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3D Histech Pannoramic SCAN 150 1.18 User Manual Download Page 107

Pannoramic SCAN 150 1.18 User’s Guide

4 Software Description

•

Use of scan everything within marked area (ON/OFF)

•

Remove coverslip function (ON/OFF)

•

Filling of holes (ON/OFF)

•

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

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Use saved scan area

•

Use selection box (ON/OFF)

Fluorescent settings

•

Filter position(s)

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Selected focus channel

•

Selected stitching channel

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Flat field correction (ON/OFF)

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Sharpening (ON/OFF)

•

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

•

Limitation of focus range (ON/OFF)

•

Enable/disable Multilayer options

•

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

April 3, 2014 - Rev. 1

3DHISTECH Ltd.

107(131)

Summary of Contents for Pannoramic SCAN 150 1.18

Page 1: ...PS1 18 UG EN Rev1 Pannoramic SCAN 150 1 18 User s Guide April 3 2014 Rev 1 ...

Page 2: ...tware 21 2 Installation 22 2 1 Control computer ports 22 2 2 Connectors and cables 23 2 3 Coupling the Lumencor Spectra 6 unit with the scanner 24 3 Operating Slides and Magazines 25 3 1 Preparing Slides and Magazines 25 3 2 Affixing Barcode Stickers to Slides 26 3 3 Inserting and Removing Slides 27 4 Software Description 31 4 1 Starting Exiting Pannoramic Scanner Software 31 4 1 1 Starting the so...

Page 3: ...ic Mode 91 4 6 1 Routine work panel 91 4 6 2 Barcodes panel 96 4 6 3 Preview panel 99 4 6 4 Focus panel 100 4 6 5 Service panel 100 4 7 Scan To Server 101 4 8 Using Profiles 106 5 Troubleshooting and Maintenance 108 5 1 Safety Information 108 5 1 1 Cleaning the device 109 5 1 2 Cleaning the magazine 109 5 1 3 Preventive maintenance 109 5 2 Troubleshooting 110 5 2 1 Fluorescent Applications optiona...

Page 4: ...Pannoramic SCAN 150 1 18 User s Guide Index 131 April 3 2014 Rev 1 3DHISTECH Ltd 4 131 ...

Page 5: ...P are the sole properties of the 3DHISTECH Ltd 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including the results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitalized slide s that stems from or is a...

Page 6: ... KIND EXPRESSED IMPLIED OR OTHERWISE INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL INCIDENTAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR FOR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE AND ON A...

Page 7: ...function keys such as F11 or the Ctrl 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 C...

Page 8: ...ory 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 sam...

Page 9: ...authorized service personnel All claims for warranty and warranty 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 SCAN 150 has a built in protection which must not be rendered ineffective by extension cables without ...

Page 10: ...off before you put the cover on Caution Avoid touching the lamp bulb Disconnect power and let the lamp cool down for about 15 minutes before replacing the lamp 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 insert W...

Page 11: ...y 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 void the user ...

Page 12: ...cal Aperture 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 name evaluate annotate mark comment send it to a colleague electronically for co operation or advice and so on April 3 2014 Rev 1 3DHISTECH Ltd 12 131 ...

Page 13: ...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 SCAN 150 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 equi...

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 150 is an optimal choice for customers who need high quality daily throughput granted by the loading capacity o...

Page 15: ...3 Warning and Information Labels The following figure contains the labels used on the Pannoramic SCAN 150 main unit the external mains power supply unit and the HXP 120 illumination unit Figure 1 Warning and information labels April 3 2014 Rev 1 3DHISTECH Ltd 15 131 ...

Page 16: ...nput stack for magazines 4 Protective cover for magazine loader 5 Magazine feeder door cover 6 CIS VCC FC60FR19CL scan camera 7 Protectiverails Fluorescence option A 8 HXP 120 fiber coupled illumination unit optional use with AxioCam MRm Rev3 and Stingray cameras only 9 HXP 120 illumination adapter optional use with AxioCam MRm Rev3 and Stingray cameras only 10 Fiber optic cable April 3 2014 Rev 1...

Page 17: ...ation adapter optional use with pco edge 4 2 camera only 10 Fiber optic cable 1 2 System Overview The standard scope of delivery of the product includes the following hardware and software components 1 2 1 Pannoramic SCAN 150 system The following figure shows the main parts of the Pannoramic SCAN 150 system Figure 3 Pannoramic SCAN 150 system overview April 3 2014 Rev 1 3DHISTECH Ltd 17 131 ...

Page 18: ...n of the control computer and monitor can vary depending on the product order Cameras AxioCam MRm Rev 3 1 CCD scientific cooled monochrome camera for high quality sensitive fluorescent applications CIS VCC FC60FR19CL CMOS camera for high quality brightfield applications allowing fast scanning pco edge 4 2 Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast sc...

Page 19: ...nstallation carried out by an unprofessional person Base Unit options Pannoramic SCAN 150 Basic Brightfield Option Fast Option Base unit equipped with Stingray or CIS VCC FC60FR19CL cameras for Brightfield scanning no fluorescent accessories included Pannoramic SCAN 150 Basic Fluorescence Option Base unit completely equipped with AxioCam camera and HXP 120 illumination unit trigger cable and filte...

Page 20: ... filters for fluorescence scanning NOTE If Lumencor light source is ordered the custom light source and filter modules can be variable For more information contact 3DHISTECH customer service Objectives Carl Zeiss Plan Apochromat 20 NA 0 8 Carl Zeiss Plan Apochromat 40 Corr NA 0 95 Warning Do not change correction collar settings on the 40 NA objective if you need it to be set contact customer serv...

Page 21: ...rescence Extended focus Z stack Barcode reader licensed feature Pannoramic Viewer software fully functional Optional CaseCenter TMA module 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules TumorBoard module E School Encoder April 3 2014 Rev 1 3DHISTECH Ltd 21 131 ...

Page 22: ...out by an unauthorized 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 components from each other Fig...

Page 23: ...Preview camera USB cable between scanner and control computer Stingray FireWire 1394 B cable between Stingray camera and control computer AxioCam FireWire 1394 A cable between AxioCam 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 monito...

Page 24: ...instrument to avoid the risk of electrical shock 2 3 Coupling the Lumencor Spectra 6 unit with the scanner To operate the Lumencor Spectra 6 Light Engine fluorescent illumination unit it has to be connected to the Pannoramic SCAN 150 base unit the camera and the control computer 1 Turn the control computer off and disconnect power supply of the pco edge 4 2 camera 2 Connect both ends of the fiber ...

Page 25: ... beveled corners Edges Grounded or cut 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 loading less reliable Not compl...

Page 26: ...scent reagents e g VECTASHIELD Fluorescent 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...

Page 27: ...and the label area outer limits It is 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 ...

Page 28: ...the side of the magazine demonstrate 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 150 To insert or remove a filled magazine from the device or when transporting it without its cover 4 slightly tilt it to...

Page 29: ...fore you insert magazines Caution Replace 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 ma...

Page 30: ...stack can be filled with a maximum of 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 April 3 2014 Rev 1 3DHISTECH Ltd 3...

Page 31: ...initialized After successful initialization the program displays a Mode selection window Figure 10 Mode selection window The selection window displays two Brightfield or Fluorescent scan modes depending on the camera installed on the microscope Automatic for digitizing multiple slides Manual for digitizing individual slides where contrast ratio is critical due to specimen staining and where ideal ...

Page 32: ...4 2 Options The Options menu can be activated from the main menu of the Mode selection window Figure 11 Options menu 4 2 1 Barcode Settings Barcode settings can be modified in the Barcode Settings window 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 Note You can only scan th...

Page 33: ...o 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 To display an image of the 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 ...

Page 34: ...ftware will display the following error message Barcode detection unsuccessful There might be no barcode present 1D Barcode Types You can select the following 1D barcode types Code 128 Code 93 EAN 8 EAN 13 UPC A 2D Barcode Types You can select the following 2D barcode types Data Matrix PDF417 MicroPDF417 Maxicode QR code April 3 2014 Rev 1 3DHISTECH Ltd 34 131 ...

Page 35: ...tion 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 Prepare 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 whenever compensation ...

Page 36: ...ompensation Figure 13 Brightfield compensation Camera Selection This field displays the active camera Currently there is only one active camera for Brightfield mode Objective Selection This field displays the objective used for scanning April 3 2014 Rev 1 3DHISTECH Ltd 36 131 ...

Page 37: ...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 pr...

Page 38: ...type and the magnification level of the objectives Camera type If Pannoramic SCAN 150 features a manual camera changer first activate the Use manual camera changer option then set the appropriate camera types both for Brightfield and Fluorescent scanning modes in Pos 1 Camera type and Pos 1 Camera type fields The software automatically loads the camera settings upon clicking the Test and Apply Cam...

Page 39: ...s displayed on the form The function Enable HXP 120 fluorescent light source shutter is available only for AxioCam MRm Rev 3 The AxioCam and the HXP 120 must be connected by a trigger cable to enable this function Filter Settings Figure 16 Filter Settings panel On this panel you can define which filters occupy which turret positions April 3 2014 Rev 1 3DHISTECH Ltd 39 131 ...

Page 40: ... 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 service support and do not modify these settings yourself April 3 2014 Rev 1 3DHISTECH Ltd 40 131 ...

Page 41: ... 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 18 Z Difference panel April 3 2014 Rev 1 3DHISTECH Ltd 41 131 ...

Page 42: ...oval 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 Removing the protective cover Slide Removed Manually Click this button to notify the software that you have removed the slide manually 4 2 4 Event Call Settings Figure 20 Event Call Settings April 3 2014 Rev 1 3DHISTECH Ltd 42 131 ...

Page 43: ...g For Scan Finished Call SLIDENAME transfers the slide name For Error Occurred Call ERRORTEXT transfers the error message Run defines the window mode that the external application will start in The following window modes can be set Normal window Minimized Maximized You can test whether the Scanning Error Occurred settings work by clicking By moving the mouse cursor over the buttons the software di...

Page 44: ...meters can be set Message Type E mail SMTP Host Address Authentication User ID and User Password are required Secure connection SSL If activated the messages will be sent through secured connection Send Test e mail Click this button to send test e mail to the specified address There are 2 feedback messages that come up after sending the e mail An e mail has been sent to the recipient An error has ...

Page 45: ...roperly set messenger settings click OK then click Users in the Message Call section of the Event Call Settings window to address functions to the recipients that can be selected under the Send Message when field Figure 22 Users window April 3 2014 Rev 1 3DHISTECH Ltd 45 131 ...

Page 46: ...ettings or single slides You can also define profiles here which can be used in the Automatic mode For more information on profiles see section 4 8 Using Profiles For more information on Automatic mode see section 4 4 Using Brightfield Automatic Mode Figure 23 Main window of control software 1 Panel with scanner functions and settings 2 Scan camera live image display area 3 Preview image recorded ...

Page 47: ...ion 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 April 3 2014 Rev...

Page 48: ...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 the ...

Page 49: ...l slide You can choose the following 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 April 3 2014 Rev 1 3DHISTECH Ltd 49 131 ...

Page 50: ...a It is not accessible for configurations installed with CIS camera Image fields will be saved with native pixel resolution If this function is disabled you will work with reduced pixel resolution These resolution differences are not really visible with the human eye what is important in this feature is the resulting smaller file size Brightfield Compensation The Use saved compensation image funct...

Page 51: ...ed in the specified folder You can browse for the folder with the Browse button If you specify a folder that does not exist the software will create it All parameter inputs are saved for the next software session 4 3 3 Preview panel The Preview panel offers options for threshold setting and selection of the area to be scanned Figure 27 Preview panel Use threshold Scan specimen with auto threshold ...

Page 52: ... smaller specimen areas will not be digitized Scan area inside the marker If the specimen cannot be identified as required for digitization for example 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 ...

Page 53: ...nate those areas Warning Do not use 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 predetermine...

Page 54: ...d 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 enabl...

Page 55: ...le 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 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 ...

Page 56: ... on the area 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 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 option from the righ...

Page 57: ...selection settings on the following four tabs Select panel Figure 34 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 35 TMA tool Block April 3 2014 Rev 1 3DHISTECH Ltd 57 131 ...

Page 58: ...µm fields or select the appropriate values with the arrows 4 Enter the average diameter of the spots in the Diameter of spots μm field or select the appropriate value with the arrows Grid panel The Grid panel displays the previously set grid settings Figure 36 TMA tool Grid Move panel The Move panel allows the rotation and moving of the TMA selection spots that are displayed on the preview image T...

Page 59: ...Pannoramic SCAN 150 1 18 User s Guide 4 Software Description Figure 37 TMA tool Move panel with preview April 3 2014 Rev 1 3DHISTECH Ltd 59 131 ...

Page 60: ...User s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degrees checkbox Figure 38 Label area 4 3 5 Focus panel Figure 39 Focus panel April 3 2014 Rev 1 3DHISTECH Ltd 60 131 ...

Page 61: ...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 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 St...

Page 62: ...ng between focus levels One step is around 0 2 µm The default settings are Number of focus levels 7 Focus step size 5 4 3 6 Service panel Figure 41 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 Removing the p...

Page 63: ...r 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 or Show images during scanning option is enabled Figure 42 Display field and toolbar for live images April 3 2014 Rev 1 3DHISTECH Ltd 63 131 ...

Page 64: ...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 noise l...

Page 65: ...k 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 panel 4 4 1 Routine work panel Figure ...

Page 66: ...t 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 use the Scan Profiles field The current prof...

Page 67: ...c SCAN 150 1 18 User s Guide 4 Software Description 4 4 2 Barcodes panel Figure 44 Barcodes panel Identification features and profiles for slides can be set on this panel April 3 2014 Rev 1 3DHISTECH Ltd 67 131 ...

Page 68: ...e used by barcodes The positions of the characters in the barcode can be defined in the Folder 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 subdirecto...

Page 69: ...f_n Folder is the folder for saving Vir is the name of the virtual slide 123_prof_n is the profile name 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 April 3 2014 Rev...

Page 70: ...Names Barcodes You can also define profiles in the selection boxes in column Profiles if you intend to use different profiles for slides NOTE If the Continuous scanning mode is activated this function is not available Current Profile is the profile loaded in Routine Work Scan Profiles You can save the entered names and assigned profiles by clicking You can define a name before saving The informati...

Page 71: ...ptions in Automatic mode are the 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 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 settings April 3 2014 Rev 1 3DHISTECH Ltd...

Page 72: ...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 depth o...

Page 73: ...een 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 48 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 Removing the protecti...

Page 74: ...og window in the right bottom of the application window a timestamp is added to each 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 49 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 If you have inte...

Page 75: ... User s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work panel Figure 50 Routine work panel The Routine work panel provides basic digitization functions April 3 2014 Rev 1 3DHISTECH Ltd 75 131 ...

Page 76: ...e 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 To administer profiles use the Scan Profi...

Page 77: ... 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 default selection is Focus channel The Objective positi...

Page 78: ...ere 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 settings can be activated in this field accordingly yo...

Page 79: ...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 52 Multilayer Settings window Set the focus level value under the Number of focus levels box and the Focus step size one step 0 2 µm ...

Page 80: ...iption 4 5 2 Scan Options Figure 53 Scan options panel These settings determine the resulting quality and storage location of the virtual slide Image Encoding You can set the image format parameters within this group April 3 2014 Rev 1 3DHISTECH Ltd 80 131 ...

Page 81: ...rmat BMP Lossless uncompressed image format but larger files due to less effective compression It is a raw data file JPEG 2000 It supports both the 8 bit and 16 bit image formats 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 compres...

Page 82: ... scanning process is increased Caution If the specimen area is barely visible it is possible that 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 enables seamless stitching of digitized tiles Focus ...

Page 83: ...ange 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 a dedicated CaseCenter server For information on how to use the ScanToServer application see section 4 7 Scan To Server If you enable the Folder func...

Page 84: ...pecimen with auto threshold This automatically detects the specimen in the preview image Important Make sure that the detection result 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 For more information see section 4 3 4 Preview area scanned by preview camera Preview Toolbar April 3 2014 Rev ...

Page 85: ...lack 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 the Marker threshold level selection box in the range of 0 255 This sets th...

Page 86: ...gitized by adjusting the Speck size slider Scan area dilation Adjust the slider to the desired value to enlarge or decrease 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 mo...

Page 87: ...Pannoramic SCAN 150 1 18 User s Guide 4 Software Description 4 5 4 Hardware panel Figure 57 Hardware panel selected mode User controlled April 3 2014 Rev 1 3DHISTECH Ltd 87 131 ...

Page 88: ...r will be rotated into position only after displaying the live image by clicking Click to display Filter properties window for more information see 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 s...

Page 89: ...l microscope Define the manual focus step size by adjusting the Step size slider Search for the sharpest focus on the current field of view automatically by clicking Manual Focus 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...

Page 90: ...e specimen and define a representative value You can accept the value for presetting by clicking Set Value Repeat the procedure for all other filters 4 5 5 Service panel Figure 58 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 after open...

Page 91: ...re 59 Routine work panel The Routine work panel provides some basic digitization functions To insert and remove slides In Automatic mode a preloaded magazine has to be placed into the main unit This magazine is the first one irrespectively of the total number of magazines 1 6 to be loaded April 3 2014 Rev 1 3DHISTECH Ltd 91 131 ...

Page 92: ...is recommended to go through all the settings before clicking it Scan Range You can select a range of slides to be scanned here by entering the first and last slides in the selection boxes 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 sele...

Page 93: ...me 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 default selection is Focus Channel 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 previousl...

Page 94: ...iven 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 or Z stack values for each channel separately Digital Gain Note This function is camera dependent works with AxioCam MRm Rev3 camera Index value ranges from 0 to 4 and pc...

Page 95: ...us or Z stack value for the specific channel Figure 61 Filter properties window Set the focus level value under the Number of focus levels box and the Focus step size one step 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 April ...

Page 96: ...18 User s Guide 4 Software Description 4 6 2 Barcodes panel Figure 62 Barcodes panel On this panel you can set identification features to the various slides and for assigning profiles April 3 2014 Rev 1 3DHISTECH Ltd 96 131 ...

Page 97: ...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 subdirectories by the barcode If you use long strings for defining the pro...

Page 98: ...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 names for the slides in the tabl...

Page 99: ...ve the entered names and assigned profiles 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 Excel where you can change the data and save it again in CSV format Delete Names and Profiles You can delete all entries from the table by clicking 4 6 3 Preview panel Figure 63 Preview panel April...

Page 100: ...e Use 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 because settings cannot be modified in Automatic mode 4 6 4 Focus panel Figure 64 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 the selection box...

Page 101: ...hat 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 se...

Page 102: ...wn menu and give the User name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 68 Server Log in window 4 Click the Connect button in the Scan Options window to connect to the server If the connection is established the server status will be modified from Not connected to Connected Click OK to close the Scan Options window Figure 69 C...

Page 103: ...ed in a form for each magazine If in Manual Mode only the data of the actually loaded slide can be set see Figure 70 Figure 70 Scan To Server window in Manual Mode When in Automatic Mode the form contains 25 rows for all the slots per magazine Figure 71 To additional magazines click the Add tab next to the Magazine 01 tab Figure 71 Scan To Server window in Automatic Mode April 3 2014 Rev 1 3DHISTE...

Page 104: ...ill be read and set in the Barcode field Use masks for automatic fills Activate the Use mask option and the mask fields turn fillable To save masks click the Save Mask button To modify masks click Set Mask For example by creating a string for the slide name fields based on the characters of the barcode a unique name will be generated The barcode 1234567890 and a mask 1 3 result that the first four...

Page 105: ...ngs while the Ctrl button on your keyboard is pressed down or select the entire form by clicking the gray field at the top left corner To erase reset fields to default click the Reset all button If modification is done to the folder tree in the CaseCenter server click Update Tree to refresh the tree view Server side barcode parsing option can be selected if CaseCenter is connected with the support...

Page 106: ...red to and used on another control computer and if using a different type of scanner If you want to scan a group of slides it is advised to save your settings previously in a profile and continue scanning in Automatic mode You can save the following settings in a profile Scan Mode Brightfield Fluorescent Scan Options Focus frequency in Fluorescent mode Focus frequency in Brightfield mode Compressi...

Page 107: ...ea Use selection box ON OFF Fluorescent settings Filter position 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 Enable disable Multilayer options Use of extended focus or Z stack step size and focus leve...

Page 108: ...e infectious materials after use 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 There is crush hazard during operation in the area of inp...

Page 109: ...To clean greasy surfaces it is recommended to apply Isopropanol or Ethanol on a piece of lint 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 ...

Page 110: ...xit control software 2 Switch off control computer and 24V power supply disconnect power cable 3 Remove protective covers Follow the steps in section 5 3 1 Removing the protective covers 4 Remove slide manually 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 cont...

Page 111: ...y the lamp has burned out Please turn off the scanner and check the lamp Halogen lamp is defective Replace the halogen lamp see section 5 3 2 Replacing the halogen lamp Image is black Halogen lamp is defective Replace the halogen lamp see section 5 3 2 Replacing the halogen lamp Virtual slide is improperly focused almost across its entire surface Focus range enabled Disable Limiting focus range Po...

Page 112: ...ine Contact 3DHISTECH Service for support Digitization process is extremely slow Extended focusing option is activated Deactivate the Extended focusing option if not required Z stack option is activated Deactivate the Z stack option if not required Image is out of focus in Manual mode Focus range limit is activated Deactivate the Limiting focus range option Focus range setting is incorrect Change ...

Page 113: ...te 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 Intensity is too low Increase intensity with the ro...

Page 114: ... jamming the protective covers of the Pannoramic SCAN 150 need to be opened in 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 75 Removal of covers Five eccentric screws 3 are located on the bottom face of the base plate 4 They attach the...

Page 115: ...use both hands to carefully raise and take cover 2 off 4 After finishing the necessary maintenance or repair work put the covers cover 2 at first then cover 1 back into place and lock them in their positions To do this turn the eccentric screws clockwise A Caution Make sure that no cables of the scan camera are squeezed as you replace the covers 5 3 2 Replacing the halogen lamp Figure 76 Replacing...

Page 116: ...he hole 5 on the heat sink body 7 Remove the lamp mount with the lamp 8 First remove the defective lamp 4 from the lamp mount then insert a new bulb into its mount Warning Do not touch the bulb with your bare fingers Use a dry clean lint free cloth or gloves when inserting the bulb into the mount 9 Taking care that the two clamps 3 on the lamp mount are correctly aligned to the hole 5 on the heat ...

Page 117: ...that manual Also no alignment is required for the lamp 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 77 Figure 77 Removing the l...

Page 118: ...eping the lever pressed remove lamp module 2 see Figure 79 Figure 79 Removing the lamp module 5 Carefully retrieve the new lamp module from its transporting container Hold the lamp module only by its ceramic part 6 Insert the new lamp module Make sure that the groove 1 in the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 80 Figure 80 Inserting the lamp mod...

Page 119: ...1 Set hour meter time counter to zero 5 3 4 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 jammed slide c...

Page 120: ...he protective covers 2 Push locking lever 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 April 3 2014 Rev 1 3DHISTECH Ltd 120 131 ...

Page 121: ...ve 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 5 3 5 Installing and Removing the Filter Module Fluo...

Page 122: ...ury 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 filter 5 emission fil...

Page 123: ... 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 2 If the magazine is in horizontal position tilt plate 7 with the drive assembly for horizontal magazine drive motion to the front far enough for the driving gear 5 to di...

Page 124: ...l 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 150 initialization routine software restart 5 3 7 Transporting Pannoramic SCAN 150 The following procedure shows how to tran...

Page 125: ...pacity limitations You can find the weight data of the base unit in section 6 Technical Data To transport the Pannoramic SCAN 150 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 150 with the help of another person...

Page 126: ... Base 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 s...

Page 127: ...e with EN 61326 2 6 2005 Base unit input voltage 24V DC 1V Power consumption of the complete device 75 VA 24V external mains power supply unit Intended 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 CI...

Page 128: ...d as a substitute light source Slide identification Slides are identified by a VRmagic VRmC 8 PRO preview camera Label area is saved as image and barcode is interpreted as a character string with capability for interpretation of the following types of 1D and 2D barcodes Interleaved 2 of 5 Code39 ASCII encoding Code93 ASCII encoding Code128 UCC EAN128 ASCII encoding EAN8 Numeric encoding EAN13 Nume...

Page 129: ...40 pixel Camera max speed 5 frames per second Bit depth 12 bit Pixel resolution with 20 objective and 1 C mount adapter 0 32µm Cooling Peltier element Connection type FireWire 1394 A CIS VCC FC60FR19CL camera Global Shutter Type CMOS Diagonal 15 930mm Pixel size 5 5µm 5 5µm Camera resolution 2048 H 2048 V pixel Frame rates 17fps 34fps 68fps 135fps Bit depth 10 bit Pixel resolution with 20x objecti...

Page 130: ...aps 85MHz 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 8 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 2xDouble CameraLink port 1 FireWire 1394 A 4 USB 2 0 GB Ethernet 2014 April 3 3D...

Page 131: ...logen lamp 111 114 115 128 HXP 120 15 16 18 19 20 23 24 39 109 113 117 121 128 L Lumencor 19 20 24 88 108 113 128 Lumencor Spectra 6 Light Engine 13 20 128 M Marker 52 55 85 106 P Pannoramic SCAN 150 8 9 10 11 13 14 15 17 18 19 20 22 24 28 38 110 114 124 125 Pannoramic Viewer 21 62 73 112 Pco edge 13 129 Pco edge 4 2 81 Preview 23 26 31 37 46 51 52 53 54 55 56 58 59 61 71 84 86 89 99 100 128 R RGB...

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