Tour 1: Basics

designed for beginners

This chapter should help you to go familiarly with the Pannoramic scanners P250, SCAN 150, MIDI and DESK and to do the first steps in optics, brightfield illuminated and fluorescent excited microscopy.

Overview of Pannoramic scanners

Use Microscope or Scanner instead?

In our descriptions, the term “microscope” and “scanner” is often used likewise. All of our microscopes are scanners also and all of our scanners include magnifying of the tissue like a microscope does. Often the relevant expression is used to focusing the attention to the more important task at the appropriate moment, but this is not done consequently. So we can assume, the used term “microscope” or “scanner” has no important difference in our aspects.

What is a scanner?

The term “scanner” used by 3DHISTECH includes a microscope unit to magnifying the object (tissue) to be scanned. The tissue itself is scanned FOV by FOV (FOV means field of view; the area of the tissue, captured by the scan camera with 1exposure) and then, these fields are assembled by the software to a virtual slide (or virtual tissue).

To reach this, because each virtual tissue may be assembled from more 100 FOVs, the tissue must be moved in X- and Y-direction in relation to the objective pupil. So we can say, the X-Y-stage unit, equipped with the specimen holder is a part of the scanner.

In opposite to this, the focus unit (contains the objective, the condenser and the focusing mechanics) is a part of the microscope unit; a part of the optical path.

Both units are mounted together on the scanner plate and the assembled scanner plate makes the scanner unit.

This example shows that the term is floating or, the boarder between scanner and microscope can often not be defined exactly.

Watch video: Scan a tissue_P250

A short history

The development of the first scanner started in the early 2000’s years.

The goal should be to create a microscope that is able to scan glass slides with tissues automatically; to creating a virtual tissue and this virtual tissue (or virtual slide) should be stored on a HDD.

Furthermore, the removal of the finished slide and the insertion of the next slide to be scanned should be done automatically, without interaction of the user.

Allowed slide dimensions was defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

After some development and test versions, the scanner MIRAX SCAN was born in the year 2004.

If the scan procedure of a slide is finished, the virtual slide (the result of the scan process) can be made visible on the computer screen with the viewer program.

The viewer program with its various features and options is used to analyze, qualify and to prepare the virtual tissue with annotations regarding interesting or abnormal passages in the tissue.

Pannoramic viewer options and features; today

· 3D

· OnlineTeleconsultation

· TMA

· FLViewer

· BookmarkExport

· IHLab the new name is “TumorBoard”

· HistoQuant

· DataVisualisation

· MarkerCounter

· CytoFISHQuant

· NuclearQuant

· MembraneQuant

· TumorBoard

MIRAX SCAN

This scanner (distributed and serviced by Carl Zeiss G.m.b.H) uses magazines with 50 slide positions, and 6 magazines could be loaded in the input stack. With this solution, 300 slides could be scanned during 1 scan session.

· Since 2004 on the market

· The slides are hold in magazines with 50 slide positions

· 6 magazines can be hold in the input / output stack during 1 session.

· Designed for brightfield an fluorescent scan sessions.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

The SCAN exists in a full version (SCAN_FL) where the Reflector turret unit is included and a more cost-effective version (SCAN _BF) without the Reflector turret unit, so only brightfield scan sessions are possible.

Today, these machines are almost all upgraded to the version SCAN 150.

The magazines used in the scanners “MIRAX SCAN”, before upgrading to SCAN 150

· The magazine contains 50 slide positions

The external dimensions of the magazines are unchanged; only the construction of the slide positions was modified and changed to the half.

“SCAN 150”, “Pannoramic SCAN” and “P250” scanners using all the same type of magazines.

· To reduce the amount of different magazines, all the magazines with 25 slide positions has a permanent magnet implemented, but this magnet acts only in the P250.

SCAN 150

To improve the slide loading stability of the MIRAX SCAN the magazine and the slide loading mechanics was modified for the use of magazines with only 25 slide positions. This way, the stability of the slide insert and slide removal procedure could be improved.

· Since the end of the year 2008 on the market; almost all MIRAX SCAN scanners are upgraded to this version.

· The slides are hold in magazines with 25 slide positions; the useable slide dimensions are unchanged.

· 6 magazines can be hold in the input and output stack during 1 session.

· Designed for brightfield and fluorescent scan sessions.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

The SCAN 150 exists in a full version (SCAN_FL) where the Reflector turret unit is included and a more cost-effective version (SCAN _BF) without the Reflector turret unit, so only brightfield scan sessions are possible.

MIRAX DESK

For small pathology laboratories the MIRAX DESK version was created. This scanner contains in practice a scanner unit only and the slides are inserted or exchanged manually; the fluorescent illumination unit (Reflector turret unit) is left out.

· Since 2006 on the market

· The slides are inserted or removed manually via the slide door.

· Used in small laboratories with a small amount of slides to be scanned.

· Designed for brightfield scan sessions only.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

MIRAX MIDI

The two versions, MIRAX SCAN and MIRAX DESK are used in very big and very small pathology laboratories. The users asked for a machine that can be used in middle large laboratories, where the manual handling of slides is too slow and the capacity of the MIRAX SCAN is not efficiently used.

These requirements resulted in the MIRAX MIDI.

· Since 2007 on the market

· The slides are inserted / removed automatically, via a slide holder tray.

· 12 slide bays in the slide holder tray allowing an automatic scan session of about ½ to ¾ hour, depending on the tissue size.

· Used in laboratories with middle large amount of slides to be scanned.

· Designed for brightfield scan sessions and fluorescent scan sessions likewise.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

The MIDI exists in a full version (MIDI_FL) where the Reflector turret unit is included and a more cost-effective version (MIDI_BF) without the Reflector turret unit, so only brightfield scan sessions are possible.

Slide tray of the MIDI; allows an automatic scan session of about ½ to ¾ hour, depending on the tissue size and the speed of the scan camera.

At the end of the year 2009 the contract with Carl Zeiss G.m.b.H was finished. Because MIRAX™ is a trademark of Carl Zeiss G.m.b.H, the name “Pannoramic” (a combination of Pannonia (Latin name of Hungary), panorama and microscope) was created for our products.

In this time, the name of the scanners changed to Pannoramic SCAN, Pannoramic MIDI and Pannoramic DESK and 3DHISTECH contracted distributors world wide for distribution and services of Pannoramic scanners and 3DHISTECH products.

· Since 2009 on the market

· The slides are hold in magazines with 25 slide positions

· 6 magazines can be hold in the input / output stack during 1 session.

· Designed for brightfield an fluorescent scan sessions.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

· Today, all references to the SCAN, PSCAN or SCAN150 referring to this version of scanner.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

· Since 2009 on the market

· The slides are inserted / removed automatically, via a slide holder tray.

· 12 slide boxes in the slide holder tray

· Used in laboratories with middle large amount of slides to be scanned.

· Designed for brightfield scan sessions and fluorescent scan sessions likewise.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

· Since 2009 on the market

· The slides are inserted / removed manually via the slide door.

· Used in small laboratories with a small amount of slides to be scanned.

· Designed for brightfield scan sessions only.

· The scan speed depends highly on the used computer configuration and the speed of the camera.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

The P250 includes all possibilities and features like different camera selection for fluorescent scan sessions and brightfield scan sessions software controlled, selection of the objective 20x or 40x magnification for brightfield and fluorescent scan sessions likewise.

· The possible slide thickness was extended to be 1.20mm maximal

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.20 mm

· Since 2011 on the market

· The slides are hold in magazines with 25 slide positions

· 9 magazines can be hold in the input / output stack and 1 magazine in the feeder channel, so the amount of slides in 10 magazines can be scanned during 1 session.

· The specimen holder is modified; so slides with a thickness of 1.20mm can be inserted.

· Flashlight BF illumination and the use of higher speed cameras allows higher scan speeds.

· Designed for brightfield an fluorescent scan sessions.

· Exchange of the objective 20x or 40x magnification; software controlled between 2 slide scan sessions.

· Exchange of the camera, software controlled, between BF and FL slide scan sessions.

The P250 exists in a full version (P250_FL) where the Reflector turret unit is included and a more cost-effective version (P250_BF) without the Reflector turret unit, so only brightfield scan sessions are possible.

· In opposite to the SCAN, the presence of the permanent magnet is now required.

The permanent magnet signals in the magazine input stack the presence of a magazine while in the output stack the state “output stack full” is so detected.

The Pannoramic Confocal (PCON) scanner is the youngest member of the Pannoramic scanners family and gives the possibility to scan slides in confocal mode.

The scanner is based on a modular MIDI scanner and uses a Spinning Disk System to create a reflected and a passed thru image path. By subtracting the two generated images of the same field of view from each other, light rays, created by elements out of focus can be eliminated from the observed field of view and the depth of sharpness will be increased.

Since 2014 on the market

· The slides are inserted and removed automatically via a slide holder tray.

· 12 slide bays in the slide holder tray allowing a more or less autonomic work of the scanner.

· Used in laboratories with middle large amount of slides to be scanned and for research and development purposes in pathology, pharmacy and biology.

· Designed for brightfield scan sessions, fluorescent and con-focal fluorescent scan sessions.

Allowed slide dimensions are defined as:

Length: 75.00 to 76.00 mm

Width: 25.00 to 26.00 mm

Thickness: 00.95 to 01.05 mm

Slide holder tray of the PCON; it allows an automatic scan session of about ¾ to 1 hour, the scan time of the entirely filled tray depends highly on the tissue size .

Optics and illumination

For beginners (as well as for experienced technicians) it is very important to know the influence of optical means like lenses, mirrors and filters on light rays; the most efficient illumination of the tissue and other techniques in microscopy.

A lot of excellent prepared explanations about optics, illumination, microscopy, brightfield illuminated and fluorescent excited scan methods and others can be found in the internet.

The second main part is fine mechanics, stepper motors and step control of stepper motors.

The following chapters are highly recommended:

Ernst Abbe und das Mikroskop YouTube German language

Bildentstehung bei der Sammellinse © Dr. Andreas Rueff more chapters, German; Schrittweise, graphische Erläuterung der Bildentstehung bei Verwendung von Linsen

Picturing by converging lens YouTube with English subtitles; explanations are also visualized graphically in steps

Image Formation with Converging Lenses Interactive Java tutorial

Other chapters related to optics and microscopes are also very interesting and the interactive tutorials are very helpful to understand the behavior of the light rays.

Bayer mosaic and “Debayering” see: “Bayer filter” Wikipedia