3D Histech Pannoramic MIDI 1.15 User manual

Pannoramic MIDI
1.15
User’s Guide
March 13, 2012
Rev. 1

Pannoramic MIDI 1.15 User’s Guide
Contents
Disclaimer....................................................................................................................... 5
Declaration Of Conformity............................................................................................... 7
Character Formats and ymbols....................................................................................... 8
Notes Regarding Operational afety................................................................................9
Notes on Warranty........................................................................................................ 11
Terms and Abbreviations............................................................................................... 12
1 Product Description.................................................................................................... 13
1.1 Product Overview....................................................................................................................13
1.1.1 Intended Use..................................................................................................................................................13
1.1.2 Features and Benefits.....................................................................................................................................13
1.1.3 Warnin and Information Labels....................................................................................................................14
1.1.4 Base Unit........................................................................................................................................................15
1.2 System Overview......................................................................................................................15
1.2.1 Pannoramic MIDI system................................................................................................................................16
1.2.2 Hardware Options..........................................................................................................................................17
1.2.3 Control Software............................................................................................................................................19
2 Installation................................................................................................................. 21
2.1 Control computer ports...........................................................................................................21
2.2 Connectors and cables.............................................................................................................22
3 Operating lides and Trays.......................................................................................... 24
3.1 Preparin Slides and Trays.......................................................................................................24
3.2 Affixin Barcode Stickers to Slides...........................................................................................25
3.3 Insertin and Removin Slides.................................................................................................27
4 oftware Description.................................................................................................. 29
4.1 Startin / Exitin Pannoramic MIDI Software Application.......................................................29
4.1.1 Startin the software......................................................................................................................................29
4.1.2 Exitin the software........................................................................................................................................30
4.2 Options.....................................................................................................................................30
4.2.1 Barcode Settin s.............................................................................................................................................30
4.2.2 Ima e Compensation.....................................................................................................................................33
4.2.3 Microscope Settin s.......................................................................................................................................38
4.2.4 External Application Call Settin s...................................................................................................................43
4.3 Usin Bri htfield Manual Mode...............................................................................................44
4.3.1 Routine work tab............................................................................................................................................46
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Pannoramic MIDI 1.15 User’s Guide
4.3.2 Scan Options window.....................................................................................................................................48
4.3.3 Preview tab.....................................................................................................................................................50
4.3.4 Preview area scanned by preview camera.....................................................................................................53
4.3.5 Focus tab........................................................................................................................................................59
4.3.6 Service tab......................................................................................................................................................61
4.3.7 Display field and toolbar for live ima es........................................................................................................62
4.3.8 Start scan........................................................................................................................................................63
4.4 Usin Bri htfield Automatic Mode..........................................................................................64
4.4.1 Routine work tab............................................................................................................................................64
4.4.2 Barcodes tab...................................................................................................................................................66
4.4.3 Preview tab.....................................................................................................................................................70
4.4.4 Focus tab........................................................................................................................................................71
4.4.5 Service tab......................................................................................................................................................72
4.4.6 Start scan........................................................................................................................................................73
4.5 Usin Fluorescent Manual Mode.............................................................................................74
4.5.1 Routine work tab............................................................................................................................................74
4.5.2 Scan Options...................................................................................................................................................79
4.5.3 Preview tab.....................................................................................................................................................83
4.5.4 Hardware tab..................................................................................................................................................86
4.5.5 Service tab......................................................................................................................................................90
4.6 Usin Fluorescent Automatic Mode........................................................................................91
4.6.1 Routine work tab............................................................................................................................................91
4.6.2 Barcodes tab...................................................................................................................................................96
4.6.3 Preview tab...................................................................................................................................................100
4.6.4 Focus tab......................................................................................................................................................101
4.6.5 Service tab....................................................................................................................................................101
4.7 Scan To Server........................................................................................................................102
4.8 Usin Profiles.........................................................................................................................108
5 Troubleshooting and Maintenance............................................................................110
5.1 Safety Information.................................................................................................................110
5.1.1 Cleanin the device......................................................................................................................................111
5.1.2 Cleanin the trays.........................................................................................................................................111
5.1.3 Preventive maintenance...............................................................................................................................111
5.2 Troubleshootin .....................................................................................................................112
5.2.1 Fluorescent Applications (optional).............................................................................................................114
5.3 Maintenance..........................................................................................................................115
5.3.1 Removin the protective covers...................................................................................................................115
5.3.2 Replacin the halo en lamp.........................................................................................................................117
5.3.3 Replacin Lamp Module (for Fluorescent Option).......................................................................................118
5.3.4 Removin a slide...........................................................................................................................................121
5.3.5 Installin and Removin the Filter Module (Fluorescent Option)................................................................122
5.3.6 Transportin Pannoramic MIDI....................................................................................................................124
6 Technical Data........................................................................................................... 126
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Pannoramic MIDI 1.15 User’s Guide
Index........................................................................................................................... 131
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Pannoramic MIDI 1.15 User’s Guide
Disclaimer
Copyri ht © 2001-2012 3DHISTECH Ltd.
All ri hts reserved.
Intellectual property related to the 3DHISTECH products 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 ranted patents, ranted utility model, re istered trademarks, pendin
international and national patent applications and the other correspondin IP are the sole properties
of the 3DHISTECH Ltd.
3DHI TECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general
or specific damage, indirect damage, consequential damage or incidental damage, including the
results of the analysis of the digitized slides, for example, change of health status related to
erroneous diagnosis from the digitalized slide(s)) that stems from or is associated with use of
Product, digitalized slides, quality of staining, quality of stained slides, quality of used method of
staining. 3DHI TECH Ltd. assumes no responsibility for the functionality and fault-free condition of
your “application programs” (Workflows, VBA macros, Commander scripts).
CAUTION
This product has not been approved or cleared as a medical device by the U.S. Food and Dru
Administration.
Do not use this device in close proximity to sources of stron electroma netic radiation (e. .
unshielded intentional RF sources), as these may interfere with the proper operation.
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Pannoramic MIDI 1.15 User’s Guide
Third-Party Disclaimer (LibTIFF – TIFF Library and Utilities)
3DHISTECH Ltd. is not liable for dama e of whatever nature (includin , but not limited to, eneral or
specific dama e, indirect dama e, consequential dama e or incidental dama e, includin dama e
resultin from lost profits, interruption of business, loss of business information, pecuniary loss or
similar dama e) that stems from or is associated with the incorporated part of this Product that is
made by Silicon Graphics Inc.
THE OFTWARE I PROVIDED “A I ” AND WITHOUT WARRANTY OF ANY KIND, EXPRE ED,
IMPLIED OR OTHERWI E, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNE FOR A PARTICULAR PURPO E.
IN NO EVENT HALL AM LEFFLER OR ILICON GRAPHIC BE LIABLE FOR ANY PECIAL, INCIDENTAL,
INDIRECT OR CON EQUENTIAL DAMAGE OF ANY KIND, OR FOR ANY DAMAGE WHAT OEVER
RE ULTING FROM LO OF U E, DATA OR PROFIT , WHETHER OR NOT ADVI ED OF THE PO IBILITY
OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARI ING OUT OF OR IN CONNECTION WITH THE
U E OR PERFORMANCE OF THI OFTWARE.
Further Information
For the latest information on 3DHISTECH products and services, please visit our website at the
followin URL: http ://www.3dhistech.com .
Company Address: 29-33 Konkoly-The e Miklos street, Buildin 18
1121 Budapest – HUNGARY
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Pannoramic MIDI 1.15 User’s Guide
Declaration Of Conformity
3DHISTECH Ltd. declares that the product Pannoramic MIDI slide scanner is desi ned and produced
with consideration of specified requirements accordin to the ISO 13485:2003 and IEC 61326-2-
6:2005 standards, and conforms to the directives and other standards listed below:
IEC 61010-1:2001 (ed. 2), “Safety requirements for electrical equipment for measurement, control,
and laboratory use – Part 1: General requirements”
IEC 61010-2-101:2002 (ed. 1), “Safety requirements for electrical equipment for measurement,
control and laboratory use – Part 2-101: Particular requirements for in vitro dia nostic (IVD) medical
equipment”
EN 55011:1998, Group 1, Class A, “Limits and methods of measurement of radio disturbance
characteristics of industrial, scientific, and medical (ISM) radio-frequency equipment”
This product has been tested to the requirements of CAN/CSA-C22.2 No. 61010-1, second
edition, includin Amendment 1, or a later version of the same standard incorporatin the same level
of testin requirements.
Conformity with Directive 98/79/EC is documented by the Pannoramic MIDI -label.
Conformity with Directive IEC 61010-2-101:2002 (ed. 1) is marked by on the product
labelin .
Further information may be obtained from the manufacturer:
3DHISTECH Ltd.
29-33 Konkoly-The e Miklos street, Buildin 18
1121 Budapest – HUNGARY
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Pannoramic MIDI 1.15 User’s Guide Character Formats and ymbols
Character Formats and ymbols
Example Words or characters that appear on the screen. These include field names, screen
and window titles, push-buttons and menu names, paths or options.
Keys on the keyboard. For example, function keys (such as F11) or the Ctrl+M key
combination.
Example Cross-references within this document or to other documents.
Warning! It mi ht cause irreversible dama e or harm to the user of the product or the
product itself if this instruction is not followed.
Caution! It mi ht cause the product to not work properly if this instruction is not followed
and alerts to a potential dan er situation.
Note: Calls attention to some important features.
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Pannoramic MIDI 1.15 User’s Guide Character Formats and ymbols
Notes Regarding Operational afety
The below section of this User’s Guide contains information and warnin s of a kind that must be
followed by owner/operator personnel.
Warnin and advisory symbols which are used on the base unit of the Pannoramic MIDI and in the
section 1.1.3 Warning and Information Labels have the followin meanin s:
CAUTION
Disconnect mains plu before any kind of intervention into the device!
CAUTION
Crush hazard!
The Pannoramic MIDI, includin any of its ori inal accessory components, should not be operated in
any other way than described in section 1.1.1 Intended Use.
Any of the followin notes should be strictly observed:
Caution!
In the event of any non-conformin type of use, includin non-conformin use
of assemblies or sin le parts, no liability will be assumed by the Manufacturer.
This shall also apply to service or repair work of any kind, which is performed by
other than authorized service personnel. All claims for warranty and warranty
services will be null and void in any such case.
Warning!
Insert the power cord plu s only into a roundin outlet. The protective action
must not be rendered ineffective by extension cables without protective
conductor. The Pannoramic MIDI has a built-in protection which must not be
rendered ineffective by extension cables without protective (earth- round)
conductor.
Warning! The operation of the instrument in explosion-risk environments is not allowed.
Warning!
If protective devices are found to be ineffective, the Pannoramic MIDI must be
shut down and precautions must be taken to prevent unintended usa e. For
necessary repair work or work to restore proper operatin condition, you
should contact the 3DHISTECH Customer Service.
Note:
Electric power to the Pannoramic MIDI is supplied via an external mains power
supply unit. It allows for operation at line volta es in the ran e of 100 V to 240
V ±10%, 50/60 Hz, without any extra facilities required for volta e
transformation.
Warning! Check that your local line volta e is compatible with Pannoramic MIDI
specifications before you turn power on.
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Pannoramic MIDI 1.15 User’s Guide Character Formats and ymbols
Disconnect plug! Remember to unplu the power cord before you open the Pannoramic MIDI
base unit or replace a fuse!
Warning! Use only electric fuses which are rated for the specified nominal current. You
are prohibited from usin makeshift fuses or short-circuitin of a fuse holder.
Warning! Only connect external devices that are safety extra low volta e rated to the
instrument to avoid the risk of electrical shock.
Warning!
The Pannoramic MIDI does not include any special facilities to protect from
samples with an etchin , potentially infectious, toxic, radioactive or other
health-dama in effect. You are under obli ation to comply with all currently
bindin le islation, notably, national accident prevention rules when handlin
samples of this kind.
Caution!
Dirt or dust may adversely impact the operatin capability of the Pannoramic
MIDI. For this reason, measures must be taken to eliminate such influences to a
maximum possible de ree. Durin periods of non-use, the Pannoramic MIDI
must be protected with a dust cover. Check that power is turned off before you
put the cover on.
Caution! Avoid touchin the lamp bulb. Disconnect power and allow the bulb to cool
down by waitin for about 15 minutes before replacin it.
Crush hazard!
There is crush hazard in the movement area of the slide insert durin operation.
Please note that the di itizin process has to be interrupted and the insert
moved via software to the output position before removin the insert.
Warning!
Clo ed or covered ventilation slots may result in a heat build-up with a
dama in effect for the Pannoramic MIDI. Keep the ventilation slots always
unobstructed and do not insert or drop objects into a ventilation slot.
Warning! A defective Pannoramic MIDI is not classified as domestic waste. It must be
properly disposed in accordance with currently valid le al requirements.
Warning!
The Pannoramic MIDI may not be operated by other than properly instructed
persons. Operatin personnel must be fully aware of the potential dan ers
which a particular field of application involves. The Pannoramic MIDI is a
precision instrument which may suffer a si nificant reduction in operational
functions or even physical destruction followin intervention performed in any
nonconformin manner.
Warning! If an X-Cite 120 illuminator is used, the correspondin warnin s included in the
manufacturer’s operatin manual have to be observed.
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Pannoramic MIDI 1.15 User’s Guide Character Formats and ymbols
Notes on Warranty
3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic MIDI to be free from faults
in material and workmanship at the moment of installation. Defects must be notified immediately on
identification and maximum efforts must be undertaken in order to minimize dama e. On receivin
notice of a fault, the Product Manufacturer will be under obli ation to remove the fault, at his own
option, either by providin adequate repair services or by deliverin a faultless product for
replacement. No warranty will be accepted in cases of natural wear (notably, wear and tear) or
improper product handlin .
The Product Manufacturer will refuse any liability in the event of dama e resultin from faulty
operation, ne li ence or unauthorized intervention into the product, notably, from the replacement
of product parts or the usa e of accessory parts from other manufacturers. Any such case will void
the user’s claim for warranty.
Except for actions which are explicitly described in this User’s Guide, you are prohibited from
performin any kind of maintenance or repair work at the Pannoramic MIDI. Only authorized
3DHISTECH Service personnel or specifically authorized representatives are allowed to handle repair
work. In case of malfunction contact 3DHISTECH Service Support first.
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Pannoramic MIDI 1.15 User’s Guide Character Formats and ymbols
Terms and Abbreviations
C V Comma Separated Value
FOV Field of View
NA Numerical Aperture
Virtual lide / lide A di ital ima e of a thin lass plate on which specimens are mounted for
microscopic study:
a dynamic, interactive ima e that you can mana e, save, ma nify, zoom, name,
evaluate, annotate, mark, comment, send to a collea ue electronically for co-
operation or advice, and so on.
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
1 Product Description
1.1 Product Overview
1.1.1 Intended Use
The Pannoramic MIDI is desi ned to use transmitted li ht and reflected li ht fluorescence to di itize
biolo ical samples and specimens (typically histolo ical sections). The tar et users of the product can
work for example, in education, research, industry or medical sectors.
1.1.2 Features and Benefits
The Pannoramic MIDI offers world class bri htfield and fluorescent whole slide scannin on up to 9
channels.
An outstandin 0.12 µm/pixel resolution is achieved with the 40×/0.95 NA Carl Zeiss Plan-
Apochromat objective.
Key features of the Pannoramic MIDI scanner:
•Up to 9 freely selectable color filters for fluorescence
•Hi h-end fluorescent illumination device – Lumencor Spectra 7 Li ht En ine
•Multiband filter support
•Noiseless FL scannin with the best FL camera available – pco.ed e
•12 slide automatic loadin and scannin
•Improved permanent autofocus
•Small footprint
•Compact and robust device
•Good quality and stable manufacturin
•Barcode readin
Pannoramic MIDI is an optimal choice for customers who want to scan in bri htfield and in
fluorescent mode where the quantity of scanned slides will be re ularly over 10 slides per day. It has
the best price/performance ratio with a reliable loadin /scannin mechanism.
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
1.1.3 Warning and Information Labels
The followin fi ure contains the labels used on the Pannoramic MIDI main unit, the external mains
power supply unit, and the HXP 120 illuminator.
Figure 1 – Warning and information labels
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
1.1.4 Base Unit
The followin fi ure shows the main parts of the base unit.
Figure 2 – Main parts of base unit
1. Protective covers
2. Slide tray
3. CIS VCC-F52U25CL scan camera
4. HXP 120 fiber-coupled illuminator (option)
5. HXP 120 illumination adapter (option)
6. Fiber optic cable
1.2 ystem Overview
The standard scope of delivery of the product includes the followin hardware and software
components.
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
1.2.1 Pannoramic MIDI system
The followin fi ure shows the main parts of the Pannoramic MIDI system.
Figure 3 – Pannoramic MIDI system overview
1. HXP 120 fiber-coupled illuminator (option)
2. 24 V power supply
3. Pannoramic MIDI base unit
4. Monitor
5. Mouse
6. Control computer
7. Keyboard
8. Slide tray
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
1.2.2 Hardware Options
Note:
The confi uration of the control computer and monitor can vary
dependin on the product order.
Cameras
AxioCam MRm Rev 3
1 CCD scientific, cooled, monochrome camera for
hi h quality, sensitive fluorescent applications.
CI VCC-F52U25CL
3 CCD camera for hi h-quality bri htfield
applications allowin fast scannin .
pco.edge
Equipped with a hi h-quality sCMOS ima e sensor
for fluorescent applications allowin fast scannin
and an outstandin low read out noise. Cooled
with Peltier element.
tingray F146C IRF Medical camera
1 CCD camera for normal bri htfield application
and entry level fluorescent applications.
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
Camera adapters
0.63× adapter 1× adapter
Warning!
The installation of the cameras in Pannoramic MIDI must be carried out
by trained professionals!
In any other case the warranty will be automatically voided. The
supplier or distributor is not liable for any dama es caused by an
installation carried out by an unauthorized person.
Base Unit options
•Pannoramic MIDI Basic Scan Option / Fast Option – base unit equipped with Stin ray or CIS
cameras for Bri htfield scannin (no fluorescent accessories included)
•Pannoramic MIDI Basic Fluorescence Option – base unit completely equipped with Stin ray
or CIS VCC-F52U25CL camera for Bri htfield scannin ; with AxioCam camera and HXP 120
illuminator, tri er cable and filters for fluorescence scannin
•Pannoramic MIDI Advanced Fluorescence Option – base unit completely equipped with CIS
VCC-F52U25CL camera for Bri htfield scannin , and with pco.ed e camera and Lumencor
fluorescence illuminator, tri er cable and filters for fluorescence scannin
NOTE: In case Lumencor li ht source is ordered, the custom li ht source and filter modules
can be variable. For more information, please contact 3DHISTECH customer service.
Objectives
•Carl Zeiss Plan-Apochromat 20×/NA 0.8
•Carl Zeiss Plan-Apochromat 40× Corr/NA 0.95
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
Fluorescent Option for Pannoramic MIDI
Fluorescent unit (internal part)
HXP 120 Fluorescent illumination
unit (can be used with AxioCam
MRm Rev3 only)
Lumencor Spectra 7 Li ht En ine
illumination unit (can be used with
pco.ed e camera only)
1.2.3 Control oftware
•Pannoramic canner control software
Optional:
•Fluorescence
•Extended focus
•Z-stack
•Barcode reader (licensed feature)
•Scan To Server
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Pannoramic MIDI 1.15 User’s Guide 1 Product Description
•Pannoramic Viewer software (fully functional)
Optional:
•CaseCenter
•Pannoramic Viewer TMA module
•3D Reconstruction module
•HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, and DensitoQuant modules
•ImmunoScreener module
•E-School Encoder
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