A “Hands-on Workshop on FISH and its application in Pathology and Clinical Medicine” was organized by MetaSystems and Department of Pathology, Himalayan Institute of Medical Sciences (HIMS) to demonstrate the applications of FISH in hematological malignancies and solid tumors.
Pathology and Tissue Imaging
- Sample Digitization
- Digital Pathology and FISH
MetaSystems has designed a system of FISH, imaging, and visualization tools to be integrated in the routine workflow of pathology labs. Smart slide scanning, networking, and documentation of results help to generate faster and better diagnoses.
The renowned scanning platform Metafer combines the advantages of a motorized microscope with modern, high-quality imaging automation. Therefore, the system is not restricted to certain magnifications or contrasting modes. Even Z-stacks can automatically be acquired, thus, providing the possibility to virtually 'focus' through the digitized sample.
Sample digitization with Metafer is very easy. The system automatically reads and interprets bar code labels and uses the encoded information to perform smart, multi-stage scanning workflows. Alternatively, dedicated imaging protocols can be provided from external software, e.g.by a LIMS. All images are accessible immediately after scanning and can be opened on any workstation with the free viewer software.
Though Metafer's virtual slides are stitched from individual image fields to achieve an unrivaled image quality, the system is extremely fast. A combination of a high-resolution camera, ultra-fast scanning hardware, and the high-capacity SlideFeeder x80 make Metafer the fastest, yet most precise system of its kind.
Metafer’s flexibility predestines the system for being used for complex and particular imaging tasks, within pathology and beyond. No matter whether diatom images from the sea floor shall be visualized and identified, or fruit fly larvae are to be detected and digitized using a combination of Nomarski phase contrast and fluorescence – there is almost no conceivable imaging application Metafer could not cover.
Based on the wishes of users and lab managers, MetaSystems has developed a dedicated system to analyze FISH signals in tissue sections. Core of the MetaSystems solution is a combination of dedicated DNA probes (MetaSystems Probes‘ XL range of locus-specific FISH probes target amplifications, deletions, or translocations of gene regions involved in solid tumors) with the innovative platform Neon Metafer.
The analysis workflow is based on the powerful analysis engine of Metafer, extended with a new, convenient analysis environment. The user interface supports either conventional mouse control or the optional interactive pen display.
As initial step a digital brightfield, e.g. H&E slide is generated by Neon Metafer. The pathologist calls up the digital slide and selects on screen the tumor region on the virtual slide that needs to be FISH-scored.
Next, the FISH slide (from a subsequent section of the same block) is being scanned at low magnification to generate an overview. Displayed side by side to the marked digital H&E image the tumor region can easily be transferred to the FISH slide.
Neon Metafer now has all the information to start automatic image acquisition of the FISH slide at higher magnification. Cell nuclei that are isolated or slightly connected will be separated automatically and spot-counted. Manual tools for segmentation help to separate touching nuclei for immediate automatic scoring until the preset number of cells to be analyzed has been reached. The module can be easily set up to match the individual analysis standards. For instance, it is possible to define a minimum number of cells to be analyzed, and also to define a number of independent readers.
For final review the system presents a full synopsis to the pathologist, comprising the cell gallery with the scoring results, the virtual DAPI slide showing the positions of analyzed cells, and the corresponding H&E virtual slide. Every cell can be traced back to the tissue section to confirm its location within the preselected tumor region. Final results can either be exported as raw data, allowing for being processed in external software, or be summarized in comprehensive, user-adaptable reports.
Once a pathology sample is digitized, it can be easily shared with others. The Metafer image file format makes this even more convenient: it contains a lot of additional information, e.g. on focus planes, on analyzed cells and signals, on annotations, and much more. Thus, any colleague who has access to the file, and who is opening the image in the viewer, can see all this information. Additionally important image and meta data are stored digitally, and can be retrieved anytime for inspection.
But MetaSystems can do even more for the pathologist: how about sharing your data with your colleague abroad? How about teaching your students from your home? How about sharing an example gallery of interesting cases?
The Virtual Microscope Database (VMD) is a browser-based software solution for the display of digital sample images. To access an image database, no extra hard- or software is needed – just a valid user account provided by the administrator. Images can be loaded, visualized, and annotated online. Meta data can be entered by any authorized user in customizable forms. The integrated conferencing module allows for collective sessions over the same image, including a convenient IRC function.
VMD is highly secure, as all users have defined roles and corresponding access rights (e.g., supervisors, workers, read-only users). Data are organized in institutes, and each institute is only accessible for and even only visible to the authorized users. This way many groups can easily share the same VMD server without the risk of interference.