3D Histech Pannoramic 250 FLASH III User manual

Pannoramic 250 FLASH
1.14 SP1
User’s Guide
March 30, 2011
Rev. 1

Pannoramic 250 FLASH 1.14 SP1 User’s Guide
Contents
Disclaimer....................................................................................................................... 5
Charac er Forma s and Symbols.......................................................................................7
1 Produc Descrip ion...................................................................................................... 8
1.1 Product Overview......................................................................................................................8
1.1.1 Intended Use....................................................................................................................................................8
1.1.2 Features and Benefits.......................................................................................................................................8
1.1.3 Main arts of the Base Unit.............................................................................................................................9
1.2 System Overview......................................................................................................................10
1.2.1 Pannoramic 250 FLASH system......................................................................................................................10
1.2.2 Hardware O tions..........................................................................................................................................11
1.2.3 Control Software............................................................................................................................................15
2 Ins alla ion................................................................................................................. 17
2.1 Control com uter orts...........................................................................................................17
2.2 Connectors and cables.............................................................................................................18
2.3 Mounting the Lumencor S ectra unit......................................................................................18
3 Opera ing Slides and Magazines..................................................................................21
3.1 Pre aring Slides and Magazines..............................................................................................21
3.2 Affixing Barcode Stickers to Slides...........................................................................................22
3.3 Inserting and Removing Slides.................................................................................................23
3.3.1 Insert slides into a magazine..........................................................................................................................23
3.3.2 Insert and remove magazines........................................................................................................................24
3.3.3 O ening/Closing the FL rotective cover.......................................................................................................27
4 Sof ware Descrip ion.................................................................................................. 28
4.1 Starting / Exiting Pannoramic Scanner Software.....................................................................28
4.1.1 Starting the software......................................................................................................................................28
4.1.2 Exiting the software........................................................................................................................................29
4.2 O tions.....................................................................................................................................29
4.2.1 Barcode Settings.............................................................................................................................................29
4.2.2 Image Com ensation.....................................................................................................................................33
4.2.3 Microsco e Settings.......................................................................................................................................36
4.2.4 External A lication Call Settings...................................................................................................................41
4.3 Using Brightfield Manual Mode...............................................................................................42
4.3.1 Routine work tab............................................................................................................................................43
4.3.2 Scan O tions window.....................................................................................................................................45
4.3.3 Preview tab.....................................................................................................................................................46
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide
4.3.4 Preview area scanned by review camera.....................................................................................................49
4.3.5 Focus tab........................................................................................................................................................56
4.3.6 Service tab......................................................................................................................................................58
4.3.7 Dis lay field and toolbar for live images........................................................................................................59
4.3.8 Start Scan........................................................................................................................................................61
4.4 Using Brightfield Automatic Mode..........................................................................................62
4.4.1 Routine work tab............................................................................................................................................62
4.4.2 Barcodes tab...................................................................................................................................................64
4.4.3 Preview tab.....................................................................................................................................................68
4.4.4 Focus tab........................................................................................................................................................69
4.4.5 Service tab......................................................................................................................................................70
4.4.6 Start Scan........................................................................................................................................................71
4.5 Using Fluorescent Manual Mode.............................................................................................73
4.5.1 Routine work tab............................................................................................................................................73
4.5.2 Scan O tions...................................................................................................................................................78
4.5.3 Preview tab.....................................................................................................................................................82
4.5.4 Preview area scanned by review camera.....................................................................................................84
4.5.5 Hardware tab..................................................................................................................................................85
4.5.6 Service tab......................................................................................................................................................88
4.6 Using Fluorescent Automatic Mode........................................................................................90
4.6.1 Routine work tab............................................................................................................................................90
4.6.2 Barcodes tab...................................................................................................................................................95
4.6.3 Preview tab.....................................................................................................................................................99
4.6.4 Focus tab......................................................................................................................................................100
4.6.5 Service tab....................................................................................................................................................100
4.7 Scan To Server........................................................................................................................102
4.8 Using Profiles.........................................................................................................................108
5 Troubleshoo ing and Main enance............................................................................110
5.1 Safety Information.................................................................................................................110
5.1.1 Cleaning the device......................................................................................................................................111
5.1.2 Cleaning the magazine.................................................................................................................................111
5.1.3 Preventive maintenance...............................................................................................................................111
5.2 Troubleshooting.....................................................................................................................112
5.2.1 Fluorescent A lications (o tional).............................................................................................................114
5.3 Maintenance..........................................................................................................................115
5.3.1 O ening the rotective cover.......................................................................................................................115
5.3.2 Re lacing fuses of the main ower switch...................................................................................................116
5.3.3 Re lacing Lam Module (for Fluorescent O tion).......................................................................................117
5.3.4 Removing a slide...........................................................................................................................................119
5.3.5 Installing and Removing the Filter Module (Fluorescent O tion)................................................................121
5.3.6 Removing a Magazine from the Trans orting System..................................................................................122
5.3.7 Trans orting.................................................................................................................................................124
Technical Da a............................................................................................................. 126
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide
Index........................................................................................................................... 130
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide
Disclaimer
Co yright © 2001-2011 3DHISTECH Ltd.
All rights reserved.
Intellectual ro erty related to the 3DHISTECH roducts are as follows:
EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007-
516451; US7,327,515; EP 1,994,398; JP 2008-557835; US 12/281,566; U0700210; US 6,246,785;
HU0900142; HU0700404; PCT/HU2007/000065; EP 08762668.5; US 12/663,537;
PCT/AT2006/000492; JP 2008-542552; EP 06817469; US 12/095,545; PCT/AT2006/000493; EP
06817470.5; US 12/095,596; HU0900741; US 61/264,732; US 11/826,752; P0401870;
PCT/IB2005/050344; US 11/662,976; HU0700409; US 12/042,050; US 77/636,144 and 007502032.
The above mentioned granted atents, granted utility model, registered trademarks, ending
international and national atent a lications and the other corres onding IP are the sole ro erties
of the 3DHISTECH Ltd.
3DHISTECH L d. is no liable for damage of wha ever na ure (including, bu no limi ed o, general
or specific damage, indirec damage, consequen ial damage or inciden al damage, including he
resul s of he analysis of he digi ized slides, for example, change of heal h s a us rela ed o
erroneous diagnosis from he digi alized slide(s)) ha s ems from or is associa ed wi h use of
Produc , digi alized slides, quali y of s aining, quali y of s ained slides, quali y of used me hod of
s aining. 3DHISTECH L d. assumes no responsibili y for he func ionali y and faul -free condi ion of
your “applica ion programs” (Workflows, VBA macros, Commander scrip s).
CAUTION
For research and education uses only, not for use in diagnostic rocedures. This roduct has not been
a roved or cleared as a medical device by the U.S. Food and Drug Administration, nor any other
regulatory authority. The data and images obtained or viewed using this roduct are not intended for
clinical or diagnostic use.
For erformance evaluation only, the erformance characteristics of this roduct have not been
established.
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide
Third-Party Disclaimer (LibTIFF – TIFF Library and Utilities)
3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general or
s ecific damage, indirect damage, consequential damage or incidental damage, including damage
resulting from lost rofits, interru tion of business, loss of business information, ecuniary loss or
similar damage) that stems from or is associated with the incor orated art of this Product that is
made by Silicon Gra hics Inc.
THE SOFTWARE IS PROVIDED “AS IS” AND WITHOUT WARRANTY OF ANY KIND, EXPRESSED,
IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL, INCIDENTAL,
INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR FOR ANY DAMAGES WHATSOEVER
RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY
OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE
USE OR PERFORMANCE OF THIS SOFTWARE.
Fur her Informa ion
For the latest information on 3DHISTECH roducts and services, lease visit our website at the
following URL: htt ://www.3dhistech.com .
Com any Address: 29-33 Konkoly-Thege Miklos street, Building 18
1121 Buda est – HUNGARY
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide Character Formats and Symbols
Charac er Forma s and Symbols
Example Words or characters that a ear on the screen. These include field names, screen
and window titles, ushbuttons and menu names, aths or o tions.
Keys on the keyboard. For exam le, function keys (such as F11) or the C rl+M key
combination.
Example Cross-references to other documents.
Warning! It might cause irreversible damage or harm to the user of the roduct or the
roduct itself if this instruction is not followed.
Cau ion! It might cause the roduct not to work ro erly if this instruction is not followed.
No e: Calls attention to some im ortant features.
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
1 Produc Descrip ion
1.1 Produc Overview
1.1.1 In ended Use
Pannoramic 250 FLASH is designed to use transmitted light and reflected light fluorescence to digitize
biological sam les and s ecimens (ty ically histological sections). The target users of the roduct can
work for exam le, in education, research, industry or medical sectors.
1.1.2 Fea ures and Benefi s
The Pannoramic 250 FLASH offers world class brightfield and fluorescent whole slide scanning on u
to 9 channels.
An outstanding 0.16 µm / ixel resolution is achieved with 0.95 NA (equivalent to 62× magnification)
Carl Zeiss Plan-A ochromat objective.
Key features of the Pannoramic 250 FLASH Scanner:
•Extreme fast brightfield scanning mode:
•Continuously moving stage during scanning
•The new brightfield camera sees 30% larger field of view with better ixel resolution
and has double frame rate
•Light source is a Xenon flash lam
•Im roved image quality:
•Image shar ening feature which im rove the visual a earance of digital slides
•New faster focus algorithm find the focus which is more a ealing to the human
eye
•Motorized camera changer for a 3CCD camera for brightfield and a cooled monochrome CCD
camera for fluorescence
•Motorized Objective changer for two objectives
•10 times higher resolution for barcode reading and review image
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
•Com act design:
•Cameras are laced inside the unit
•Built-in ower su ly
•Fewer cables
•Im roved fluorescent scanning mode:
•3 times faster and more silent filter change
•Magazine stack cover to rotect every slides against hoto bleaching
•250 slide automatic loading and scanning
This device is recommended for customers, who need high quality daily through ut granted by the
biggest loading ca acity of 250 slides. The device has many advanced im rovements like software
controlled motorized camera- and objective changer, and high resolution color review.
1.1.3 Main par s of he Base Uni
The following figures show the main arts of the base unit.
Figure 1 – Main parts of base unit
1. Protective FL cover
2. In ut and out ut stack for magazines
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
3. Cover release hole
4. Power su ly switch
5. Main ower switch
6. Power su ly cable connector
1.2 Sys em Overview
The standard sco e of delivery of the roduct includes the following hardware and software
com onents.
1.2.1 Pannoramic 250 FLASH sys em
The following figure shows the main arts of the Pannoramic 250 FLASH system.
Figure 2 – Pannoramic 250 FLASH system overview
1. Pannoramic 250 FLASH base unit
2. monitor
3. mouse
4. control com uter
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
5. keyboard
6. slide magazine with cover
7. HXP 120 fiber-cou led fluorescent illuminator (o tional)
8. Lumencor S ectra illuminator (o tional)
1.2.2 Hardware Op ions
The configuration of the control com uter and monitor can vary de ending on the roduct order.
Cameras
AxioCam Mrm Rev 3
1 CCD scientific, cooled, monochrome camera for
high quality, sensitive fluorescent a lications.
CIS VCC-F52U25CL
3 CCD camera for high-quality brightfield
a lications allowing fast scanning.
Camera adap ers
0.63x ada ter 1x ada ter
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
Camera changer
Figure – Camera changer
You can fit two cameras into the Pannoramic 250 FLASH on the first ada ter (1) (fluorescent osition)
and the second ada ter (2) (brightfield osition) at the same time. They are set and switched by the
software automatically, without any human assistance.
This system also enables switching between brightfield and fluorescent scanning by one click.
Warning!
The installation of the cameras in Pannoramic 250 FLASH must be
carried out by trained rofessionals!
In any other case the warranty will be automatically voided.
Su lier/Distributor is not liable for any damages caused by an
installation not carried out by rofessional erson.
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
Objec ives
Figure 4 – Objective changer
You can select two different objectives to be equi ed with the Pannoramic 250 FLASH, the first
objective (1) and the second objective (2).
20x/NA 0.80 and 40x/NA 0.95 objectives can be used; you can change between the objectives with
one click. This hel s you to select the magnification and resolution that is the most suitable for your
requirements.
Impor an !
Note, that higher resolution results in slower digitization rocess.
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
Preview
Figure 5 – Preview camera (1), Brightfield preview (2) with Dark-field preview ( )
At fluorescent sections the dark-field review makes the fluorescent sam les detectable even for the
user and for the automatic marking algorithm. By detecting the sam le the fluorescent scanning will
be much faster since the software will not waste time on em ty FOVs.
Base Uni op ions
•Pannoramic 250 FLASH Base Unit
•Pannoramic 250 FLASH Scan O tion – base unit equi ed with CIS VCC-F52U25CL camera
for Brightfield scanning (no fluorescent accessories included)
•Pannoramic 250 FLASH Fluorescence O tion – base unit com letely equi ed with CIS VCC-
F52U25CL camera for Brightfield scanning, and with AxioCam camera, HXP 120 or Lumencor
fluorescence illuminator, trigger cable and filters for fluorescence scanning
NOTE: In case Lumencor light source is ordered, the custom light source and filter modules
can be variable. For more information, lease contact 3DHISTECH customer service.
Objec ives
•Plan-A ochromat 20x/0.8
•Plan-A ochromat 40x/0.95 Corr
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
Fluorescen Op ions for Pannoramic 250 FLASH
Fluorescent unit (internal art)
HXP 120 illumination unit
Lumencor S ectra 7 Light Engine
illumination unit
1.2.3 Con rol Sof ware
•Pannoramic Scanner control software
Op ional:
•Fluorescence
•Extended focus
•Z-stack
•Barcode reader (licensed feature)
•Scan To Server
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product escription
•Pannoramic Viewer software (fully functional)
Op ional:
•Fluorescence slide viewer (built-in with hardware, o tional without hardware)
•CaseCenter
•Pannoramic Viewer TMA module
•3D Reconstruction module
•HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, DensitoQuant modules
•ImmunoScreener module
•E-School Encoder
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation
2 Ins alla ion
Warning!
The installation of Pannoramic 250 FLASH must be carried out by
trained rofessionals!
In any other case the warranty will be automatically voided.
Su lier/Distributor is not liable for any damages caused by an
installation not carried out by rofessional erson.
Only qualified service assistants are allowed to install the hardware and software. The roduct is
ready for use after installation.
The following figures show the location of the connectors in order to enable easier trans ortation of
the roduct for a short distance, by disconnecting cables and detaching hardware com onents from
each other.
2.1 Con rol compu er por s
Figure 6 – Ports on control computer
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation
1. Status dis lay
2. DVD drive (RW)
3. Power on/off button
4. Ear hone and micro hone 3.5mm Jack orts
5. 2x USB ort
6. Power su ly connector
7. PS/2 mouse ort
8. PS/2 keyboard ort
9. 4x USB ort
10. 2x USB ort
11. Network ort
12. Matrox Solios CameraLink orts
13. 2x FireWire ort (IEEE 1394 A/B)
2.2 Connec ors and cables
•Control – USB (between scanner and control com uter)
•Preview camera – FireWire 1394 A cable (between review camera and control com uter)
•AxioCam – FireWire 1394 A cable (between AxioCam camera and control com uter)
•CiS – a air of CameraLink cables (between CiS camera and control com uter)
•Video cable (between monitor and control com uter)
•Power su ly cable (between 230V/110V and monitor)
•Power su ly cable (between 230V/110V and control com uter)
•Power su ly cable (between 230V/110V and Pannoramic 250 FLASH main unit)
•O tical cable (between fluorescent illuminator and scanner)
•Trigger cable (between AxioCam and fluorescent illuminator)
•Power su ly cable (between 230V/110V and fluorescent illuminator)
2.3 Moun ing he Lumencor Spec ra uni
To o erate the Lumencor S ectra unit, it has to be attached to the Pannoramic 250 FLASH base unit.
1. Switch off the main ower su ly on the rear anel of the Pannoramic 250 FLASH and
disconnect the ower cables (see section 1.1.3 Main parts of the Base Unit).
2. O en rotective cover (see section 5.3.1 Opening the protective cover).
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation
3. Find the mounting hole (1) at the back side of the Pannoramic 250 FLASH unit and rotate the
Lumencor unit u side down.
Figure 7 – Mounting position
4. Move the lever (1) to the o en osition, which is to the right when facing the front of the unit
(see Figure 8).
Figure 8 – Positioning locking lever
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Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation
5. Attach the Lumencor unit so the contact surfaces at the mounting oint are tightly
com ressed (see Figure 9 Step 1).
6. Secure the locking lever by moving it to the left (see Figure 9 Step 2). If the lever stucks at
around the center osition, a ly a bit more ressure to the Lumencor unit.
Figure 9 – Mounting the Lumencor unit
7. Close the rotective cover of the Pannoramic 250 FLASH.
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