TissueQuest 4.0 – A short description
TissueQuest 4.0 is a new version which is much better integrated into the TissueFAXS-System workflow than anterior versions. The analysis paradigm is the same, however, so there is no need to learn a completely new workflow.
Main features
- Completely new user interface which allows the user to see and navigate a zoomable digital slide.
- Regions of interest, annotations and exclusion regions, drawn onto this digital slide, allow for greater precision and ease of analysis.
- Enhanced calculation speed due to better usage of multi-core computer workstations.
- Analysis of FISH and other “Dot in the Cell” data as mRNA, displaying results in Pathology-oriented list view, export to Excel.
- Import scan projects from Mirax and Pannoramica line scanners and analyze them in TissueQuest
- Load more samples of the same type into the analysis project, use analysis templates and profiles to re-use proven settings.
- Use of Calculated Parameters to measure ratios and the Percentile measurement parameter for intensely stained within the Measurement Mask.
- Three data export modes (Print Report, Raw Data list, Statistic Report).
- Compare Sets for side by side or overlay graphic data comparison.
- Comparative analyses of consecutive sections with different markers on the same tissue areas using Image Compare Sets.
- Fully controllable colour and thickness of all contours on the images.
- Full TMA support for fast analysis with comprehensive data export.
Modularity
TissueGnostics has made major efforts to equip its users with Software that is tailored to their needs. As the final result TissueQuest 4.0 is modularized. Taking into consideration the different applications of image analysis software around the globe, TissueGnostics defined 6 module-packages:
- Module 1 - Histology
- Module 2 - Nuclear Counting
- Module 3 - Cells & Cytoplasm
- Module 4 - Diagnostics
- Module 5 - Diagnostics Xtended
- Module 6 - TMA
Histology Module
This entry module provides the capability to import original fluorescent gray-scale images from each filter used and draw individualised regions of interest (ROI's) to measure stained areas in a sample. It also features an annotation tool. Data display is in histograms and raw data can be exported to Excel or PDF.
Stand-alone or incombination with any other module
Nuclear Counting Module
Similar to the histology module, the nuclear counting module additionally allows users to quantify stained nuclei and measure several analytical parameters, such as area and staining intensity of nuclei.
Basic module for the modules 3 to 5
Cells & Cytoplasm Module
This module adds more cell-structured analysis to the entry modules: ring mask around the nucleus and cell mask detection of cytoplasmatic markers is available through a growth algorithm. Data can now also be displayed in scattergrams.
Add-on to anterior modules
Diagnostics Module
This module additionally provides virtual channels for comparative measurements in nuclear versus cytoplasmatic compartments and a report generator. Compare sets allow the graphical comparison of diagrams. Tools such as a ruler and a scale bar make exact sample measurements possible. Propagation & grouping of ROI's makes analysis of consecutive cuts simpler and faster.
Add-on to anterior modules
Diagnostics Xtended
The entire features and capabilities (excluding TMA analysis) of the Software are provided: in addition to the diagnostics module, further automation is possible using a cutoff suggestion for the separation of positive and negative populations in the diagrams. Scattergram and histogram results can be controlled visually by using the forward and backward connection in conjunction with the images. Images can now also be imported from specific scanners and be compared using the multi-sample-viewer. A manual correction tool allows manipulation of the identified nuclei and specified regions can be excluded from analysis. Finally, ROI's and annotations can be produced quicker and more extensively with the easy-ROI tool.
Add-on to anterior modules
TMA Module
This module provides full analysis capabilities including Tissue Microarrays. TMA scanning projects from the TissueGnostics product line TissueFAXS/HistoFAXS can be imported with each spot, block or slide already identified and named. The spots in TMA images from other systems can be identified with several features, allowing for automatic detection or manual selection.
Add-on to any other module
TissueQuest - Cell Analysis Software
TissueQuest is the first software solution worldwide to identify and analyze individual cells in their native tissue environment. It supports any number of fluorescent markers used for this purpose.
Cell identification is not confined to isolated cells. TissueQuest also identifies cells that are agglomerated in dense clusters or have been reduced to ring structures (as is typical of cancer cells).
With Tissue Quest, we offer our customers a unique diagnostic tool. This is the first time that tissue can be mapped and analyzed in a truly objective and reproducible manner.
Regardless of the type and density of cells involved, TissueQuest recognizes their nuclei due to patented image processing algorithms.
By combining specific stainings and algorithms, one can measure staining intensities that are specific for various cell types.
TissueQuest can be used as stand alone application.
Cells are clearly distinguished even:
- in solid tissue structures
- if embedded in clusters
- if nuclei are uniformly stained
- if staining involves ring structures
RNA Analysis
Identifying individual cells
Selecting cellular staining patterns
Individual cells are identified by capturing distinctive staining patterns (such as nuclei, ring structures and cytoplasm). These patterns can be freely selected by the user. A dedicated master channel to identify nuclei is used for cell segmentation.
Different mask options and quantitative analysis
Analysis of staining intensities can be restricted to the area of the nucleus or can be extended into the cytoplasm. In case of cytoplasmic antigens TissueQuest provides an image processing algorithm that is growing in stained areas around the nucleus.
Representation of Data
Identified cells are immediately displayed on screen as scattergrams, indicating surface area/DNA and staining intensity. Just like in flow cytometry, each dot illustrates one individual cell.
For further analysis, cutoff parameters need to be defined based on the negative control. Then gates are set to define which parameters will be analyzed.
Any cutoffs thus defined can be conveniently copied to the other scattergrams. Several gate settings within the same scattergram can be related to each other. Their shape and color can be individually readjusted.Effective Analysis
The results are immediately displayed after setting the gates.
Calculated parameters include mean intensity, relative/absolute events, and percentage of reactive cells.
The data are output in tabular format broken down into quadrants (UL-Upper Left, UR-Upper Right, LL-Lower Left, LR-Lower Right). In the past, this type of representation could not be modified by adjusting the parameters. With TissueQuest 2.0, however, any modifications made to the cutoffs and/or gates will promptly update the results.
Backward and Forward Gating
TissueQuest offers an innovative function for visual and measurement control.
Backward Gating enables the user to connect backwards from a dot in the dotplot to the specific corresponding cell in the image. By Forward Gating the user is able to locate the dot in the plot corresponding to a specific cell in the image. The function “View event data” reads out all measurement data for an individual cell.
Numerous Applications
Specific cells or cell populations contained in fluorescence-labeled tissue specimens are individually analyzed for specific parameters such as surface-expressed or intracellular molecules.
TissueQuest covers a wide range of possible applications. Here are just a few analysis solutions:
- Individual cells
- Individual cells in tissue
- Individual cells with ring structures
- Individual cells in clusters
- Cytoplasm
Features
- TissueQuest can load complete TissueFAXS projects or import any series of .tif or .jpg images for analysis
- Powerful image processing algorithms for the identification of single cells in tissue based on nuclear staining
- Automatic generation of ”cell body” (cytoplasmatic) masks for intensity measurements
- Complete set of manual modification and correction tools (splitting, merging, deleting and creating nuclei)
- Powerful DotPlot operations -Forward Gating of cells to the DotPlots and Backward Gating of dots, gates or cutoff quadrants to the image
- Unlimited custom DotPlot and histogram generation, also based on gates in existing DotPlots, allow for near-unlimited new analyses and refinement of existing ones
- Extensive printed report and data export options
Attention: Consult operating instructions for use!