3DHISTECH Ltd. Pannoramic SCAN II 2.0 User Manual Download Page 95

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Pannoramic SCAN II 2.0 User’s Guide

5 Scanning modes and settings

5.3.1 General functions at the main menu

Microscope/Planner selector

Horizontal/Vertical selector

(Available in

Slide view with card

mode)

Stage Control

– Available after initialization, upon clicking the slide icon or entering slide position

number at the right side, the slide can be loaded.

Scan to

– Available after loading procedure, unique settings can be defined even for each

separate scanning.

Start scan

– Scanning of the actually loaded slide, or if the planner has been defined, the

whole scanning process can be initiated.

Stop scan

Stop actual process

Take all previews

– Preview images of all the slides in the magazine are taken automatically.

Select the required preview type from the following: Brightfield, Pre-scan, Pre-scan high-resolution,
Pre-scan + high-resolution.

Figure 69 – Take all preview selector

Save planner

– A scanning plan containing all parameters and profile assignment will be saved.

Load planner

– The previously saved scanning plan can be loaded.

Planner menu

– The following profile-related tasks applicable for the planner can be performed:

•

Add current profile to all racks

•

Open profile for all racks

•

Detach current profile from all racks

•

Detach profiles from racks

June 4, 2018 - Rev. 2

3DHISTECH Ltd.

95(142)

For research and education uses only, not for use in diagnostic procedures.

Summary of Contents for Pannoramic SCAN II 2.0

Page 1: ...PSII123 UG EN Rev2 Pannoramic SCAN II 2 0 User s Guide June 4 2018 Rev 2 For research and education uses only not for use in diagnostic procedures ...

Page 2: ...20 2 Installation 22 2 1 Control computer ports 22 2 2 Connectors and cables 23 2 3 Coupling the Lumencor SOLA SM II unit with the scanner 24 2 4 Coupling the Lumencor Spectra 6 unit with the scanner 24 3 Operating Slides and Magazines 26 3 1 Preparing Slides and Magazines 26 3 2 Affixing Barcode Stickers to Slides 27 3 3 Inserting and Removing Slides 28 4 Software Description 32 4 1 Starting Exit...

Page 3: ...rogress features 104 5 6 Services and Settings 104 5 6 1 Services 104 5 6 2 Settings 111 5 7 Hosting 115 5 8 Using Profiles 117 6 Troubleshooting and Maintenance 119 6 1 Safety Information 119 6 1 1 Cleaning the device 120 6 1 2 Cleaning the magazine 120 6 1 3 Preventive maintenance 120 6 2 Troubleshooting 121 6 2 1 Fluorescent Applications optional 123 6 3 Maintenance 124 6 3 1 Removing the prote...

Page 4: ...e Packing the SCAN II scanner 140 Packing the accessories 140 Closing the package 140 Handling of the package 141 Index 142 June 4 2018 Rev 2 3DHISTECH Ltd 4 142 For research and education uses only not for use in diagnostic procedures ...

Page 5: ...344 US 11 662 976 HU0700409 US 12 042 050 US 77 636 144 and 007502032 The above mentioned granted patents granted utility model registered trademarks pending international and national patent applications and the other corresponding IP are the sole properties of the 3DHISTECH Ltd CAUTION For research and education uses only not for use in diagnostic procedures This product has not been approved or...

Page 6: ...dhistech com Or contact the distributor Richard Allan Scientific Co Subsidiary of Thermo Fisher Scientific 4481 Campus Drive Kalamazoo Mi 49008 USA US Toll Free 1 800 522 7270 Tudor Road Manor Park Runcorn WA7 1TA United Kingdom 44 0 800 018 9396 44 0 1928 534 000 June 4 2018 Rev 2 3DHISTECH Ltd 6 142 For research and education uses only not for use in diagnostic procedures ...

Page 7: ... M key combination Example Cross references within the document or to other documents Warning It might cause irreversible damage or harm to the user of the product or the product itself if this instruction is not followed Caution It might cause the product to not work properly if this instruction is not followed and alerts to a potential danger situation Note Calls attention to some important feat...

Page 8: ...art 2 081 Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes IEC 62471 2006 Photobiological safety of lamps and lamp systems IEC 61326 2 6 2012 Electrical equipment for measurement control and laboratory use EMC requirements Part 2 6 Particular requirements In vitro diagnostic IVD medical equipment There is no further operator user action ...

Page 9: ...other than duly authorized service personnel All claims for warranty and warranty services will be null and void in any such case Note The safety level of the equipment after servicing will be identical with level of the original equipment Warning Insert the power cord plugs only into a grounding outlet The protective action must not be rendered ineffective by extension cables without protective c...

Page 10: ... power is turned off before you put the cover on Caution Do not position the equipment so that it is difficult to operate and to disconnect the device if necessary Crush hazard There is crush hazard in the movement area of the slide insert during operation Please note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the inse...

Page 11: ...y provisions necessarily vary to comply with differences in national and regional legislation Specific details can be found in the delivery documentation or from your dealer or representative Please note that your warranty may be invalidated if This instrument is modified in any way Accessories and reagents which have not been approved by Thermo Fisher Scientific are used The instrument is not ope...

Page 12: ...gital image of a thin glass plate on which specimens are mounted for microscopic study a dynamic interactive image that you can manage save magnify zoom name evaluate annotate mark comment send it to a colleague electronically for co operation or advice and so on June 4 2018 Rev 2 3DHISTECH Ltd 12 142 For research and education uses only not for use in diagnostic procedures ...

Page 13: ...ty of the scanner program 1 1 2 Features and Benefits The Pannoramic SCAN II offers world class brightfield and fluorescent whole slide scanning on up to 9 channels An outstanding 0 12 µm pixel in Brightfield and 0 16 µm pixel in Fluorescent resolution is achieved with the 40 NA 0 95 equivalent to 80 magnification in BF and 62 magnification in FL Plan Apochromat objective Key features of the Panno...

Page 14: ...and preview image Image sharpening both for Fluorescence and Brightfield feature which improve the visual appearance of digital slides Focus algorithm finds the focus which is most appealing to the human eye Compact and robust device Good quality and stable manufacturing Pannoramic SCAN II is an optimal choice for customers who need high quality daily throughput granted by the loading capacity of ...

Page 15: ... Pannoramic SCAN II main unit the external mains power supply unit and the Lumencor SOLA SM II illumination unit Figure 1 Warning and information labels NOTE The symbol at the feeder slot calls attention to biohazardous materials in use June 4 2018 Rev 2 3DHISTECH Ltd 15 142 For research and education uses only not for use in diagnostic procedures ...

Page 16: ...e loader 5 Magazine feeder door cover 6 Point Grey Grasshopper 3or pco edge5 5 camera 7 Protective rails Fluorescent option A 8 Lumencor SOLA SM II fiber coupled illumination unit can be used with Point GreyGrasshopper 3 camera only 9 Lumencor illumination adapter and cable Fluorescent option B 8 Lumencor SPECTRA 6 Light Engine fiber coupled illumination unit June 4 2018 Rev 2 3DHISTECH Ltd 16 142...

Page 17: ...N II system The following figure shows the main parts of the Pannoramic SCAN II system Figure 3 Pannoramic SCAN II system overview 1 Lumencor SOLA SM II fiber coupled illumination unit optional 2 24 V external power supply unit 3 Lumencor Spectra 6 Light Engine optional 4 Monitor 5 Mouse June 4 2018 Rev 2 3DHISTECH Ltd 17 142 For research and education uses only not for use in diagnostic procedure...

Page 18: ...ey Grasshopper 3 1 CCD monochrome camera for high quality sensitive fluorescent applications pco edge 4 2 Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast scanning and an outstanding low read out noise High quantum efficiency cooled with Peltier element Camera adapters 0 63 adapter for Point Grey Grasshopper 3 only 1 adapter June 4 2018 Rev 2 3DHISTECH Ltd...

Page 19: ...opper 3 camera and Lumencor SOLA SM II non triggered or Lumencor SPECTRA 6 fluorescent illumination unit with filters for fluorescence scanning Pannoramic SCAN II Advanced Brightfield and Fluorescence Option base unit completely equipped with pco edge 4 2 camera and Lumencor SPECTRA 6 fluorescence illumination unit trigger cable and filters for fluorescence scanning NOTE If Lumencor SPECTRA 6 is o...

Page 20: ... with Point Grey Grasshopper 3 camera only Lumencor Spectra 6 Light Engine illumination unit 1 2 3 Control Software Pannoramic Scanner control software Optional licensed features Fluorescence Extended focus Z stack Barcode reader Pannoramic Viewer software fully functional Optional CaseCenter June 4 2018 Rev 2 3DHISTECH Ltd 20 142 For research and education uses only not for use in diagnostic proc...

Page 21: ...e 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules TumorBoard module E School Encoder June 4 2018 Rev 2 3DHISTECH Ltd 21 142 For research and education uses only not for use in diagnostic procedures ...

Page 22: ...ervice assistants are allowed to install the hardware and software The product is ready for use after installation Caution Make sure that the device is placed so that there is enough space for ventilation and for safe and efficient operator maintenance 2 1 Control computer ports The following figure shows the location of the connectors in order to enable easier transportation of the product for a ...

Page 23: ...rasshopper 3 camera 2 2 Connectors and cables Caution It is not recommended to use USB and FireWire cables longer than 2 5 meters Control USB between scanner and control computer Preview camera USB cable between scanner and control computer Point Grey Grasshopper 3 USB 3 0 cable between Point Grey Grasshopper 3 camera and control computer pco edge 4 2 a pair of CameraLink cables between pco edge 4...

Page 24: ... the risk of electrical shock 2 3 Coupling the Lumencor SOLA SM II unit with the scanner To operate the Lumencor SOLA SM II fluorescent illumination unit it has to be connected to the Pannoramic SCAN II base unit 1 Turn the control computer and the Pannoramic SCAN II unit off 2 Connect both ends of the fiber optic cable to the coupling ports of the scanner and the illumination unit see Figure 2 op...

Page 25: ...pco edge 4 2 camera out 4 or Point Grey Grasshopper 3 camera and the Lumencor SPECTRA 6 unit TTL port and USB to RS232 communication cable between the Lumencor SPECTRA 6 unit and the computer Figure 5 Lumencor SPECTRA 6 Light Engine connecting ports June 4 2018 Rev 1 3DHISTECH Ltd 25 142 ...

Page 26: ...gloves and coat when working with biohazardous material or slides Warning Do not use a slide when it is broken or its edges are not properly cut or grounded Using such slides can lead to injury Warning Ensure that no part of the mounted coverslip protrudes from the edges of the slide Use slides only with completely dried embedding medium If not so the coverslip can be shifted that makes slide load...

Page 27: ...nt Mounting Medium by Vector Laboratories and ProLong Gold and SlowFade Gold antifade reagents by Invitrogen during the FISH protocol For further information see the homepages of the manufacturers http www vectorlabs com and http www invitrogen com 3 2 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides Barcodes enable virtual slide identification Fig...

Page 28: ...vital for barcode identification Do not let barcode sticker protrude from slide edges or stick on the coverslip surface 3 The thickness of the barcode sticker on the slide must not exceed 0 4 mm Do not stick more than 4 barcode stickers over each other and the overall thickness must must be kept below 1 65 mm including the barcodes and the slide 3 3 Inserting and Removing Slides To insert slides i...

Page 29: ...the proper way of inserting slides Note You should insert several slides into a magazine without empty slots Begin the insertion on position 1 of the magazine Caution Only original 3DHISTECH magazines are allowed for use with Pannoramic SCAN II To insert or remove a filled magazine from the device or when transporting it without its cover 4 slightly tilt it to its closed side to prevent the slides...

Page 30: ...ace magazine cover when magazine is not currently used or is stored for a longer period The cover prevents soiling and mechanical damage 2 Open the door of the input stack 5 and put a magazine 1 into the input stack 4 The magazine s rack the back side of the magazine 2 must contact with the guide rails with its open side towards the scanner 3 Slide down the magazine on the input guide rails until ...

Page 31: ...6 magazines in addition to the one in the magazine loader Figure 9 Misplaced magazine Caution Do not place magazines into the output stack 3 or remove magazines with already digitized slides from there during the digitization process Only remove magazines from the output stack when you have finished digitization of all slides June 4 2018 Rev 2 3DHISTECH Ltd 31 142 For research and education uses o...

Page 32: ...tion icons are displayed These two mode buttons represent Microscope and Planner scanner modes Microscope mode for digitization of individual slide or individual rack set scanning profile of the slide run Live teleconsultation use Live microscope Planner mode plan the entire scanning procedure assign one or more profiles to each slide define Brightfield and Fluorescence or mixed scanning mode with...

Page 33: ...and Planner modes Microscope initialization Initialization All motors and the preview camera during start up BF mode In BF mode the camera for brightfield scanning is initialized FL mode In FL mode the camera for fluorescence scanning is initialized Hosting Start and host a live Teleconsultation session magazine Slide loading June 4 2018 Rev 2 3DHISTECH Ltd 33 142 For research and education uses o...

Page 34: ...d Click this button to inform the control software that the slide has been removed manually Objective changer Live view is on Live view is on with the shutter closed Toolbar for live images The toolbar is only available for the displayed live image but not available for camera images during digitization One pixel on the monitor corresponds to one pixel on the camera The live image completely fills...

Page 35: ...ifier Window Ruler Image Processor Plugin functions Convolute gray scale image by custom kernel Multi channel histogram with normalization Invert image for testing purposes Mark overexposed pixels Scan Properties included as well on the profile cards added to the slide in Planner mode unique settings can be defined even for each separate scanning Scan to Local Select the Slide save Path Folder fro...

Page 36: ...an to server settings Server Editor The user define here the following details of the Server Display Name Host Name Protocol Server Editor stores each of the created server in a list List entries can be removed or a new entry can be added if required With the Filters function you can narrow down the results by searching for a specific server data By double clicking a list item server data will be ...

Page 37: ...nd other settings Server Side Barcode Parsing option can be selected if CaseCenter is connected with the supported HIS LIS This way the barcode read by the software is being identified and the predefined location of that specific case in CaseCenter is automatically selected as scanning destination based on the CaseID containing slide and patient data stored on HIS LIS Therefore Folder Case Block a...

Page 38: ...owing barcode types 1D barcode types Code 39 Code 128 Code 16K Interleaved 2 of 5 Standard 2 of 5 IATA 2 of 5 Matrix 2 of 5 Telepen Code 93 Code 11 MSI Codabar Patch Code Pharmacode EAN 13 EAN 8 UPC A UPC E June 4 2018 Rev 2 3DHISTECH Ltd 38 142 For research and education uses only not for use in diagnostic procedures ...

Page 39: ...initiated Stop Scan Stop actual progress Take All Preview Each preview of slides in the magazine is taken automatically Preview types are the following Brightfield Pre Scan FL Pre Scan High Resolution FL Pre Scan High Resolution FL Figure 15 Take all preview selector Auto attach Actual profile is assigned to the loaded slide automatically June 4 2018 Rev 2 3DHISTECH Ltd 39 142 For research and edu...

Page 40: ...d into two clusters Brightfield and Fluorescence Additional profiles can be created here as well and you can also search for a specific profile by filtering based on the following data Objective type Multilayer mode Illumination Filters Modify date Last use date Figure 16 Profile browser window June 4 2018 Rev 2 3DHISTECH Ltd 40 142 For research and education uses only not for use in diagnostic pr...

Page 41: ...o the text field and clicking Save as Reset Zoom This function is active only in Live view at 1 1 magnification Live image magnification Preferences This panel contains user settings that have global effect on the GUI and some of its functions June 4 2018 Rev 2 3DHISTECH Ltd 41 142 For research and education uses only not for use in diagnostic procedures ...

Page 42: ...egacy live image is displayed in an external window Profile settings Use profile history save With this function each profile modification is saved in Profile History from which the different stages can be reloaded Save interval Profile content is automatically saved at the specified time frames Enable setting of focus time Parameters Short Normal Long related to focus time will be enabled on the ...

Page 43: ...barcode image creation Exposure times will be recalculated each time thus creating prefect light conditions for barcode reading so to make sure that barcode identification is successful Scanning History Hardware log Scanner hardware operations are contained in this log To enable this function first the database from the following folder must be loaded C ProgramData 3DHISTECH SlideScanner HWLogData...

Page 44: ...D is the sequence number of scanning performed on the scanner in use Profile Name Illumination mode Scan type Scan Start Scan Finished URL Error Filtering for the following parameters is available Scanning date Profile name Illumination mode URL Slide name Slide index Rack index June 4 2018 Rev 2 3DHISTECH Ltd 44 142 For research and education uses only not for use in diagnostic procedures ...

Page 45: ...t automatically about every failure and error that is occurred during scanning to the specified address The log files are compressed into a ZIP file that is attached to the mail Help June 4 2018 Rev 2 3DHISTECH Ltd 45 142 For research and education uses only not for use in diagnostic procedures ...

Page 46: ... Settings see section 5 6 Services and Settings for more information In accordance with the selected mode the Profile Settings Panel and the Microscope Control Panel views are modified 5 1 Brightfield Scanning Mode Microscope View consist of three different sections Main functions Located at below the window header these functions are identical in both modes Profile Settings panel Profile settings...

Page 47: ...s This is useful if focusing was not targeted on the specimen but on a spot on the coverslip Focus distance the distance of focal points can be set to create a focus map based on which the software calculates interpolated focus values one step in distance means one FOV Sample detection This panel offers options for threshold setting and selection of the area to be scanned Source Brightfield previe...

Page 48: ...nel Specimen threshold This value is definable manually This sets the sensitivity of the specimen detection To set the desired threshold value manually change the setting in the Specimen threshold level selection box in the range of 0 255 The default value is 220 Smaller values result in a more sensitive scanning meaning that more areas will be digitized however this may also include specks or oth...

Page 49: ...ction easier by limiting the scanned area If this option is selected only the area encircled with a marker pen will be scanned You can define the threshold level by changing the threshold value in the Use marker with threshold selection box in the range of 0 255 This sets the sensitivity of the specimen detection inside the marker area To set the desired threshold value manually change the setting...

Page 50: ...T use Remove coverslip function on TMA slides The layout of TMA slides may mislead the detecting algorithm Fill holes inside the scanmap If selected the holes inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filter...

Page 51: ... is used for scanning Use selection box restriction If selected only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned Multilayer mode Single layer mode Select Single layer option if you want to scan a single layer of the slide Extended focus By choosing the Extended focus optio...

Page 52: ...scanning from the drop down menu Settings according to the profile has effect on the color set color temperature and gamma value of the scanned image Separate color matrix can be defined and used for each profile and scanning Preset profiles are the following Calibrated Linear Color scheme is defined by calibration Gamma value is not included sRGB standard Color scheme is defined by calibration st...

Page 53: ...overed by the specimen for example blood smear thereby making compensation image capture impossible For such slides use an empty slide with coverslip to grab a compensation image If you select this the software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading Save focus quality The measurement of focus quality corr...

Page 54: ...ned Figure 23 Preview panel Threshold options This section is located at right side of the preview window Scanmap Source is designed to set which type of scanmap is used on the preview image This scanmap is displayed automatically in the Profile Scanmap Source setting Selectable scanmap types are the following Use threshold Load previously saved scanmap from file Custom scan map June 4 2018 Rev 2 ...

Page 55: ...ip If selected the edges of the coverslip are not detected as specimen to be scanned Depending on the threshold level it is possible that the edges of the coverslip are detected as areas to be digitized Figure 24 Preview image with and without coverslip edge Caution It requires lots of time since it cannot find focus neither on the edges nor on specks to digitize coverslip edges Select Remove cove...

Page 56: ... acceptable for you Otherwise set the threshold value manually Make sure that the detection result is acceptable for you Otherwise set the threshold value manually Manual threshold Set threshold value manually or calculate value on the actual preview with Calculate Threshold function which is active only if setting the value manually This sets the sensitivity of the specimen detection To set the d...

Page 57: ...0 255 This sets the sensitivity of the specimen detection inside the marker area To set the desired threshold value manually change the setting in the Threshold selection box in the range of 0 255 The default value is 212 Everything within marker This function is available only to select if the Use marker with threshold function is activated To scan everything within the marked area check the Scan...

Page 58: ...ive image that you can access from the Live view Union Add the selected areas to the preview Mark area for scanning based on the shape selected in the Preview Toolbar This area will not be scanned Erase Delete selected areas from the preview image Deselection is made based on the selected shape from the Preview Toolbar This area will not be scanned Figure 26 Not scanned selection Edit The size of ...

Page 59: ...r Rectangle tool Draw rectangle shaped area Ellipse tool Draw ellipse selection Polygon tool Area selection by defining a polygon shape Finish area selection by double clicking with the mouse at or near the starting point TMA tool TMA tool is used for selecting TMA spots on TMA slides You can set the selection settings on the following four tabs June 4 2018 Rev 2 3DHISTECH Ltd 59 142 For research ...

Page 60: ... µm in the Core distance fields or select the appropriate values with the arrows Enter the average diameter of the spots in the Core size field or select the appropriate value with the arrows Clear scanmap The entire scanmap area will be cleared and reset to default Use selection box restriction The preview image shows the area that will be digitized with a red and or an orange mask If the Use sel...

Page 61: ...image The following colors are used in the preview image to demonstrate digitization and selection settings Figure 30 Colors in preview image and Label area switching button June 4 2018 Rev 2 3DHISTECH Ltd 61 142 For research and education uses only not for use in diagnostic procedures ...

Page 62: ... example they are outside the selection box They are detected by the selected threshold value Marker If Scan area inside the marker is selected in the Preview panel the preview camera detects the marker pen The inside areas appear in red color and will be digitized Areas scanned in This color is only displayed during scanning Hide all layers All the layers will be hidden existing but not visible S...

Page 63: ...men but on the coverslip Also this makes the focusing sequence faster For manual focusing define the manual focus step size by adjusting the Step size slider and use the two arrow buttons to focus manually This is useful when you are interested in an area that remained blurry with Auto Focus for example the specimen is thicker in that area This does not influence the way slides are digitized in Au...

Page 64: ...ning Click to activate Stage Positioning Tool to navigate on the slide so to perform microscope movements on the Live image with this control function The number at the center of the controller defines the step size by which the stage is moved Value can be entered by hand or with the slider Figure 35 Stage positioning tool This tool offers easy and punctual slide navigation in distinctive steps Se...

Page 65: ...ns Drag Draw Erase Retake preview Settings Toggle deletion always on top Reset zoom Window auto size Clean scanmap Figure 36 Quick toolbar 5 1 3 Quick microscope functions A quick microscope functions tool can be displayed upon right clicking on the background of the main window outside the preview window It includes quick access buttons to main functions Figure 37 Quick toolset for microscope Jun...

Page 66: ...Set coarse focus point Set interpolated focus point 1 Set interpolated focus point 2 Set interpolated focus point 3 Live tools Fast mode Screenshot Magnifier Ruler Image processor plugins June 4 2018 Rev 2 3DHISTECH Ltd 66 142 For research and education uses only not for use in diagnostic procedures ...

Page 67: ...annoramic SCAN II 2 0 User s Guide 5 Scanning modes and settings Add scanmap Auto exposure June 4 2018 Rev 2 3DHISTECH Ltd 67 142 For research and education uses only not for use in diagnostic procedures ...

Page 68: ...osure time of each filter can be defined manually Values such as Calc Exposure time in Microscope Control panel and those that are specified manually are loaded in these fields Value units can be the following microsec millisec sec Exc The given value specifies the excitation intensity in percentage of the illumination unit DG Digital Gain This is camera dependent with Point Grey Grasshopper 3 the...

Page 69: ...focus position You can accept the current Z value by clicking Assign Current Interpolated focus If you select the Interpolated focus option the coarse focus level is calculated from three different focus points of the specimen Carry out a manual focusing sequence in the preview image on those three points Set the correct focus value of the desired preview position by clicking Set in the table of i...

Page 70: ...ze of the specimen Focus Exposure The exposure time during focusing it can have three states Short Normal Long Sample detection The Sample detection panel offers options for setting threshold and the selection of scannable areas Source Brightfield preview a normal type of illumination in the microscope for scanning the slide This option is recommended when scanning in Brightfield mode Fluorescent ...

Page 71: ...imperfections of the slide Greater values result in a less sensitive scanning but it is possible that some of the smaller specimen areas will not be digitized Auto Threshold By clicking the specimen will automatically be detected in the preview image Caution Make sure that the detection result is acceptable for you Otherwise set the threshold value manually or append missing areas with the help of...

Page 72: ...n everything within the marked area selected not selected Threshold enhancement Remove coverslip If selected the edges of the coverslip are not detected as specimen to be scanned Depending on the threshold level it is possible that the edges of the coverslip are detected as areas to be digitized Figure 41 Preview image with and without coverslip edge June 4 2018 Rev 2 3DHISTECH Ltd 72 142 For rese...

Page 73: ...ilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by 100 µm each time Scanmap option The previously saved scanmap can be loaded for use Use Threshold Preview settings set in Microscope Controller Panel Preview window are applied to create a scanmap Loaded scanmap This function is useful if the slides contain areas of interest that cannot be detect...

Page 74: ...nt focus value is the starting point If you set 5 for example one current two focus levels above and below FOVs are captured Therefore it is advised to choose an odd number for the focus levels Separate layers are created and stored this way and can be opened with Pannoramic Viewer The Z stack slide contains the extended focus layer Focus step size determines the spacing between focus levels One s...

Page 75: ...lide The following three options can be selected from the drop down list Intensity statistics legacy compensation algorithm Reduce intensity pixel level analyzation of the acquired image during which the background of the image is reduced based on the comparison of the image recorded by the camera and the compensation image Intensity equalization pixel level analyzation of the acquired image a one...

Page 76: ...NG or BMP image format is selected Figure 43 Image encoding window Compression BMP Lossless uncompressed image format but larger files due to less effective compression It is a raw data file PNG Lossless compressed image format JPG The quality can be set in the value box Greater values result in better quality but larger files The default setting is 80 Bit depth 8 bit Stitching Use Stitching funct...

Page 77: ... Threshold options This section is located at right side of the preview window Scanmap Source is designed to set which type of scanmap is used on the preview image This scanmap is displayed automatically in the Profile Scanmap Source setting Selectable scanmap types are the following Use threshold Load previously saved scanmap from file Custom scan map June 4 2018 Rev 2 3DHISTECH Ltd 77 142 For re...

Page 78: ... Profile Wizard window Scanning process takes a couple of minutes only and cannot be interrupted Pre scan high resolution creates a High Resolution fast FL preview image of every FOV within the selected area in single layer DAPI with an illumination time of 20ms that is displayed in the Profile Wizard window Scanning process is initiated with a simple PreScan the located sample with auto threshold...

Page 79: ...e scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filtering specks and other uninteresting objects out Set the maximum volume of specks manually in the setting window Threshold Auto threshold Select this option to automatically detect the specime...

Page 80: ... to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area Manual setting of Use marker with threshold If this option is selected only the area encircled with a marker pen will be scanned You can define the threshold level by changing the thres...

Page 81: ...on sample and then click on the area of interest on the preview image This will define the Live image that you can access from the Live view Union Add the selected areas to the preview Mark area for scanning based on the shape selected in the Preview Toolbar This area will not be scanned Erase Delete selected areas from the preview image Deselection is made based on the selected shape from the Pre...

Page 82: ... Area selection by defining a polygon shape Finish area selection by double clicking with the mouse at or near the starting point TMA tool TMA tool is used for selecting TMA spots on TMA slides You can set the selection settings on the following four tabs TMA Grid Setting This function is enabled only if a TMA grid has already been placed on the preview image Set grid parameters row and column num...

Page 83: ...e diameter of the spots in the Core size field or select the appropriate value with the arrows Clear scanmap The entire scanmap area will be cleared and reset to default Use selection box restriction If selected only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned The preview ...

Page 84: ...ple Fill holes in scan area and not detected by the selected threshold value Detected sample areas that will be scanned These areas are digitized They are detected on the basis of the selected threshold value Detected sample areas that will not be scanned These areas are not digitized on the basis of their position for example they are outside the selection box They are detected by the selected th...

Page 85: ...displayed during scanning Hide all layers Separate scanning Discrete sample areas will be scanned separately as individual slides If there are two samples on a slide two separate virtual slides will be created Show pre scans pseudo colorized Click the button to display barcode label area To rotate the label area by 180 click Figure 52 Barcode label area window June 4 2018 Rev 2 3DHISTECH Ltd 85 14...

Page 86: ...ue and the Upper limit value is set to 32 of the current focus value This is useful if Auto Focus does not find the focus on the specimen but on the coverslip Also this makes the focusing sequence faster For manual focusing define the manual focus step size by adjusting the Step size slider and use the two arrow buttons to focus manually This is useful when you are interested in an area that remai...

Page 87: ...unctions in this field Exposure Settings You can set the Exposure time weight here displayed under TW in the Channel Settings frame Set Lumencor excitation intensity at the Excitation intensity field The defined value will be used as maximum when applying Auto Exposition time if you activate the Max excit intensity option Caution To prevent over exposure the Excitation intensity value can be modif...

Page 88: ...ed by hand or with the slider Figure 57 Stage positioning panel 5 2 3 Hidden functions Use Ctrl mouse wheel to zoom in or out to the preview area or the Live image Figure 58 Settings of preview quick toolbar A Quick Toolbar pops up by right clicking any of the control menu items It allows a quick access to main functions and for FL these are the following Drag Draw Erase Retake preview June 4 2018...

Page 89: ...pon right clicking on the background of the main window outside the preview window It includes quick access buttons to main functions Figure 59 Quick toolset for microscope Focus Figure 60 Focus Autofocus Set coarse focus point Set interpolated focus point 1 Set interpolated focus point 2 Set interpolated focus point 3 June 4 2018 Rev 2 3DHISTECH Ltd 89 142 For research and education uses only not...

Page 90: ...ttings Objective type Figure 61 Objective type 20x 40x Filters Figure 62 Filters Microscope mode Brightfield Fluorescence Figure 63 Microscope mode June 4 2018 Rev 2 3DHISTECH Ltd 90 142 For research and education uses only not for use in diagnostic procedures ...

Page 91: ...ve tools Fast mode Screenshot Magnifier Ruler Image processor plugins Use pseudo color Add scanmap Figure 64 Live tools Auto exposure Figure 65 Auto exposure June 4 2018 Rev 2 3DHISTECH Ltd 91 142 For research and education uses only not for use in diagnostic procedures ...

Page 92: ...ow Figure 66 Progress of the profile modification history Once you are moving the mouse cursor over a unit all of the parameters will become visible in a pop up window Figure 67 Details of parameter modification For the easier perspicuity modifications can be observed in a pop up window by clicking the button in which both the original and the modified values are presented Click to save parameters...

Page 93: ...oramic SCAN II 2 0 User s Guide 5 Scanning modes and settings Figure 68 Profile history tree June 4 2018 Rev 2 3DHISTECH Ltd 93 142 For research and education uses only not for use in diagnostic procedures ...

Page 94: ...lso profile assignment to slides of prepared virtual magazines is available to be performed It is also possible to scan to different locations with each profile and virtual slides can be created and stored in different folder or server Planner module offers you three window layout types for planning scans located under the Preferences Planner Layout Selector menu Slide view with card Table Card co...

Page 95: ...e initiated Stop scan Stop actual process Take all previews Preview images of all the slides in the magazine are taken automatically Select the required preview type from the following Brightfield Pre scan Pre scan high resolution Pre scan high resolution Figure 69 Take all preview selector Save planner A scanning plan containing all parameters and profile assignment will be saved Load planner The...

Page 96: ...and settings Clear planner Figure 70 Planner menu Jump to scanned Loads the planner view of the actual slide during scanning Preferences Help June 4 2018 Rev 2 3DHISTECH Ltd 96 142 For research and education uses only not for use in diagnostic procedures ...

Page 97: ... from all slides Detach profiles from slides 5 3 3 General functions at the slide menu Mark empty slide positions Define range in the Empty slide range boxes to set multiple slide positions as empty For single slides enter set slide position with the arrows in the Empty single slide box or right click on a slide and select Mark as empty Click Reset empty definitions to cancel slide selections as e...

Page 98: ...lector to activate this view Depending on the actual view preference selected at slide positions can have a horizontal or vertical layout Slide preview and the list of the assigned profiles are displayed Figure 72 Vertical slide view with card June 4 2018 Rev 2 3DHISTECH Ltd 98 142 For research and education uses only not for use in diagnostic procedures ...

Page 99: ...oved for from the slide respectively The parameters of the assigned profile is displayed in a card The colors of a Brightfield and a Fluorescence profile cards are different Figure 74 Brightfield profile card and Fluorescence profile card June 4 2018 Rev 2 3DHISTECH Ltd 99 142 For research and education uses only not for use in diagnostic procedures ...

Page 100: ...de actual status of the slide is presented here If the slide is under scanning the Scanning if scanning has been interrupted by some error the Failed text is visible NOTE If slide status is marked as Failed delete status before scanning by clicking If the virtual slide is created the scanning is finished the location path of the destination folder is displayed To re scan and thus recreate the slid...

Page 101: ... or FL if the scanner is capable to operate in these two scanning modes Figure 75 Table view mode In Table view the following information are displayed in the profile strip based on the loaded profile Profile name Illumination Objective type Filters Progress Properties The location of the virtual slide with the selected profile can be defined Scan result Scan duration Scanned FOV S Total FOVs June...

Page 102: ... button each of the slide previews are displayed in the window Add profiles by clicking and detach profiles by clicking Functions are the same as with the other modes Figure 76 Card collection view mode June 4 2018 Rev 2 3DHISTECH Ltd 102 142 For research and education uses only not for use in diagnostic procedures ...

Page 103: ...e view type of the Profile Setting panel Slide preview is displayed in the Preview window in which the scanmap can be modified until beginning the scanning process Every aforementioned Profile setting can be modified depending on the scan profile type being Brightfield or Fluorescence Figure 77 Selected profile and expanded Preview window in Planner mode June 4 2018 Rev 2 3DHISTECH Ltd 103 142 For...

Page 104: ...n is included in the progress log list during scanning Filter Elapsed time Location Slide name Free space FOV number 5 6 Services and Settings Activate Services by clicking and Settings by clicking at the right side of the main menu bar 5 6 1 Services Activate Services by clicking at the right side of the main menu bar Camera settings Position Objective type Select the type and the magnification l...

Page 105: ... slide area near the edges will not be scanned to record fast preview image If inactive Fast Preview processing becomes slower Cameras Activate BF and or FL mode for the camera The software automatically loads the camera settings upon clicking the Test and apply camera settings button June 4 2018 Rev 2 3DHISTECH Ltd 105 142 For research and education uses only not for use in diagnostic procedures ...

Page 106: ...rsion is applied Custom parameters are freely customizable as follows Color Scheme Calibrated Scheme is defined by the color calibration slide Legacy a Color scheme calibrated for the previous software version is applied Raw the color information of the recorded raw image is applied White Point D65 color temperature according to a standard illuminant D65 white point value is applied 6500K daylight...

Page 107: ...on Camera rotation angle is measured Alpha blending The two images are blended Lower image position Moves the upper image sideways in distinctive steps Reset all camera rotation Click this button to set camera rotation values to default Save settings by clicking Filter settings On this panel you can define which filters occupy which turret positions Select filter hardware positions from the drop d...

Page 108: ...ocusing during scanning Barcode settings By predefining barcode type foreground color black or white the color of the barcode and other settings you enable the Read Barcode option when using the control software To display an image of the barcode area click You can redefine the barcode reading area by dragging the edges of the blue square To check whether the barcode reading settings are correct d...

Page 109: ...n unsuccessful There might be no barcode present Barcode reader library Select MIL barcode library or Embedded barcode library General Barcode settings Inverse barcode color Activate to invert foreground and background colors of the barcode Use barcode compensation A compensation image is used during barcode reading June 4 2018 Rev 2 3DHISTECH Ltd 109 142 For research and education uses only not f...

Page 110: ...identification Barcode types Linear Stacked linear Postal Two dimensional Second barcode priority The software is capable to read two barcodes at the same time If activated the second barcode will be the barcode used for slide identification Note When having two barcodes on the slide barcode layout must be consequential June 4 2018 Rev 2 3DHISTECH Ltd 110 142 For research and education uses only n...

Page 111: ...n menu bar Basic settings On this panel you can define the swap file location set shutter auto close time in FL and create new compensation image for preview camera if needed Click Apply to accept modifications Prescan settings June 4 2018 Rev 2 3DHISTECH Ltd 111 142 For research and education uses only not for use in diagnostic procedures ...

Page 112: ...Occurred For Slide scanning has finished and Scanning error has occurred you can define the external software by entering the file path in the Application box or by browsing for it by clicking If you define parameters in the Parameters field it will pass them to the software that it starts If no parameter is defined then the parameter will not be passed The default parameters are the following For...

Page 113: ...recipients on the location of the scanner or the slide set you are working with Click to test settings by sending an e mail to the address defined in the E mail To field after you have finished to check their relevancy before applying them First click SMTP setup to display the E mail settings window in which you can dedicate an e mail server through which the software sends e mails to the selected...

Page 114: ...ing medium irregularities BF cameras field displays the active camera Currently there is only one active camera for Brightfield mode Objectives field displays the objective used for scanning There might be specks or minor etches on the surface of the compensation slide that require modifying the threshold settings Therefore the scanner will not use those areas for the creation of the compensation ...

Page 115: ... far away from each other This means multiple users can connect to the device at the same time The user of the scanner will be the host with direct access to the scanner Note Both the client s and the host s scanner software version must be identical Once client users have connected they will be able to reach the following functions of scanner Live image Preview window Profile content Stage contro...

Page 116: ...e version of the scanner software 2 Type in your nickname used during the session 3 Enter Host address and Port number 4 Click Connect On Client side the following functions are unavailable inactive Selection box Scan properties Separate scanning Note During a fluorescence Live consultation the shutter of light path will be closed automatically during the host time in order to save the sample from...

Page 117: ... Options Focus frequency in Fluorescent mode Focus frequency in Brightfield mode Compression procedure Use of a fixed compensation image in Brightfield mode ON OFF Use of Save focus quality ON OFF Use of stitching ON OFF Determination of the area to be scanned Use of automatic threshold specimen Use of specimen threshold value Use of marker pen threshold and specimen threshold values Use of scan e...

Page 118: ... ON OFF Intensity statistics Intensity reducing Intensity equalization Sharpening ON OFF Use of skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Custom extended focus Other settings Limitation of focus range ON OFF Enable disable Multilayer options Use of extended focus or Z stack step size and focus level Output resolution June 4 2018 Rev 2 3DHISTECH Ltd 1...

Page 119: ...azardous materials and disposed in compliance with the currently valid legal requirements Dust specks and humidity may decrease or harm the operating capability of the device Protect it with dust cover when not in use Switch the power off before covering it Avoid touching the lamp bulb Wait for about 15 minutes to allow the bulb to cool down and disconnect the power plug before changing the bulbs ...

Page 120: ... clean greasy surfaces it is recommended to apply soapy water on a piece of lint free cotton cloth and gently rub the surface 6 1 2 Cleaning the magazine Do not clean the magazines with xylene because it might harm the plastic We recommend to apply Isopropanol on a piece of lint free cotton cloth and gently rub the surface instead In case the magazine is damaged use either order a new one as inser...

Page 121: ...ally see section 5 3 4 Removing a slide 5 Reattach protective covers 6 Reconnect 24V power supply and control computer to line power supply 7 Switch on the 24 V power supply 8 Switch on the control computer 9 Launch control software Magazine jammed 1 Exit control software 2 Switch off control computer and 24V power supply disconnect power cable 3 Remove protective covers see section 5 3 1 Removing...

Page 122: ...xture Contact Thermo Fisher Scientific Service for support Slide is often positioned incorrectly Guiding fault in transport system Check if faulty positioning disappears after the selection of a different type of magazine for example universal magazine Contact Thermo Fisher Scientific Service for support Digitization process is extremely slow Extended focusing option is activated Deactivate the Ex...

Page 123: ...on 6 2 1 Fluorescent Applications optional The switching of the Lumencor SPECTRA 6 cannot be triggered in spite of trigger connection through the camera Contact Thermo Fisher ScientificService for support No suitable exposure time can be found Signal is too weak Lumencor SOLA SM II is switched off Switch light source on otherwise contact 3Thermo Fisher ScientificService for support June 4 2018 Rev...

Page 124: ...order to eliminate the problem Before removing the covers exit the control software switch off the 24 V power supply and disconnect the power cables Warning Avoid leaning over the device when opening it Figure 79 Removal of covers Five eccentric screws 3 are located on the bottom face of the base plate 4 They attach the covers to the base plate 1 Use an open end wrench W F 10 5 to turn the screws ...

Page 125: ...n camera are squeezed as you replace the covers 6 3 2 Removing a slide If a slide got jammed or has suffered breakage during the process of digitization stop the process and if possible move the slide holder to a position where the slide can be easily removed by clicking the Emergency Manual Slide Removal Position button see section 4 3 6 Service panel Warning Crush hazard Before you remove a jamm...

Page 126: ...ever 1 to the left and keep the lever in this position 3 Seize the slide loader 2 by the end where the lever is and turn it up by the necessary degree to make the removing of slide possible 4 Remove slide loader unit 5 Press clamping lever 4 down The slide position lock releases 6 Retrieve slide 3 from the holder June 4 2018 Rev 2 3DHISTECH Ltd 126 142 For research and education uses only not for ...

Page 127: ... motor block groove again 8 Press the slide loader down to mechanical stop position in which the locking lever must engage 1 Use moderate force to press the loader part opposite the motor in clamp direction 2 until this part mechanically engages too 9 Close the protective cover again see section 5 3 1 Removing the protective covers 10 Launch the control software 6 3 3 Installing and Removing the F...

Page 128: ...l may lead to injury 5 Hold the filter module 3 by its handling pads one on the right one on the left lateral side of the module and insert it in forward tilted position from above into the upper spring loaded clamps 1 at the filter wheel 6 Press the filter module down until it safely connects to the bottom spring loaded clamps 2 of the filter wheel Mounting position of the filters excitation filt...

Page 129: ...moving the protective covers Warning Crush hazard Remember to stop the running digitization process terminate the software session and turn off the power supply before removing a jammed magazine Caution Check that the magazine is not tilted so that it rests on both of the horizontal guide rails June 4 2018 Rev 2 3DHISTECH Ltd 129 142 For research and education uses only not for use in diagnostic p...

Page 130: ...tioned if vertically aligned exactly one above each other Turn the knurled wheel 4 by hand until the tappets are in their initial position again and the magazine flatly rests on both horizontal guide rails Note Any manipulation performed on a mechanical component for example transporting system by the user must be followed by a complete Pannoramic SCAN II initialization routine software restart 6 ...

Page 131: ... carrying capacity limitations You can find the weight data of the base unit in section 6 Technical Data To transport the Pannoramic SCAN II do the following 1 Turn power supply off and detach all cables 2 Pull carrying handles out 2 until mechanical stop position A 3 Turn carrying handles by 90 B towards the base unit to secure them 4 Now you can transport Pannoramic SCAN II with the help of anot...

Page 132: ...e unit with fluorescent option approx 29 kg 24V 100W power supply approx 550 g Ambient conditions Transportation shipment packed Permissible ambient temperature 40 C to 70 C Storage Permissible ambient temperature 0 C to 60 C Permissible relative air humidity non condensing 75 Operation Permissible ambient temperature 10 C to 35 C Permissible relative air humidity 75 Altitude at installation site ...

Page 133: ...ed site closed room facilities Electrical protection class I Internal protection degree IP 20 Electrical safety in compliance with UL 2601 1 TÜV EN 60601 CE EN60601 1 2 2001 Over voltage category II Radio interference suppression in accordance with CISPR 11 EN 55011 class B Line input voltage 100 V AC to 240 V AC Line input frequency 50 60 Hz Power consumption max 100 VA Secondary voltage 24V DC S...

Page 134: ...jective and 0 63x C mount adapter 0 14µm Pixel resolution with 40x objective and 1x C mount adapter 0 09 µm Connection type USB 3 0 pco edge 4 2 13 3 mm 13 3 mm sCMOS CIS2020 Pixel size 6 5 µm x 6 5 µm Camera resolution 2048 x2048 active pixel Camera max speed 100 fps at full resolution 2048 2048 pixel Bit depth 16 bit Pixel resolution with 20x objective and 1x C mount adapter 0 33µm Pixel resolut...

Page 135: ...soft Windows 7 Professional SP1 64 bit EN CPU Xeon E5 2609v3 1 90GHz 15MB cache RAM 32 GB DDR4 Hard disk 1 5 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices Keyboard mouse Ports 2xDouble CameraLink port 1 FireWire 1394 A 4 USB 2 0 GB Ethernet 2018 June 4 Rev 1 3DHISTECH Ltd 135 142 ...

Page 136: ...ch located on the backside of the device Disconnect all the cables of the scanner 4 Remove the main camera and camera adapter 5 Turn off and disconnect all the cables of the workstation and display Main parts and their accessories 1 BOX 1 Big carton box a fixing foams for the angles of the scanner box 2 BOX 2 SCAN II scanner large carton box a Scanner unit b objective s June 4 2018 Rev 2 3DHISTECH...

Page 137: ...mera b power supply connector c power supply cable d camera adapter s e 10 wrench f objective spacer set g magazines for SCAN 150 P250 h dongles software and driver disks in 3DH SW box i slide checker j filter cubes if any 5 BOX 5 Cables a 3 m USB cable b USB cable of the scanner c trigger cable d camera protector 6 BOX 6 FL lamp if any a FL lamp b lamp power supply c power supply cable d adapter ...

Page 138: ...ith a vertical carton slab Space 1 for accessories PC cables etc Space 2 for BOX 2 scanner Figure 2 1 BOX 2 scanner box 2 Fixing foams for underneath BOX 2 3 Fixing foams for above BOX 2 4 Bottom part of BOX 1 5 Top of BOX 1 6 BOX 3 7 BOX 4 5 6 June 4 2018 Rev 2 3DHISTECH Ltd 138 142 For research and education uses only not for use in diagnostic procedures ...

Page 139: ...Pannoramic SCAN II 2 0 User s Guide Appendix Packaging instructions Figure 3 June 4 2018 Rev 2 3DHISTECH Ltd 139 142 For research and education uses only not for use in diagnostic procedures ...

Page 140: ... holding the scanner at its motherboard between its feet and taken inside the BOX 2 s lower part onto the foams inside it The shape of the rubber foam defines the orientation how they should put on After the scanner and foams are taken in you can place the upper part of the box of the scanner Now place the BOX 2 into BOX 1 and place the fixing foams around Figure 4 Packing the accessories Place in...

Page 141: ...rticularly large or bulky packages cannot be stored in warehouses or sheds they must be carefully covered with tarpaulins Recycling This indicates that an object is capable of being recycled CE The symbol shows that the device complies with the essential requirements of the relevant European health safety and environmental protection legislation in practice by many of the so called Product Directi...

Page 142: ...25 130 Focus 14 20 106 115 116 120 121 L Lumencor 19 24 117 121 Lumencor Spectra 6 Light Engine 13 20 132 M Marker 115 P Pannoramic 8 Pannoramic SCAN II 8 9 10 11 13 14 15 17 18 19 20 22 24 29 119 122 128 129 Pannoramic Viewer 20 120 Pco edge 14 132 Preview 23 27 S Scan 13 14 30 105 112 115 116 120 123 132 Scanner 8 112 June 4 2018 Rev 2 3DHISTECH Ltd 142 142 For research and education uses only n...

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3DHISTECH Ltd. Pannoramic SCAN II 2.0, User Manual, Page: 95 / 142

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Summary of Contents for Pannoramic SCAN II 2.0

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