TissueFAXS Imaging Software

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TF Logo 2017 V1 small  TissueFAXS Imaging Software

TissueFAXS is TGs software for the control of the TissueFAXS and TissueFAXS i systems.

It provides automated scanning capabilities, a state of the art sample viewer and management of the scan projects.

There are configurations of TissueFAXS for scanning slides, microtiter plates, high throughput and for TissueFAXS Confocal.

TissueFAXS software is not available as a standalone version or for the control of other microscopes (upgrades of eligible microscopes to TissueFAXS or TissueFAXS S configuration excepted).


Key icon Simplicity is key

In some large research groups and core facilities TissueFAXS is the most used and booked system for scanning images and digital slides.

This is due to its ease of use.

TG has even been approached with the idea to provide the TissueFAXS software for running a broad range of microscopes. This has not been taken up as such a "fits to everything" product inevitably would compromise the quality and performance of TissueFAXS.

 

TissueFAXS Workflow and automation

TissueFAXS workflow is based on a "preview scan - tissue or region detection - high magnification scan" approach.

Once a solution has been established for a specific batch of slides a profile containing all essential information for scanning this batch of slides can immediately be saved and reused. The profile can very easily be adapted to divergences in the batch. 

The image below shows the principal steps:

 

TissueFAXS imaging software workflow

 

TissueFAXS GUI

 The TissueFAXS GUI is well organised with tabs and static windows.

The Camera and Acquired Images tabs as well as the Preview window can be deployed to become discrete windows, with the camera window usually being deployed to the right screen in the two screen computer setups preferred by TG.

The image below shows the standard TissueFAXS GUI with the camera window integrated and visible as a tab behind the sample viewer.

 

TissueFAXS graphic user interface

 

Tissue Detection

 TissueFAXS software in all configurations provides comprehensive and robust automatic tissue detection (see image below).

 

TissueFAXS tissue detection and settings 

 

To take into account the wide variety of stainings and staining quality as well as the placement of sections on the slide the algorithm providing tissue detection has controls to provide adaptation if needed.

There also are drawing tools to add to or subtract from the automatic result to further fine tune.

If the user does not need an automatic detection of the whole tissue and prefers to identify specific parts of the tissue visually there also are comprehensive drawing tools to set such regions up for scanning.

 

Autofocus, Image Stitching & Illumination Correction

TissueFAXS systems operate with software autofocus. There are two methods, a defined area for one focus point and a focal plane.

The focal plane method has the advantage of haveing smoother focus transitions between its focal points.

The graphic below illustrates the focal plane with a simplified virtual overlay. The focal points are shown as small flags.

 

Focal plane

 

TissueFAXS software also stitches the single field of view images of a sample into a seamless digital slide which is visualised in the viewer.

Illumination correction (also known as "vignetting" or "flat field" correction) is available both in bright field and in fluorescence modes.

 

TissueFAXS scanning speed

TissueFAXS scanning speed is high for automated microscopy. This is supported on the hardware side by cost-efficient, good quality, fast cameras with large sensors, corresponding inllumination systems and SSD drives to rapidly store the images.

The TissueFAXS software is permanently optimized to integrate these often changing hardware devices.

The images below exemplify scanning speeds in brightfield and epifluorescence. The scanning speed of the TissueFAXS Confocal system is exemplified here.

 

1cm2 bf       TissueFAXS speed: 1cm2 fluorescence, 4 channels, 7 minutes 3 seconds

 

Tissue Microarray Imaging

TissueFAXS provides a specialised version of the Tissue Detection algorithm for Tissue Microarray (TMA) scanning. This algorithm recognises TMA blocks on the TMA slide provided that the alleys between the blocks are large enough.

Within each recognised TMA block the algorithm also recognises the logical block structure, i.e. how many rows and columns there are in the block. Based on this the algorithm puts placeholders core markers for missing or damaged cores into the block detection. These crosshatched markers will not be scanned, they only serve to keep the nomenclature of the cores intact.

Blocks can be moved as a whole, scaled in the x and y axes and rotated. Core markers can be moved and resized either individually, in selected groups or for the whole block. 

The images below show some of these operations.

TissueFAXS Tissue Microarray (TMA) autodetection tool results        rotate scale tmablock       resize tma cores

There is fallback manual option for placing markers for a whole block, to be used if the block is too degraded or skewed for automatic block detection to work. All options for moving and resizing the block as described above are also available for the manual option.

 

Z-Stacking & FISH Imaging

TissueFAXS also offers Extended Focus scanning (also known as focus stacking, focal plane merging, z-stacking or focus blending) and z-stacks.

In this method, as series of images above and/or below the actual focal plane of each field of view are also scanned. For each image or channel image this "image stack" is then compressed into one image containing all the areas in focus of the whole image stack, resulting in an optimal image.

This method is essential for FISH analysis as it ensures that no FISH probe above and beneath the actual focal plane is missed.

 

TissueFAXS Extended Focus Scanning ((also known as focus stacking, focal plane merging and z-stacking or focus blending))

 

 The z-stack images can optionally be saved to be used in 3D reconstruction.

 

High Throughput

TissueFAXS software is also used to scan with the TissueFAXS 120 High Throughput system in a special configuration allowing the control and management of the 60 two-slide frames in the magazine of the system.

 

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Cell culture vessel Imaging

TissueFAXS also has a dedicated scanning mode for microtiter plates. The most commonly used plate types are stored as templates in the software and can be activated. The well regions are then automatically established in the right place for scanning (first image).

There also is an inbuilt editor for creating more microtiter plate templates.

The well regions are also automatically named (2nd image). Whole well areas or groups thereof can be resized and moved, there is also an option to draw in one or a group of other regions (subregions to a well region, rectangular, spherical or polygonal) into the first well region and then propagate these into all or a selection of the other well regions.

 

 TissueFAXS standard microtiter plate well regions     TissueFAXS microtiter plate well regions automatically named

 

Finally, the well rgions or their subregions can be scanned (3rd image) and the scans results can then be passed on to TG analysis software to be analysed (TissueQuest in the 4th image).

 

TissueFAXS i 8 Slides 1 microtiter plate scanning     Whole well analysis

 

Question head 70x70Want to know more about TissueFAXS imaging software?

Please just let us know.

 

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