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3D Histech Pannoramic 250 FLASH II User Manual Download Page 115

Pannoramic 250 FLASH II 1.18.1 User’s Guide

4 Software Description

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Use of removing specks according to the set value (ON/OFF)

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Use saved scan area

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Use selection box (ON/OFF)

Fluorescent settings

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Filter position(s)

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Selected focus channel

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Selected stitching channel

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Flat field correction (ON/OFF)

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Sharpening (ON/OFF)

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Use of skip empty field-of-views (ON/OFF)

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Do not use extended focus on empty field-of-views (ON/OFF)

Other settings

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Limitation of focus range (ON/OFF)

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Use of objective position 

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Enable/disable Multilayer options

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Use of extended focus or Z-stack step size and focus level

May 29, 2014 – Rev. 1

3DHISTECH Ltd.

115

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137

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Summary of Contents for Pannoramic 250 FLASH II

Page 1: ...Pannoramic 250 FLASH II 1 18 1 User s Guide May 29 2014 Rev 1 ...

Page 2: ... 18 1 2 3 Control Software 22 2 Installation 24 2 1 Control computer ports 24 2 2 Connectors and cables 25 2 3 Mounting the Lumencor Spectra unit 26 3 Operating Slides and Magazines 29 3 1 Preparing Slides and Magazines 29 3 2 Affixing Barcode Stickers to Slides 30 3 3 Inserting and Removing Slides 31 3 3 1 Insert slides into a magazine 31 3 3 2 Insert and remove magazines 32 3 3 3 Opening Closing...

Page 3: ...utine work panel 81 4 5 2 Scan Options 86 4 5 3 Preview panel 90 4 5 4 Hardware panel 94 4 5 5 Service panel 97 4 6 Using Fluorescent Automatic Mode 98 4 6 1 Routine work panel 98 4 6 2 Barcodes panel 103 4 6 3 Preview panel 106 4 6 4 Focus panel 107 4 6 5 Service panel 107 4 7 Scan To Server 108 4 8 Using Profiles 114 5 Troubleshooting and Maintenance 116 5 1 Safety Information 116 5 1 1 Cleaning...

Page 4: ...ser s Guide 5 3 5 Installing and Removing the Filter Module Fluorescent Option 127 5 3 6 Removing a Magazine from the Transporting System 128 5 3 7 Transporting 130 6 Technical Data 132 Index 136 May 29 2014 Rev 1 3DHISTECH Ltd 4 137 ...

Page 5: ... results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitized slide s that stems from or is associated with use of Product digitized 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...

Page 6: ...ONSEQUENTIAL DAMAGES OF ANY KIND OR FOR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE AND ON ANY THEORY OF LIABILITY ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE Further Information For the latest information on 3DHISTECH products and services please visit our website at the following URL http w...

Page 7: ... 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 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 not to work properly if this instruction is not followed Note Calls attention t...

Page 8: ...atory use Part 2 101 Particular requirements for in vitro diagnostic 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 including Amendment 1 or a later version of the s...

Page 9: ...services will be null and void in any such case Warning Insert the power cord plugs only into a grounding outlet The protective action must not be rendered ineffective by extension cables without protective conductor The Pannoramic 250 FLASH II has a built in protection which must not be rendered ineffective by extension cables without protective earth ground conductor Warning The operation of the...

Page 10: ... operation Please note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the insert Warning Clogged or covered ventilation slots may result in a heat build up with a damaging effect for the Pannoramic 250 FLASH II In extreme cases this may also cause fire Keep the ventilation slots always unobstructed and refrain from inserti...

Page 11: ...t No warranty will be accepted in cases of natural wear notably wear and tear parts or improper product handling The Product Manufacturer will refuse any liability in the event of damage resulting from faulty operation negligence or unauthorized intervention into the product notably from the replacement of product parts or the usage of accessory parts from other manufacturers Any such case will vo...

Page 12: ...ical damage and covalent modification therefore fluorescent signals cannot be properly detected SWAP A file that is used as a temporary location on the computer to store information that is not currently used by the RAM Virtual Slide Slide A digital 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 nam...

Page 13: ... information loss Warning Any modification to a hardware or software component of the PC will highly affect the functionality of the scanner program 1 1 2 Features and Benefits The Pannoramic 250 FLASH II offers world class brightfield and fluorescent whole slide scanning on up to 9 channels An outstanding 0 19 µm pixel in Brightfield and 0 16 µm pixel in Fluorescent resolution is achieved with a ...

Page 14: ...orescence and Brightfield feature which improve the visual appearance of digital slides Focus algorithm finds the focus which is most appealing to the human eye Motorized camera changer for color camera for brightfield and a cooled monochrome CCD camera or a scientific CMOS camera for fluorescence Motorized Objective changer for two objectives Plan Apochromat 0 8 NA or 0 95 NA 3MP camera for barco...

Page 15: ...scription 1 1 3 Warning and Information Labels The following figure contains the labels used on the Pannoramic 250 FLASH II main unit and the HXP 120 fluorescent illumination unit Figure 1 Warning and information labels May 29 2014 Rev 1 3DHISTECH Ltd 15 137 ...

Page 16: ...it The following figures 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 magazines 3 Cover release hole 4 Power supply switch 5 USB port 6 Main power switch 7 Power supply cable connector May 29 2014 Rev 1 3DHISTECH Ltd 16 137 ...

Page 17: ...gure shows the main parts of the Pannoramic 250 FLASH II system Figure 3 Pannoramic 250 FLASH II system overview 1 Pannoramic 250 FLASH II base unit 2 Monitor 3 Mouse 4 Control computer 5 Keyboard 6 Slide magazine with cover 7 HXP 120 fiber coupled fluorescent illumination unit optional used with AxioCam MRm Rev3 8 Lumencor Spectra Light Engine illumination unit optional used with pco edge 4 2 cam...

Page 18: ... for high quality sensitive fluorescent applications CIS VCC FC60FR19CL 1 CMOS camera for high quality brightfield applications allowing ultra fast scanning up to 135fps 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 1x adapter ...

Page 19: ...e set and switched by the software automatically without any human assistance This system also enables switching between brightfield and fluorescent scanning by one click Warning The installation of the cameras in Pannoramic 250 FLASH II must be carried out by trained professionals In any other case the warranty will be automatically voided Supplier Distributor is not liable for any damages caused...

Page 20: ... FLASH II the first objective 1 and the second objective 2 20x NA 0 80 and 40x NA 0 95 objectives can be used You can change between the objectives with one click This helps you to select the magnification and resolution that is the most suitable for your requirements Important Note that higher resolution results in slower digitization process May 29 2014 Rev 1 3DHISTECH Ltd 20 137 ...

Page 21: ...unit completely equipped with CIS VCC FC60FR19CL camera for Brightfield scanning with AxioCam camera and HXP 120 illumination unit trigger cable and filters for fluorescence scanning Pannoramic 250 FLASH II Advanced Fluorescence Option base unit completely equipped with CIS VCC FC60FR19CL camera for Brightfield scanning and with pco edge 4 2 camera and Lumencor fluorescence illumination unit trigg...

Page 22: ...art HXP 120 illumination unit can be used only with AxioCam MRm Rev3 camera Lumencor Spectra 6 Light Engine illumination unit can be used only with pco edge 4 2 camera 1 2 3 Control Software Pannoramic Scanner control software Optional Fluorescence Extended focus Z stack Barcode reader licensed feature May 29 2014 Rev 1 3DHISTECH Ltd 22 137 ...

Page 23: ...c Viewer software fully functional Optional CaseCenter Pannoramic Viewer TMA module 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant FISHQuant CISHQuant and DensitoQuant modules TumorBoard module E School Encoder May 29 2014 Rev 1 3DHISTECH Ltd 23 137 ...

Page 24: ...stallation that is not carried out by a professional person Only qualified service assistants are allowed to install the hardware and software The product is ready for use after installation 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 short distance by disconnecting cables and detaching hardware ...

Page 25: ... camera and control computer CIS a pair of CameraLink cables between CIS camera and control computer pco edge 4 2 a pair of CameraLink cables between pco edge 4 2 camera and control computer Video cable between monitor and control computer Power supply cable between 230V 110V and monitor Power supply cable between 230V 110V and control computer Power supply cable between 230V 110V and Pannoramic 2...

Page 26: ... to be attached to the Pannoramic 250 FLASH II base unit 1 Switch off the main power supply on the rear panel of the Pannoramic 250 FLASH II and disconnect the power cables see section 1 1 4 Main parts of the Base Unit 2 Open protective cover see section 5 3 1 Opening the protective cover 3 Find the mounting hole 1 at the back side of the Pannoramic 250 FLASH II unit and rotate the Lumencor unit 2...

Page 27: ...locking lever by moving it to the left see Figure 10 Step 2 If the lever stucks at around the center position apply a bit more pressure to the Lumencor unit Figure 10 Mounting the Lumencor unit 7 Close the protective cover of the Pannoramic 250 FLASH II 8 Connect power supply cables both of the scanner and the illumination unit 9 Connect TTL trigger cable between pco edge 4 2 camera out 4 and the ...

Page 28: ...Pannoramic 250 FLASH II 1 18 1 1 User s Guide 2 Installation Figure 11 Lumencor Spectra 6 LE connecting ports May 29 2014 Rev 1 3DHISTECH Ltd 28 137 ...

Page 29: ...led or 90 cut corners Edges Grounded or cut Note The distance between slide edges and the edges of the mounted coverslip should be 1 2 mm and they should be parallel with each other Caution 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 loading less rel...

Page 30: ...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 Figure 12 Slide with a barcode sticker The label area 1 is recorded by the preview camera and can be displayed by the c...

Page 31: ...arcode identification Do not let barcode sticker protrude from slide edges or stick on the coverslip surface 3 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 3 3 1 Insert slides into a magazine Figure 13 Inserting slides into a magazine May 29 2014 Rev 1 3DHIS...

Page 32: ...n actuating it by the magnet in the side of the magazine 4 Note You should insert several slides into a magazine without empty slots Begin the insertion on position 1 of the magazine Caution To insert or remove a filled magazine from the device or when transporting it without its cover 5 slightly tilt it to its closed side to prevent the slides from accidentally falling out Magazines should always...

Page 33: ...If the system does not detect the inserted magazine in the input stack check whether you have inserted it correctly If the magazine is placed correctly there may be a problem with the sensor In this case contact 3DHISTECH Service Support 1 Remove magazine cover before you insert magazines Caution Replace magazine cover when magazine is not currently used or is stored for a longer period The cover ...

Page 34: ...heels 6 or magazines Figure 15 Gear wheels Caution Make sure that the magazines are properly placed between the rails because it can cause serious damages in the feeding mechanism Figure 16 Misplaced magazine Note The input stack can be filled with a maximum of 9 magazines in addition to the one in the magazine loader May 29 2014 Rev 1 3DHISTECH Ltd 34 137 ...

Page 35: ...osing the FL protective cover Figure 17 Opening the FL protective cover Open the protective cover by moving it upwards and lay it down to the upper cover of the unit then insert magazines When scanning slides close the FL protective cover 1 of the base unit after inserting the magazine s into the input stack 1 Mount the protective cover properly 2 After finishing the digitization process open the ...

Page 36: ...ramic Scanner 2 During start up all motors the preview camera and the scan camera are initialized After successful initialization the program displays a Mode selection window Figure 18 Mode selection window The selection window displays two Brightfield and Fluorescent scan modes Automatic for digitizing multiple slides Manual for digitizing individual slides where contrast ratio is critical due to...

Page 37: ...ed Note It is recommended to use specimens with identical staining for a given batch of magazines in Automatic mode 4 1 2 Exiting the software If you close a mode or one of the options window the Mode selection window turns active again To exit the software click X in the title bar of the Mode selection window and the magazine s on the input stack can be unloaded to the output stack automatically ...

Page 38: ...ng the 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 Note You can only scan the barcode type that you have previously set If you want to read several barcode types you always have to set the current barcode type before reading it May 29 2014 Rev 1 3DHISTECH Ltd 38 137 ...

Page 39: ... barcode area click You can redefine the barcode reading area by dragging the edges of the green square To check whether the barcode reading settings are correct display the barcode digits in the Barcode field by clicking Note If you did not set the barcode type correctly or there is no barcode in the barcode area the software will display the following error message Barcode recognition unsuccessf...

Page 40: ... Use barcode compensation image to use the previously created compensation image for scanning the label area You can take a new compensation image from a slide with blank barcode sticker by clicking You need a slide with a label area covered fully by a white sticker The compensation image improves the effectiveness of barcode reading 4 2 2 Image Compensation You can use a saved compensation image ...

Page 41: ...re 21 Image compensation Camera Selection This field displays the active camera Currently there is only one active camera for Brightfield mode Objective Selection To select the objectives to be used for creating a new compensation image select the checkbox es May 29 2014 Rev 1 3DHISTECH Ltd 41 137 ...

Page 42: ...ld level in the box Use Selection Box Select this if you have a compensation slide that has only certain predefined areas for creating compensation images due to the type of the compensation slide or because the compensation slide has faded in some areas To create the compensation image s click Click the Stop button to interrupt the process The Progress bar at the bottom of the window displays the...

Page 43: ...terested in Base Settings Figure 23 Base Settings panel Objective type You can select the type and the magnification level of the objectives Camera type Select the correct camera types in Pos 1 and Pos 2 fields then the software automatically loads the camera settings upon clicking the Test and Apply Camera Settings button Save the settings by clicking May 29 2014 Rev 1 3DHISTECH Ltd 43 137 ...

Page 44: ...cor is configured as illumination unit the corresponding Enable Lumencor hardware trigger option is displayed on the form Filter Settings Figure 24 Filter Settings panel On this panel you can define which filters occupy which turret positions May 29 2014 Rev 1 3DHISTECH Ltd 44 137 ...

Page 45: ... Rotation panel Caution If you have transported the product or changed the camera there is a possibility that the camera does not display the images properly If you experience such problems contact 3DHISTECH service support Do not modify these settings yourself May 29 2014 Rev 1 3DHISTECH Ltd 45 137 ...

Page 46: ...on Z Difference This function is available only for fluorescence settings it enables you to set the basic focus differences between the filters This facilitates more precise focusing during scanning Figure 26 Z Difference panel May 29 2014 Rev 1 3DHISTECH Ltd 46 137 ...

Page 47: ...oved manually after opening the cover see section 5 3 1 Opening the protective cover Slide Removed Manually Click this button to notify the software that you have removed the slide manually New Compensation Image for Preview Camera By clicking this button you can create a new compensation image if the preview camera fails to display a satisfactory preview image Note The software asks you to remove...

Page 48: ...Slide Scanning Finished Scanning Error Occurred For Slide Scanning Finished and Scanning Error 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 box it will pass them to the software that it starts If no parameter is defined then the parameter will not be passed The default par...

Page 49: ...xt for example to inform recipients on the location of the scanner or the slide set you are working with Click Test 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 Setup to display the Messenger Setup window in which you can dedicate an e mail server through which the software send...

Page 50: ...ts that can be selected under the Send Message when field Figure 30 Users window 4 3 Using Brightfield Manual Mode You can use Brightfield Manual mode to set the scanning preview and image quality settings You can also set profile settings here and start scanning in Brightfield Manual mode This Manual mode is perfect for digitizing slides that require unique settings or single slides You can also ...

Page 51: ...ain window of control software 1 Panel with scanner functions and setting 2 Scan camera live image display area 3 Preview image recorded by the preview camera 4 Preview image editor toolbar 5 Information area about the digitization progress May 29 2014 Rev 1 3DHISTECH Ltd 51 137 ...

Page 52: ...section To insert and remove slides To move the lowest magazine in the input stack to the loading position click To move the magazine into the output stack click To move a selected slide from its magazine to the specimen holder either enter its position number to the Current slide field and click To return the slide to its magazine click To move all magazines to the output stack click May 29 2014 ...

Page 53: ...rt scanning with but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from the selection menu click Load To delete the current profile click Delete The Objective position field sets t...

Page 54: ...ng predefined image formats and a subsequent custom option from the Image Quality drop down list in the Image Encoding section of the window Excellent JPEG 90 Good JPEG 80 Medium JPEG 60 Low JPEG 30 Custom If choosing this option the Image encoding window is displayed on which you can select from different image formats Accordingly further adjustments can be made except if PNG or BMP image format ...

Page 55: ...h illumination during continuous stage movement Stop and go mode The stage stops its movement at each FOV while the image is acquired and then goes to the next field to acquire the following FOV Note The Stop and go mode is useful to digitize coarse textured specimen and to create detailed images although scanning takes more time Scan Settings Focus distance in field of views the distance of focal...

Page 56: ... software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading The Scanned slide destination field determines where to digitize the virtual slides Select the Scan To CaseCenter function to scan directly to a dedicated CaseCenter server For information on how to use the ScanToServer application see section 4 7 Scan To S...

Page 57: ...tted Darkfield illumination This option is recommended for you to choose in case the sample is not correctly stained for example the specimen is lacking contrast when using Brightfield illumination The image is created within a minute Scan specimen with auto threshold This automatically detects the specimen in the preview image Important Make sure that the result of detection is acceptable for you...

Page 58: ...le weak contrast it can help 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 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 th...

Page 59: ...se Remove coverslip function on TMA slides The layout of TMA slides may mislead the detecting algorithm Fill holes in scan area 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 filtering speck...

Page 60: ...load preview mask or TMA grid Use selection box 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 4 3 4 Preview area scanned by preview camera The preview image shows the area that will be digitized with a red and or an orange mask If the Use selection box is en...

Page 61: ...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 threshold value Marker If Scan marker specified area 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 on...

Page 62: ...rea of interest on the preview image This will define the Live image that you can access from the Focus panel To display the original image created by the preview camera Brightfield or Darkfield click To shrink or enlarge the preview image set the zoom level at the left Size selection box 100 600 To fit the preview image to the preview area click Fit Choose from the Scanned or the Not scanned opti...

Page 63: ...the selection settings on the following four tabs Select panel Figure 42 TMA tool Select To create a new TMA object click New To select an existing TMA object click on the object name The selected object name will highlight To delete an existing TMA object click Delete Block panel Figure 43 TMA tool Block May 29 2014 Rev 1 3DHISTECH Ltd 63 137 ...

Page 64: ...ppropriate values with the arrows 3 Enter the distance between two spots on the X and the Y axis in μm in the Spot distance X μm and Spot distance Y μm fields or select the appropriate values with the arrows 4 Enter the average diameter of the spots in the Side length of μm field or select the appropriate value with the arrows Grid panel The Grid panel displays the previously set grid settings Fig...

Page 65: ...oving of the TMA selection spots that are displayed on the preview image To move the spots enter the pixel value in the Move field or use the arrows To rotate the spots enter the degree value in the Rotate field or use the rotation arrows Figure 45 TMA tool Move panel with preview May 29 2014 Rev 1 3DHISTECH Ltd 65 137 ...

Page 66: ... 1 User s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degrees checkbox Figure 46 Label area 4 3 5 Focus panel Figure 47 Focus panel May 29 2014 Rev 1 3DHISTECH Ltd 66 137 ...

Page 67: ...d 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 Automatic mode The manual focus is mainly for setup purposes not for using the product as a traditional microscope Define the manual focus step size by adjusting the Step size slider or search for the sharpest focus on the current field of view ...

Page 68: ...f focus levels 7 Focus step size 5 4 3 6 Service panel Figure 49 Service panel This panel contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective cover Slide Removed Manually Click this button to notify the software that...

Page 69: ...Display field and toolbar for live images The display field for live images displays images of the scan camera The live image is displayed if no current digitization process is running Figure 50 Display field and toolbar for live images May 29 2014 Rev 1 3DHISTECH Ltd 69 137 ...

Page 70: ...ves the current image as BMP or JPEG file Fast live mode live images are displayed with a frequency of at least 10 images second If an exposure time is set to more than 100 ms the pixel values are multiplied accordingly for example if an exposure time of 200 ms is set the pixel values are multiplied by 2 and the exposure time is reset to 100 ms Therefore the resulting images will have a higher noi...

Page 71: ... disk space in the last line Available disk space of the information area of Current Slide Scan Progress You can interrupt a running digitization process by clicking This button is only enabled if a digitization process is in progress 4 4 Using Brightfield Automatic Mode Compared to Manual mode it has less options in some dialogs but it has an additional Barcodes tab 4 4 1 Routine work panel Figur...

Page 72: ...de parsing during scanning If you do not want to load all slides you can specify the first and last slide to be loaded in the Scan Range by entering the appropriate slide numbers in the selection boxes of First slide and Last slide Start scanning by clicking the button but before that it is recommended to go through all the settings and make sure everything is set correctly To administer profiles ...

Page 73: ...Pannoramic 250 FLASH II 1 18 1 User s Guide 4 Software Description 4 4 2 Barcodes panel Figure 52 Barcodes panel May 29 2014 Rev 1 3DHISTECH Ltd 73 137 ...

Page 74: ...output directory the name and the profile to be used by barcodes The positions of the characters in the barcode are defined in the mask fields It is possible to define areas using the character Characters located at different places of the barcode may be combined by using a comma Mainly 2D barcodes are used for this purpose It is possible to use 1D barcodes however it can contain less information ...

Page 75: ...The barcode control will then look like the following Folder mask 1 1 6 Folder mask 2 empty Folder mask 3 empty Folder mask 4 empty Folder mask 5 empty Name mask 8 10 Profile mask 12 21 Note The Profile mask row is inactive if the option Apply one profile to all slides is active Generate name if no name was defined By choosing this option a name is generated automatically in the following format i...

Page 76: ...to use different profiles for slides Current Profile is the profile loaded in Routine Work Scan Profiles Note If the Continuous scanning mode is activated this function is not available Save entered names and assigned profiles by clicking You can define a name before saving The information will be saved in a CSV format 1 slide position slide name profile name You can export this information into E...

Page 77: ...same as described in Manual mode In Automatic mode you cannot change the threshold values it will use the threshold values that were set previously in the Manual mode and when activating the Use selection box option the area cannot be set For more information see section 4 3 3 Preview panel Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check se...

Page 78: ...ut on a spot on the coverslip Multilayer mode Select Single layer option if you want to scan a single layer of the slide By choosing the Extended focus option the software selects the sharpest image from each focus level for each image field and combines them into one single image Therefore those parts that were blurry in auto manual focus will also be sharp This method guarantees the maximum dept...

Page 79: ...er Focus step size determines the spacing between focus levels One step is around 0 2 µm The default settings are Number of focus levels 7 Focus step size 5 4 4 5 Service panel Figure 56 Service panel This panel contains the following control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually aft...

Page 80: ...step of the scanning process The logs can be erased by clicking the Clear button or saved as a text file by selecting Save to file Figure 57 Information on scan progress You can interrupt a running digitization process by clicking This button is only enabled if a digitization process is in progress If you have interrupted a digitization process the slide currently being digitized is placed back in...

Page 81: ...Pannoramic 250 FLASH II 1 18 1 User s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work panel Figure 58 Routine work panel May 29 2014 Rev 1 3DHISTECH Ltd 81 137 ...

Page 82: ... access the Scan Options window click Note These settings are only applicable if you do not use profiles If you use profiles the profile settings are used Scanning Mode Full automatic focus and exposure time are automatically determined by the software User controlled you can define focus and exposure time manually The selection of scanning mode influences the number of options on the Focus panel ...

Page 83: ...titching channel This is done on one channel You can choose whether you want to do stitching on the focus channel or on another channel It is recommended to choose another channel if the focus channel was determined on the basis of exposition time and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of the specimen The def...

Page 84: ...w Filter name The name of the filter is displayed here Exposure Settings You can set the Exposure time weight here displayed under TW in the Channel Settings frame In full automatic mode the system automatically calculates the exposition time to the given channel You can increase or decrease this amount here in a range of 50 200 Multilayer Settings Enable Multilayer function and the concerning set...

Page 85: ...between the filters click Previous Filter or Next Filter Multilayer Settings By clicking the button the Multilayer Settings window is displayed The containing settings are the same as in Brightfield mode but you can select Extended focus or Z stack value for the specific channel Figure 60 Multilayer Settings window Set the focus level value under the Number of focus levels box and the Focus step s...

Page 86: ...ng quality and storage location of the virtual slide Image Encoding You can set the image format parameters within this group Select an item from the Image quality drop down list There are four predefined quality types and a custom settings option on the list Excellent JPEG XR 90 Good JPEG XR 80 Medium JPEG XR 60 May 29 2014 Rev 1 3DHISTECH Ltd 86 137 ...

Page 87: ...rmats The quality can be adjusted with the JPEG 2000 quality factor slider Greater values result in better quality but larger files The default setting is 80 You can create lossless image by selecting the Lossless image compression Not recommended checkbox You can select the desired Image Bit Depth for the applied camera 8 bit or 12 bit when using AxioCam MRm Rev 3 and 8 bit or 16 bit when using p...

Page 88: ...hat the software will analyze that area as an empty one Do not use multilayer mode on empty field of views If selected the multilayer mode function will not run on the empty not containing specimen field of views Use stitching By selecting this function it enables seamless stitching of digitized tiles Focus Exposure Time This function is used for defining time length used for determination of focu...

Page 89: ...the Change filters at each field of view option if using multi band filter for multi channel digitization Digital Slide Destination This field determines where to digitize the virtual slides Select the Scan to CaseCenter function to scan slides directly to the dedicated server For information on how to use the ScanToServer application see section 4 7 Scan to Server If you enable the Folder functio...

Page 90: ...II 1 18 1 User s Guide 4 Software Description 4 5 3 Preview panel The Preview panel offers options for threshold setting and selection of the area to be scanned Figure 63 Preview panel May 29 2014 Rev 1 3DHISTECH Ltd 90 137 ...

Page 91: ...ult of detection is acceptable for you Otherwise set the threshold value manually or append missing areas with the help of Scanned function located at the preview toolbar Scan specimen with user set threshold 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 defa...

Page 92: ...is sets the sensitivity of the specimen detection inside the marker area 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 35 To scan everything within the marked area check the Scan everything within marked area selection box Note This step is recommended when using FL mode as the application is ...

Page 93: ...ease the scanned area The edge is extended discretely by 100 µm each time Use saved scan area This function is useful if the slides contain areas of interest that cannot be detected by the preview camera This function along with saving profiles helps to scan all slides with the most adequate settings To save a new mask click Save It will display a drop down menu Select whether to save preview mask...

Page 94: ... s Guide 4 Software Description 4 5 4 Hardware panel Figure 66 Hardware panel selected mode User controlled Live Click to display a live image of the current specimen in the Live image display field May 29 2014 Rev 1 3DHISTECH Ltd 94 137 ...

Page 95: ...e section 4 5 1 Routine work panel Note After 10 seconds an empty position is rotated into position instead of the filter However the last snapshot is still displayed In case Lumencor illumination unit is used it is triggered by the pco edge 4 2 camera so it will not emit light Exposure You can automatically detect the appropriate exposure time by clicking You can also enter the exposure time manu...

Page 96: ...cus By selecting the Use manual focus box you can preset the coarse focus value By activating the Coarse focus function the lower limit value is set to 64 and the upper limit value is set to 64 of the current focus value Note Before entering coarse focus value turn live image on and set a suitable focus position You can accept the current z value by clicking Set Value If you select the Interpolate...

Page 97: ...anel Figure 67 Service panel This panel contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective cover Slide Removed Manually Click this button to notify the software that you have removed the slide manually Show images d...

Page 98: ... User s Guide 4 Software Description 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work panel Figure 68 Routine work panel The Routine work panel provides some basic digitization functions May 29 2014 Rev 1 3DHISTECH Ltd 98 137 ...

Page 99: ...but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from the selection menu click Load You can delete the current profile by clicking Delete To access the Scan Options window click N...

Page 100: ...e position Set the objective changer to the appropriate position in this field Channel Settings Select what types of filters you want to use during scanning You can select the filter types and the number of channels to be used Those filters are displayed automatically that you have previously defined in the Options Microscope Settings at the mode selection screen For more information on predefinin...

Page 101: ... given channel You can increase decrease this amount here in a range of 50 200 Multilayer Settings Enable Multilayer function and the concerning settings can be activated in this field accordingly you can set the Extended focus and Z stack values for each channel separately Digital Gain Note This function is camera dependent works only with AxioCam MRm Rev 3 camera Index value ranges from 0 to 4 a...

Page 102: ...pecific channel Figure 70 Multilayer Settings window Set the focus level value under the Number of focus levels box and the Focus step size 0 2 µm Once you have set the correct values tick the multilayer checkbox EF or ZS column of the channel for which you want to apply these settings or activate Enable Multilayer function in the Filter Properties window For more information about Extended Focus ...

Page 103: ... 18 1 User s Guide 4 Software Description 4 6 2 Barcodes panel Figure 71 Barcodes panel On this panel you can set identification features to the various slides and for assigning profiles May 29 2014 Rev 1 3DHISTECH Ltd 103 137 ...

Page 104: ...the barcode are defined in the mask fields It is possible to define areas using the character Characters located at different places of the barcode may be combined by using a comma Mainly 2D barcodes are used for this purpose It is possible to use 1D barcodes however it can contain less information You can create up to five sub directories by the barcode If you use long strings for defining the pr...

Page 105: ...te name if no name was defined By choosing this option a name is generated automatically in the following format if no name was defined and there is no barcode magazine number M slide position for example 1M10 The number before M represents the magazine number The number after M represents the slide position In this example the name indicates a slide in magazine 1 position 10 You can also define n...

Page 106: ...saved in a CSV format 1 slide position slide name profile name You can export this information into Excel where you can change the data and save it again in CSV format Load Names and Profiles from File You can import previously saved names and assigned profiles by clicking Delete Names and Profiles You can delete all entries from the table by clicking 4 6 3 Preview panel Figure 72 Preview panel Ma...

Page 107: ...e selection box option the area cannot be set For more information see section 4 5 3 Preview panel Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings 4 6 4 Focus panel Figure 73 Focus panel Focus You can define focus limits by selecting Limit focus range checkbox You can set the upper and lower limits by selecting the desired value in...

Page 108: ...e that you have removed the slide manually Show images during scanning If you select this option you will be able to see the currently scanned image field during scanning in the live image display field This slows down digitization process and should be activated only with purpose 4 7 Scan To Server The ScanToServer function is available for you to scan directly to a dedicated CaseCenter server To...

Page 109: ...ow then click Connect Figure 76 Scan to CaseCenter option 3 Type in or select the server address from the Connect to drop down menu and give the User name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 77 Server Log in window May 29 2014 Rev 1 3DHISTECH Ltd 109 137 ...

Page 110: ...K to close the Scan Options window Figure 78 Connected to server Slide settings in the Scan To Server window 1 Click in the Routine work panel Slide data is displayed in a form in the Scan To Server window If in Manual Mode only the data of the actually loaded slide can be set see Figure 79 Figure 79 Scan To Server window in Manual Mode May 29 2014 Rev 1 3DHISTECH Ltd 110 137 ...

Page 111: ...e 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 Upon activating this option Slide name Folder Case and Block field data cannot be modified only a profile can be selected 2 The Generate slide name if no name was defined option can b...

Page 112: ...data fields press TAB to move to the next cell Figure 81 Profile selection Profiles can be added by selecting a list entry from the Profile drop down list Select a folder where the slide will be scanned to After clicking the Folder drop down list a path will be displayed in which the destination folder can be selected Figure 82 Folder selection Fill in the Case and Block fields in case you do not ...

Page 113: ...ields to default click the Reset all button If modification is done to the folder tree of the CaseCenter server while the Scan To Server window is open click Update Tree to refresh the tree view Figure 83 Scan To Server window during the barcode parsing process Click Done when finished or Cancel to quit the Scan To Server window If you save the form slides will be scanned to server according to th...

Page 114: ...ode Brightfield Fluorescent Scan 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 stitching ON OFF Determination of the area to be scanned Use of automatic threshold specimen Use of specimen threshold value Use of Brightfield Darkfield preview image Use of marker pen threshold a...

Page 115: ...on s Selected focus channel Selected stitching channel Flat field correction ON OFF Sharpening ON OFF Use of skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Other settings Limitation of focus range ON OFF Use of objective position Enable disable Multilayer options Use of extended focus or Z stack step size and focus level May 29 2014 Rev 1 3DHISTECH Ltd 11...

Page 116: ...the device Protect it with dust cover when not in use Switch the power off before covering it There is crush hazard during operation in the area of input or output Inserts magazines should be moved through software The protective shield of the magazine feed unit can be unmounted when slide scanning has stopped The device can be opened for service reasons only when switched off and in cases stated ...

Page 117: ...t free cotton cloth and gently rub the surface 5 1 2 Cleaning the magazine Do not clean the magazines with xylene because it might harm the plastic We recommend to apply Isopropanol or Ethanol 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 inserting a deteriorated magazine could lead into unsafe loading of slide...

Page 118: ...e see section 1 1 4 Main parts of the Base Unit 3 Remove protective covers see section 5 3 1 Opening the protective cover 4 Remove slide or magazine manually see sections 5 3 4 Removing a jammed or broken slide or 5 3 6 Removing a magazine from the transporting system If a jammed magazine cannot be removed contact service personnel 5 Reattach protective covers 6 Reconnect power supply cable of the...

Page 119: ...ng in Pannoramic Viewer Scan camera is not properly adjusted for example due to loose fixture Contact 3DHISTECH Service for support Preview image is too dark too bright Invalid compensation image for preview camera Capture a new compensation image for the preview camera see section 4 3 6 Service panel Digitization process is extremely slow Extended focusing option is activated Deactivate the Exten...

Page 120: ... in spite of trigger connection through the camera Contact 3DHISTECH Service for support No suitable exposure time can be found Signal is too weak HXP 120 Shutter is closed The opening of the iris contained in the lamp module for fluorescent applications can be varied by means of the wheel located at the front side of the module Open the iris completely HXP 120 Intensity is too low Increase intens...

Page 121: ...he power cables see section 1 1 4 Main parts of the Base Unit Warning The opening mechanism is operated by a pre tensioned hinge Be sure that before opening the protective cover open the FL cover first so it will not lash to the cover during opening For information on how to open the FL cover see section 3 3 3 Opening Closing the FL protective cover Figure 85 Opening the cover To open the cover yo...

Page 122: ...s located next to the main power supply switch at the back side of the Pannoramic 250 FLASH II 3 Release lock 1 by pushing the lever to the left so the insert 2 can be pulled out Figure 86 Fuse compartment 4 Remove insert from the compartment Figure 87 Removing the fuse insert 5 Replace fuses put the insert back into its mounting and push it inwards until you hear a snap so the lever locks Figure ...

Page 123: ...amp module Accordingly the module is fully operational after lamp replacement Warning Hot surface Wait at least twenty minutes to allow the lamp surface to cool down sufficiently 1 Disconnect power plug separate all poles from the mains 2 Unfix screws of lateral cover plate and remove it from the unit housing see Figure 89 Figure 89 Removing the lateral cover of the HXP 120 3 Press plug securing l...

Page 124: ...e sure that the groove 1 in the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 92 Figure 92 Inserting the lamp module Caution Incorrect handling may considerably reduce the lamp module s useful life Hold it by the ceramic part in all cases Never touch the lamp s glass surface or the inside surface of the reflector Skin oil is harmful to these parts 7 Tighte...

Page 125: ... Service panel Warning Crush hazard Before you remove a jammed slide cancel the running digitization process terminate the software session and turn the power off Any manipulation performed on a mechanical component must be followed by a complete device initialization routine software restart Figure 93 Removing the slide loader 1 Open the protective cover see section 5 3 1 Opening the protective c...

Page 126: ... and pull it inwardly to the Pannoramic 250 FLASH II until the guiding pin connects with the motor block groove again 8 Press the slide loader 2 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 until this part mechanically engages too 9 Close the protective cover again see section 5 3 1 Openi...

Page 127: ... the desired filter in the corresponding software window see section 4 2 3 Microscope Settings Filter Settings panel The filter will be positioned in such a way that the user can access it without having to turn the filter wheel manually 4 Enter the respective parameters in the input fields 5 Hold the filter module 3 by its handling pads one on the right one on the left lateral side of the module ...

Page 128: ...ver see section 5 3 1 Opening the protective cover 9 If an HXP 120 illumination unit is used turn it on again consider the cooling time possibly required 5 3 6 Removing a Magazine from the Transporting System Figure 96 Removing a magazine 1 Open the protective cover see section 5 3 1 Opening the protective cover Warning Crush hazard Remember to stop the running digitization process terminate the s...

Page 129: ... magazine is tilted because of twisted tappets 1 first restore the tappets to their initial position They are correctly positioned if vertically aligned exactly one above each other Turn the gear 5 by hand until the tappets are in their initial position again and the magazine flatly rests on both horizontal guide rails Warning Danger of pinching Turn the knurled wheel slowly with caution and take ...

Page 130: ...aintenance 5 3 7 Transporting The following procedure shows how to transport Pannoramic 250 FLASH II Figure 97 Transporting handles Caution Do not use the FL protective cover 2 to raise shift or transport Pannoramic 250 FLASH II May 29 2014 Rev 1 3DHISTECH Ltd 130 137 ...

Page 131: ...n find the weight data of the base unit in section 6 Technical Data To transport Pannoramic 250 FLASH II do the following 1 Switch power supply off see section 1 1 4 Main parts of the Base Unit and detach all other cables 2 Pull carrying handles out 1 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 250 FLASH I...

Page 132: ...ption Approx 50 kg Ambient conditions Transportation shipment packed Permissible ambient temperature 20 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 max 2000 m Atmospheric pressure 500 hPa to 1060 hPa Degree o...

Page 133: ...sion Aligned Pulsed Xenon Light Source Average service life of halogen lamp 2 x 109 flashes Lamp module for HXP 120 fluorescent option 120 W Average service life of Mercury short arc reflector lamp 2000h Lumencor light source SPECTRA Light Engine 6 Estimated service life of the Lumencor s light source 75 000 h This User s Guide describes Lumencor Spectra and HXP 120 as light sources The X Cite 120...

Page 134: ... 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 325µm Cooling Peltier with forced air fan Connection type Dual Camera Link Full 10 taps 85MHz AxioCam MRm Rev3 2 3 progressive scan CCD Pixel size 6 45µm 6 45µm Camera...

Page 135: ...ctive and 1x C mount adapter 0 19µm Connection type Dual Camera Link Full 10 taps Control computer minimum system requirements Operating System Microsoft Windows 7 Professional SP1 64 bit EN CPU 2x Intel Xeon processor 6 core 12 MB l2 cache RAM Recommended 16 GB DDR3 Hard disk Min 1 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices Keyboard mouse Ports 2xDoubl...

Page 136: ... 66 67 68 78 79 82 83 84 85 87 88 95 96 99 100 101 102 107 114 115 119 120 H Halogen lamp 133 HXP 120 15 17 21 22 25 116 117 120 123 127 133 L Lumencor 14 17 21 22 25 26 27 44 95 116 120 133 M Marker 58 61 92 114 P Pannoramic 250 FLASH II 8 9 10 11 13 15 17 19 20 21 22 24 25 26 27 32 33 118 121 122 126 129 130 131 Pannoramic Viewer 23 68 79 119 Pco edge 4 2 14 17 18 21 22 25 85 87 88 95 101 134 Pr...

Page 137: ...Pannoramic 250 FLASH II 1 18 1 User s Guide Index ScanToServer 56 89 108 May 29 2014 Rev 1 3DHISTECH Ltd 137 137 ...

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