BIOQUANT Life Science
Following is a list of new features and enhancements added to BIOQUANT Life Science from BIOQUANT Life Science 2014, v 14.5.6, to BIOQUANT Life Science 2019, v 19.5.6. For complete release notes, see Version History.
Life Science Version 19.5.6
JENOPTIK GRYPHAX® PROKYON Camera Support
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.
IMAGING EXTENSIONS ARE NOW PART OF BIOQUANT Life Science
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.
The Life Science 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 Life Science 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 Life Science 2019 Video Handbook.
New Tutorial Sets
New Myofiber Tutorial: Myofiber BF H&E Regenerated. This new tutorial demonstrates myofiber analysis over multiple fields of view when central nuclei are plentiful and when myofibers are densely clustered. It is a good introduction to the editing tools introduced in this version.
New Measure Cells Tutorial: Measure Cells - Editing. This slightly more advanced version of the cell counting tutorial introduces some of the editing tools that help separate clusters of cells.
Life Science Version 18.5.6
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 Life Science 2017.
Life Science Version 17.5.6
BIOQUANT Life Science 2017 now has integrated video within the BIOQUANT Life Science 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.
On the Tool Ribbon, Click the Video Tutorial Help Button
From the Help Menu, Choose Tutorial Videos
On the Desktop, Double Click the Life Science Video Tutorials Manual
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.
In BIOQUANT Life Science 2017, the Sample Datasets have been replaced with Tutorial Sets that are opened directly using the Open a Tutorial Set box.
Welcome Screen - Open a Tutorial Set
On the Welcome splash screen that comes up when you open BIOQUANT Life Science, 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 Life Science. 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 Life Science 2017.
Color Palette Changes
The Color palette has changed to offer brighter colors.
Life Science Version 16.5.6
WINDOWS 10 SUPPORT
BIOQUANT Life Science 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.
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.
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.
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 measurement region at a high resolution.
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
Using Auto ROI with the Large Image Navigator has been improved so that if you move the Pan box completely outside of the Tissue Volume redraw, the system now snaps the Pan box to the nearest field with Tissue Volume tracing.
Life Science Version 15.5.6
The new Measure Cells measurement type is used to measure cell populations from field to field. This tool enables quick cell measurement by ensuring that only cells within the sampling area are counted, automatically filtering out partial cell profiles cells cut by the region of interest, and preventing duplicate measurements on overlapping fields of view.
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 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.
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.
Several LIFE SCIENCE Templates and sample data sets have been updated to use the Measure Cells type instead of the Object type. The PDF and eBook Manual protocols and guides for the templates and sample datasets have also been updated.
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.
Life Science Version 14.5.6
Now when BIOQUANT Life Science is opened the “Welcome to BIOQUANT” box opens. From this box you can choose to open the current data set, create a new data volume and set, use Quick Data Set, or open a different data set.
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.
If you are measuring on a very large digital image of your slide in the Large Image Navigator, there is an enhancement that will auto generate the region of interest for you at high power within a Sampling Area based on the topography of the sampling area. If the Sampling Area boundary IS NOT within the field of view, the system automatically changes the ROI to Full Field. If the Sampling Area boundary IS within the field of view, the system automatically generates an ROI based on the Sampling Area boundary. Auto ROI currently does not support live imaging from the microscope.
Cut Edge Objects
Cut Edge Objects is a new Threshold Editing tool that cuts the threshold of objects touching the edge of the region of interest. The cut threshold goes to the Threshold Backup Buffer and can be retrieved later using Paste or Mask, as long as it is not overwritten by another Cut, Copy, or Copy All operation.
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 following templates are new. They each have an assigned Selected List, Calculation List, and Guide, if available.
Auto Width Type-Retinal Layers
Cell Counting-2 Cell Types
Density Wand Type-Cells
Planar and Contour Conversion
Trace Type-Specimen Area
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.