3D Histech Pannoramic 250 User manual

Pannoramic 250
1.15
User’s Guide
March 13, 2012
Rev. 1

Pannoramic 250 1.15 User’s Guide
Contents
Disclaimer....................................................................................................................... 5
Character Formats and Symbols....................................................................................... 7
otes Regarding Operational Safety................................................................................8
otes on Warranty........................................................................................................ 10
Terms and Abbreviations............................................................................................... 11
1 Product Description.................................................................................................... 12
1.1 Product Overview....................................................................................................................12
1.1.1 Intended Use..................................................................................................................................................12
1.1.2 Features and Benefits.....................................................................................................................................12
1.1.3 Warnin and Information Labels....................................................................................................................14
1.1.4 Main parts of the Base Unit...........................................................................................................................15
1.2 System Overview......................................................................................................................15
1.2.1 Pannoramic 250 system.................................................................................................................................16
1.2.2 Hardware Options..........................................................................................................................................16
1.2.3 Control Software............................................................................................................................................21
2 Installation................................................................................................................. 23
2.1 Control computer ports...........................................................................................................23
2.2 Connectors and cables.............................................................................................................24
2.3 Mountin the Lumencor Spectra unit......................................................................................25
3 Operating Slides and Magazines..................................................................................27
3.1 Preparin Slides and Ma azines..............................................................................................27
3.2 Affixin Barcode Stickers to Slides...........................................................................................28
3.3 Insertin and Removin Slides.................................................................................................29
3.3.1 Insert slides into a ma azine..........................................................................................................................29
3.3.2 Insert and remove ma azines........................................................................................................................30
3.3.3 Openin /Closin the FL protective cover.......................................................................................................33
4 Software Description.................................................................................................. 34
4.1 Startin / Exitin the Pannoramic Scanner Software...............................................................34
4.1.1 Startin the software......................................................................................................................................34
4.1.2 Exitin the software........................................................................................................................................35
4.2 Options.....................................................................................................................................35
4.2.1 Barcode Settin s.............................................................................................................................................36
4.2.2 Ima e Compensation.....................................................................................................................................39
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Pannoramic 250 1.15 User’s Guide
4.2.3 Microscope Settin s.......................................................................................................................................44
4.2.4 External Application Call Settin s...................................................................................................................49
4.3 Usin Bri htfield Manual Mode...............................................................................................50
4.3.1 Routine work tab panel..................................................................................................................................51
4.3.2 Scan Options window.....................................................................................................................................53
4.3.3 Preview tab panel...........................................................................................................................................54
4.3.4 Preview area scanned by preview camera.....................................................................................................58
4.3.5 Focus tab panel...............................................................................................................................................64
4.3.6 Service tab panel............................................................................................................................................66
4.3.7 Display field and toolbar for live ima es........................................................................................................66
4.3.8 Start Scan........................................................................................................................................................68
4.4 Usin Bri htfield Automatic Mode..........................................................................................69
4.4.1 Routine work tab panel..................................................................................................................................69
4.4.2 Barcodes tab panel.........................................................................................................................................71
4.4.3 Preview tab panel...........................................................................................................................................75
4.4.4 Focus tab panel...............................................................................................................................................76
4.4.5 Service tab panel............................................................................................................................................77
4.4.6 Start Scan........................................................................................................................................................78
4.5 Usin Fluorescent Manual Mode.............................................................................................79
4.5.1 Routine work tab panel..................................................................................................................................79
4.5.2 Scan Options...................................................................................................................................................84
4.5.3 Preview tab panel...........................................................................................................................................88
4.5.4 Hardware tab panel........................................................................................................................................91
4.5.5 Service tab panel............................................................................................................................................94
4.6 Usin Fluorescent Automatic Mode........................................................................................96
4.6.1 Routine work tab panel..................................................................................................................................96
4.6.2 Barcodes tab panel.......................................................................................................................................101
4.6.3 Preview tab panel.........................................................................................................................................105
4.6.4 Focus tab panel............................................................................................................................................106
4.6.5 Service tab panel..........................................................................................................................................106
4.7 Scan to Server........................................................................................................................107
4.8 Usin Profiles.........................................................................................................................113
5 Troubleshooting and Maintenance............................................................................115
5.1 Safety Information.................................................................................................................115
5.1.1 Cleanin the device......................................................................................................................................116
5.1.2 Cleanin the ma azine.................................................................................................................................116
5.1.3 Preventive maintenance...............................................................................................................................116
5.2 Troubleshootin .....................................................................................................................117
5.2.1 Fluorescent Applications (optional).............................................................................................................119
5.3 Maintenance..........................................................................................................................120
5.3.1 Openin the protective cover.......................................................................................................................120
5.3.2 Replacin fuses of the main power switch...................................................................................................121
5.3.3 Replacin Lamp Module (for Fluorescent Option).......................................................................................122
5.3.4 Removin a slide...........................................................................................................................................124
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Pannoramic 250 1.15 User’s Guide
5.3.5 Installin and Removin the Filter Module (Fluorescent Option)................................................................126
5.3.6 Removin a Ma azine from the Transportin System..................................................................................127
5.3.7 Transportin .................................................................................................................................................129
6 Technical Data........................................................................................................... 131
Index........................................................................................................................... 135
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Pannoramic 250 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.
3DHISTECH 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. 3DHISTECH Ltd. assumes no responsibility for the functionality and fault-free condition of
your “application programs” (Workflows, VBA macros, Commander scripts).
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.
CAUTIO
For research and education uses only, not for use in dia nostic procedures. This product has not been
approved or cleared as a medical device by the U.S. Food and Dru Administration, nor any other
re ulatory authority. The data and ima es obtained or viewed usin this product are not intended for
clinical or dia nostic use.
For performance evaluation only, the performance characteristics of this product have not been
established.
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Pannoramic 250 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 SOFTWARE IS PROVIDED “AS IS” A D WITHOUT WARRA TY OF A Y KI D, EXPRESSED,
IMPLIED OR OTHERWISE, I CLUDI G WITHOUT LIMITATIO , A Y WARRA TY OF
MERCHA TABILITY OR FIT ESS FOR A PARTICULAR PURPOSE.
I O EVE T SHALL SAM LEFFLER OR SILICO GRAPHICS BE LIABLE FOR A Y SPECIAL, I CIDE TAL,
I DIRECT OR CO SEQUE TIAL DAMAGES OF A Y KI D, OR FOR A Y DAMAGES WHATSOEVER
RESULTI G FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR OT ADVISED OF THE POSSIBILITY
OF DAMAGE, A D O A Y THEORY OF LIABILITY, ARISI G OUT OF OR I CO ECTIO WITH THE
USE OR PERFORMA CE OF THIS SOFTWARE.
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 250 1.15 User’s Guide
Character Formats and Symbols
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 not to work properly if this instruction is not followed.
ote: Calls attention to some important features.
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Pannoramic 250 1.15 User’s Guide
otes Regarding Operational Safety
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 250 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 250, 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 duly 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 250 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 250 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.
ote:
Electric power to the Pannoramic 250 is supplied via an internal 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 250
specifications before you turn power on.
Disconnect plug! Remember to unplu the power cord before you open the Pannoramic 250 or
replace a fuse!
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Pannoramic 250 1.15 User’s Guide
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!
The Pannoramic 250 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
250. For this reason, measures must be taken to eliminate such influences to a
maximum possible de ree. Durin periods of non-use, the Pannoramic 250
must be protected with a dust cover. Check that power is turned off before you
put the cover on.
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 250. In extreme cases, this may also cause
fire. Keep the ventilation slots always unobstructed and refrain from insertin or
droppin objects into a ventilation slot.
Warning! A defective Pannoramic 250 is not classified as domestic waste. It must be
properly disposed in accordance with currently valid le al requirements.
Warning!
The Pannoramic 250 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 250 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 250 1.15 User’s Guide
otes on Warranty
3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic 250 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 the amount of dama e as small
as possible. 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 parts) 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 action which is explicitly described in this User’s Guide, you are prohibited from
performin any kind of maintenance or repair work at the Pannoramic 250. Only 3DHISTECH Service
personnel or specifically authorized representatives are allowed to handle repair work. In case of
malfunction, contact the 3DHISTECH Service Support first.
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Pannoramic 250 1.15 User’s Guide
Terms and Abbreviations
CSV Comma Separated Value
FOV Field of View
A Numerical Aperture
Virtual Slide / Slide 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 and comment, send to a collea ue electronically for co-
operation or advice, and so on.
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Pannoramic 250 1.15 User’s Guide 1 Product Description
1 Product Description
1.1 Product Overview
1.1.1 Intended Use
Pannoramic 250 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 250 offers world class bri htfield and fluorescent whole slide scannin on up to 9
channels.
An outstandin 0.16 µm / pixel resolution is achieved with a 40×/0.95 NA (equivalent to 62×
ma nification) Carl Zeiss Plan-Apochromat objective.
Key features of the Pannoramic 250 Scanner:
•Extreme fast bri htfield scannin mode:
•Continuously movin sta e durin scannin
•The new bri htfield camera sees 30% lar er field of view with better pixel resolution
and has double frame rate
•Li ht source is a Xenon flash lamp
•Improved fluorescent scannin mode:
•Hi h-end illumination device – Lumencor Spectra 7 Li ht En ine
•3 times faster and more silent filter chan e
•Multiband filter support
•Noiseless FL scannin with the best FL camera available – pco.ed e
•Ma azine stack cover to protect every slides a ainst photo bleachin
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Pannoramic 250 1.15 User’s Guide 1 Product Description
•Improved ima e quality:
•Ima e sharpenin feature which improve the visual appearance of di ital slides
•New faster focus al orithm find the focus which is more appealin to the human
eye
•Motorized camera chan er for a 3CCD camera for bri htfield, a cooled monochrome CCD
camera or a sCMOS camera for fluorescence
•Motorized Objective chan er for two objectives
•10 times hi her resolution for barcode readin and preview ima e
•Compact desi n:
•Cameras are placed inside the unit
•Built-in power supply
•250 slide automatic loadin and scannin
This device is recommended for customers, who need hi h quality daily throu hput ranted by the
bi est loadin capacity of 250 slides. The device has many advanced improvements like software
controlled motorized camera- and objective chan er, and hi h resolution color preview.
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Pannoramic 250 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 250 main unit and the HXP 120
fluorescent illuminator.
Figure 1 – Warning and information labels
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Pannoramic 250 1.15 User’s Guide 1 Product Description
1.1.4 Main parts of the Base Unit
The followin fi ures show the main parts of the base unit.
Figure 2 – Main parts of base unit
1. Protective FL cover
2. Input and output stack for ma azines
3. Cover release hole
4. Power supply switch
5. USB port
6. Main power switch
7. Power supply cable connector
1.2 System Overview
The standard scope of delivery of the product includes the followin hardware and software
components.
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Pannoramic 250 1.15 User’s Guide 1 Product Description
1.2.1 Pannoramic 250 system
The followin fi ure shows the main parts of the Pannoramic 250 system.
Figure 3 – Pannoramic 250 system overview
1. Pannoramic 250 base unit
2. Monitor
3. Mouse
4. Control computer
5. Keyboard
6. Slide ma azine with cover
7. HXP 120 fiber-coupled fluorescent illuminator (optional, used with AxioCam MRm Rev3)
8. Lumencor Spectra 7 Li ht En ine illuminator (optional, used with pco.ed e camera)
1.2.2 Hardware Options
The confi uration of the control computer and monitor can vary dependin on the product order.
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Pannoramic 250 1.15 User’s Guide 1 Product Description
Cameras
AxioCam MRm Rev 3
1 CCD scientific, cooled, monochrome camera for
hi h quality, sensitive fluorescent applications.
CIS 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.
Camera adapters
0.63x adapter 1x adapter
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Pannoramic 250 1.15 User’s Guide 1 Product Description
Motorized camera changer
Figure – Motorized camera changer
You can fit two cameras into the Pannoramic 250 on the first adapter (1) (fluorescent position) and
the second adapter (2) (bri htfield position) at the same time. They are set and switched by the
software automatically, without any human assistance.
This system also enables switchin between bri htfield and fluorescent scannin by one click.
Warning!
The installation of the cameras in Pannoramic 250 must be carried out
by trained professionals!
In any other case the warranty will be automatically voided.
Supplier/Distributor is not liable for any dama es caused by an
installation not carried out by professional person.
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Pannoramic 250 1.15 User’s Guide 1 Product Description
Objectives
Figure 5 – Objective changer
You can select two different objectives to be equipped with the Pannoramic 250, the first objective
(1) and the second objective (2).
20x/NA 0.80 and 40x/NA 0.95 objectives can be used (the 40x objective cannot be used in Bri htfield
mode, but only in Fluorescent). You can chan e between the objectives with one click. This helps you
to select the ma nification and resolution that is the most suitable for your requirements.
Important!
Note, that hi her resolution results in slower di itization process.
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Pannoramic 250 1.15 User’s Guide 1 Product Description
Preview
Figure 6 – Preview camera (1), Brightfield preview lamp (2), and Dark-field preview lamp (3)
At fluorescent sections the dark-field preview makes the fluorescent samples detectable even for the
user and for the automatic markin al orithm. By detectin the sample the fluorescent scannin will
be much faster since the software will not waste time on empty FOVs.
Base Unit options
•Pannoramic 250 Base Unit
•Pannoramic 250 Scan Option – base unit equipped with CIS VCC-F52U25CL camera for
Bri htfield scannin (no fluorescent accessories included)
•Pannoramic 250 Basic Fluorescence Option – base unit completely equipped with CIS VCC-
F52U25CL camera for Bri htfield scannin ; with AxioCam camera and HXP 120 illuminator,
tri er cable and filters for fluorescence scannin
•Pannoramic 250 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
OTE: 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
•Plan-Apochromat 20× / NA 0.8
•Plan-Apochromat 40× / NA 0.95
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