequence now automatically uncompress and open LZW compressed TIFs. When the system detects and LZW compressed TIF, it automatically creates an uncompressed version and opens it in BIOQUANT. Consequently, it will bit longer than opening an uncompressed TIF. The uncompressed version of the TIF is saved in the same directory with the same name as the compressed TIF, with “uncompressed” appended. In prior versions of BIOQUANT, LZW compressed TIF images could not be opened.

OPEN DATA SET DEFAULTS TO CURRENT Data VOLUME

Data Region: Data Set> Open a Different Data Set The Open a Different Data Set dialog box now opens with the current Data Volume and current Data Set already selected.

This makes it easier to open other data sets in the same volume. If a Tutorial Set is open, then use the Data Set>Open a Tutorial Data Set menu instead of Open a Different Data set to open another Tutorial Set.

Remove SOURCE Images After a SCAN IS MADE

On the Scan Multiple Slides box, on the Options menu, there is a new menu item, “Delete Source Files after Montage.” If it is checked, the images of individual field of view used to create the montage will be deleted after the montage has been successfully generated. This helps save on disk space.

BIOQUANT OSTEO 2019: Version 19.9

BIOQUANT OSTEO 2019 v 19.9.6 for Windows 10/7 was released on September 25, 2019. If your system was covered by an active Technical Services Plan on September 1, 2019, your lab can receive this upgrade free of charge. Download the complete release notes.

JENOPTIK GRYPHAX® KAPELLA AND SUBRA SUPPORT

BIOQUANT is excited to announce support for the biggest camera technology upgrade since the introduction of the first high resolution digital cameras.

In addition to the PROKYON camera, BIOQUANT now supports the KAPELLA and SUBRA cameras from Jenotpik. These Jenoptik cameras all use a next generation scientific CMOS sensor that eliminate the compromises inherent to all the prior CCD sensor cameras.

BIOQUANT OSTEO 2019: Version 19.6

BIOQUANT OSTEO 2019 v 19.6.6 for Windows 10/7 was released on June 28, 2019. If your system was covered by an active Technical Services Plan on June 1, 2019, your lab can receive this upgrade free of charge. Download the complete release notes.

JENOPTIK GRYPHAX® PROKYON Camera Support

BIOQUANT is excited to announce support for the biggest camera technology upgrade since the introduction of the first high resolution digital cameras.

BIOQUANT now supports the GRYPHAX® PROKYON cameras from Jenotpik. These Jenoptik cameras all use a next generation scientific CMOS sensor that eliminate the compromises inherent to all the prior CCD sensor cameras.

Threshold Slider Box

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 2019: Version 19.2

BIOQUANT OSTEO 2019 v 19.2.6 for Windows 10/7 was released on February 28, 2019. If your system was covered by an active Technical Services Plan on February 1, 2019, your lab can receive this upgrade free of charge. Download the complete release notes.

IMAGING EXTENSIONS 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. Features include support for uncompressed TIF and BMP images larger than 250 MB, the Imaging Toolkit, Dicom imaging support, Histograms, and Pseudocolor.

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.

TWAIN Image Capture Support

In the Image region, a new Type has been added, TWAIN. TWAIN is a standards based way of transferring images between imaging devices and imaging software. If the camera or printer/ scanner in the lab has a TWAIN interface, BIOQUANT can likely connect to it now.

BIF Images now Display the mag Factor

The magnification factor (the number of microns per pixel) in a BIF image is now displayed on the title bar of the Image window.

Enhanced DATA REGION

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.

DATA SET MENU OPTIONS
Create New Project, Modify this Data Set, Create a Template from this Data Set, Open a Tutorial Data Set, Open a Different Data Set, Add Quick Data Set to Project.

SELECTED MENU OPTIONS
Open Selected List for this Data Set, Save Selected List for this Data Set.

VIEW DATA MENU OPTIONS
Open the Calculate Box, Open the Raw Data Window

ASSIGN MENU OPTIONS
Clear Assignments from Current Selected Array, Assign the Settings File to this Data Set.

EXPORT MENU OPTIONS
Export Data Table for this Project, Export Raw Data for this Data Set, Export Raw Data for this Project, Export Individual Arrays.

Data Export Enhancements

EXPORT DATA TABLE FOR THIS PROJECT
The “Export Data Table for this Project” option opens the Export Data Table for Volume box. Export Data Table for this Project exports all the calculation arrays for the current data volume in a data table format to the clipboard. Then, you can click a cell in your spreadsheet program and paste.

EXPORT RAW DATA FOR THIS DATA SET
The “Export Raw Data for this Data Set” option opens the Export Data Set box. Export Raw Data for this Data Set exports all the data in the current data set, except for Topo arrays, to the clipboard. Then, you can click a cell in your spreadsheet program and paste. If you need to export Topo arrays, use the Data Manager.

EXPORT RAW DATA FOR THIS PROJECT
The “Export Raw Data for this Project” option opens the Export Data Volume box. Export Raw Data for this Project exports all the data in the current data volume, except for Topo arrays, to the clipboard. Then, you can click a cell in your spreadsheet program and paste. If you need to export Topo arrays, use the Data Manager.

EXPORT INDIVIDUAL ARRAYS
The “Export Individual Arrays” option opens the Choose Arrays for Export box. Previously, this was the “Available Arrays to Clipboard” box, which was opened by clicking the Edit menu and choosing Copy Data, then Choose Available Arrays.

EDITING REGIOn 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 Region 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

New TEMPLATES and PROTOCOLS

Density - Average 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. 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 - 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. This is a handy way to analyze the stain intensity of cells when they are difficult to threshold individually.

Density - Average Bright Field Stain Intensity
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.

Tutorial IMPROVEMENTS

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 2018: Version 18.2

BIOQUANT OSTEO 2018 v 18.2.6 for Windows 10/7 was released on February 28, 2018. If your system was covered by an active Technical Services Plan on February 1, 2018, your lab can receive this upgrade free of charge. Download the complete release notes.

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.

Batch CONVERT Images 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.

TEMPLATES/PROTOCOLS

A new Myofibers Template has been added. This template replaces the Muscle Phenotyping template found in BIOQUANT OSTEO 2017.

BIOQUANT OSTEO 2017: Version 17.2

BIOQUANT OSTEO 2017 v 17.2.6 for Windows 10/7 was released on February 28, 2017. If your system was covered by an active Technical Services Plan on February 1, 2017, your lab can receive this upgrade free of charge. Download the complete release notes.

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.

TEMPLATES/PROTOCOLS

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.

Image CROP

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.

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 2016: Version 16.1

BIOQUANT OSTEO 2016 v 16.1.6 for Windows 10/7 was released on January 31, 2016. If your system was covered by an active Technical Services Plan on January 1, 2016, your lab can receive this upgrade free of charge. Download the complete release notes.

WINDOWS 10 SUPPORT

BIOQUANT OSTEO now supports Windows 10 and Windows 7.

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.

TEMPLATES/PROTOCOLS

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.

Doule Label Surface - 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.

INCREASED MONTAGE Size TO 4GB

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

BIOQUANT OSTEO 2015: Version 15.1

BIOQUANT OSTEO 2015 v 15.1.6 for Windows 7 was released on January 31, 2015. If your system was covered by an active Technical Services Plan on January 1, 2015, your lab can receive this upgrade free of charge. Download the complete release notes.

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.

Change Threshold Edit BRUSH SIZE with SCROLL WHEEl

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.

TEMPLATES/PROTOCOLS

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 Stop

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 2014: Version 14.1

BIOQUANT OSTEO 2014 v 14.1.6 for Windows 7 was released on February 1, 2014. If your system was covered by an active Technical Services Plan on January 1, 2014, your lab can receive this upgrade free of charge. Download the complete release notes.

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 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.

GUIDES - IMPROVED INTERFACE ON EDITOR

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

BATCH SCRIPT - IMPROVED INTERFACE ON EDITOR

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

BIOQUANT OSTEO 2013: Version 13.2

BIOQUANT OSTEO 2013 v 13.2.6 for Windows 7 was released on February 1, 2013. If your system was covered by an active Technical Services Plan on January 1, 2013, your lab can receive this upgrade free of charge. Download the complete release notes.

Imaging Extensions Add-on

The Imaging Extensions Add-on combines the Imaging Toolkit plug-in and Stereology Toolkit plug-in. Users with either of these features now have both features. Features include: Imaging Toolkit box, MicroCT Navigator box, Stereology Grids.

BIOQUANT SCAN Add-on

Non‐commercial License Users: If you had the Automated Imaging Toolkit plug‐in and a motorized stage, you have been upgraded to BIOQUANT SCAN.

BIOQUANT SCAN performs automated imaging on fixed tissue sections on glass slides and fixed cells in well plates. It supports bright‐field, wide‐field fluorescence, darkfield, polarized, and phase contrast imaging. Scans are stored in the calibrated BIF image format for analysis and may be exported to the BMP format for publications. BIOQUANT

SCAN includes the BIOQUANT Imaging Extensions add‐on. BIOQUANT SCAN requires an ASI motorized stage. It can be used with a Ludl motorized stage, however the stitching quality will be degraded.

The Auto Sequential Imaging and Time Lapse Imaging boxes are no longer available. The functionality of Auto Sequential Imaging is found in BIOQUANT SCAN. Time Lapse Imaging can still be performed at one location using the Imaging Toolkit box.

Threshold Editing New Feature: Clean

Clean deletes all thresholded objects less than a user‐specified minimum size. This makes it easier to remove non‐specific thresholding from marrow space.

OSTEOID Measurement Type Enhancements

FILL THRESHOLD WHEN PREVIEW
When the user clicks the Preview button and then clicks on an osteoid, any holes in the osteoid automatically fill with threshold. Then the system preview outlines the osteoid.

OSTEOID TYPE ARRAY CONTINUITY
The Width, Surface, and Volume arrays are now remembered across BIOQUANT sessions.

REVERSE OSTEOID SURFACE
A “Reverse” feature has been added that allows the user to reverse the slide of the osetoid seam that designates the osteoid surface. For most osteoid seams, the shorter side is the cellular surface. In some pathologies, however, the cellular side is longer. Clicking the Reverse button automatically switches the cellular surface to the longer side.

Double Labeled Surface TYPE ENHANCEMENTS

DLS TYPE ARRAY CONTINUITY
The Width and Surface arrays are remembered across BIOQUANT sessions.

FASTER DLS DEFINITION
The “Draw 1” and “Draw 2” buttons have been combined into a single “Draw” button by default.

BATCH MEASUREMENT ENHANCEMENTS

QUICK BATCH SCRIPT BUTTON
A new Quick Batch Script button/arrow combo has been added to the General Type. If you click the Quick Batch Script button directly, BIOQUANT immediately runs the batch script assigned as the Quick Batch Script.

NEW BATCH SCRIPT STEPS
The following steps can now be added to a Batch Script: Editing: Threshold: Clean, Editing: Threshold: Keep Objects, Editing: Threshold: Draw Threshold, Editing: Threshold: Erase Threshold, Navigation: Load Next Dicom Image (Available with the BIOQUANT Imaging Extensions add‐on.)

ASSIGN TO QUICK BATCH SCRIPT BUTTON
The current Batch Script can be assigned as the Quick Batch Script that is associated with the Quick Batch Script button in the Measurement region (General Type).

QIMAGING CAMERA ENHANCEMENTS

CAMERA SETTINGS: R/G/B GAIN
Using the new R/G/B Gain controls, the brightness of different fluorescent labels can be adjusted in the image. This makes measuring interlabel width easier with multiple fluorochromes like calcein and alizarin red labeling since red labels often appear dimmer than green labels.

QIMAGING EXI AQUA CAMERA SUPPORT
BIOQUANT now has QImaging EXi Aqua camera support. The EXi Aqua provide regulated cooling to 0 degrees Celsius and a 14‐bit dynamic range.

IMAGE MENU ENHANCEMENTS

The Background feature on the Image region (Live Image Type) has been enhanced. The Background Correct button has been renamed Background and is now a drop list that contains the following: Save Full Field + Enable Capture Correction, Define Region + Disable Capture Corrections, Background Box.

IMAGING EXTENSIONS ADD-ON ENHANCEMENTS

IMAGE SIZE ENHANCEMENT
The BIOQUANT Imaging Extensions have special algorithms that allow the user to open BIF or BMP images up to 4 GB in size.

DICOM IMAGE SUPPORT / MICROCT NAVIGATOR
BIOQUANT now supports the dicom image format. Single images, such as X‐rays, can be opened into the Large Image Navigator. Series of images, such as a MicroCT image set, can be loaded into the MicroCT Navigator.

STEREOLOGY FOR BONE
The Stereology Tools have been modified for use with bone and added to the BIOQUANT Imaging Extensions add‐on.

SCAN ADD-ON ENHANCEMENTS

SCAN MULTIPLE SLIDES / SCAN WELL PLATE BOX
The user interface has improved.

SETUP BOX: NEW FOCUS AND CAMERA REGION
There is a new Focus and Camera region on both the Scan Multiple Slides Setup and Scan Well Plate Setup boxes. This region offers enhanced options for choosing auto focus patterns and allowing the user to manually focus on field based on a focus pattern. It also activates the Auto Exposure box.This region replaces the Auto Focus and Pre Focus check boxes from the previous version.

CALIBRATE FOCUS BOX ENHANCEMENTS
New Pattern (Normal Mode, Hill Detect), Contrast, Speed %, Hill, and Focus Range options.

OSTEOIMAGER Enhancements

Software control over the bright field light source has been added.

Software control over the objective lens selection has been added.

BIOQUANT OSTEO 2012: Version 12.5

BIOQUANT OSTEO 2012 v 12.5.6 for Windows 7 was released on May 1, 2012.

BIOQUANT OSTEO 2012: Version 12.1

BIOQUANT OSTEO 2012 v 12.1.6 for Windows 7 was released on January 1, 2012.

BIOQUANT OSTEO 2011: Version 11.2

BIOQUANT OSTEO 2011 v11.2.6 for Windows 7 was released on February 28, 2011.

BIOQUANT OSTEO 2010: Version 10.3

BIOQUANT OSTEO 2010 v10.3.6 for Windows 7 and Windows Vista was released March 31, 2010.

BIOQUANT OSTEO 2009: Version 9.7

BIOUANT OSTEO 2009 v9.7.6 for Windows Vista was released July 16, 2009.

BIOQUANT OSTEO 2009: Version 9.0 for Windows XP

BIOUANT OSTEO 2009 v9.00.XP for Windows XP was released September 1, 2008.

BIOQUANT OSTEO 2008: Version 8.4 for Windows XP

BIOQUANT OSTEO II v8.40.20 was released February 1st, 2008. This was the final version of BIOQUANT OSTEO available to most labs without a technical services plan.

Registration Update for All Systems Prior to Version 8.4.2

Your BIOQUANT System License will periodically require an update. To update your software, you must update your registration information and request the free update for your software.

OSTEO II Version 8.12.20
OSTEO II Version 8.11.20
OSTEO II Version 8.10.20
OSTEO II Version 8.00.20