3DHISTECH Pannoramic SCAN 150 User Manual Download Page 88

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Pannoramic SCAN 150 1.17 User’s Guide

4 Software Description

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.

4.6 Using Fluorescent Automatic Mode

4.6.1 Routine work tab

Figure 53 – Routine work tab

The Routine work tab panel provides some basic digitization functions.

July 4, 2013 - Rev. 1

3DHISTECH Ltd.

88(130)

Summary of Contents for Pannoramic SCAN 150

Page 1: ...PS1 17 UG Rev1 Pannoramic SCAN 150 1 17 User s Guide July 4 2013 Rev 1 ...

Page 2: ...ontrol Software 20 2 Installation 21 2 1 Control computer ports 21 2 2 Connectors and cables 22 3 Operating Slides and Magazines 24 3 1 Preparing Slides and Magazines 24 3 2 Affixing Barcode Stickers to Slides 25 3 3 Inserting and Removing Slides 26 4 Software Description 30 4 1 Starting Exiting Pannoramic Scanner Software 30 4 1 1 Starting the software 30 4 1 2 Exiting the software 31 4 2 Options...

Page 3: ... tab 88 4 6 2 Barcodes tab 93 4 6 3 Preview tab panel 96 4 6 4 Focus tab panel 97 4 6 5 Service tab panel 97 4 7 Scan To Server 98 4 8 Using Profiles 105 5 Troubleshooting and Maintenance 107 5 1 Safety Information 107 5 1 1 Cleaning the device 108 5 1 2 Cleaning the magazine 108 5 1 3 Preventive maintenance 108 5 2 Troubleshooting 109 5 2 1 Fluorescent Applications optional 112 5 3 Maintenance 11...

Page 4: ...Pannoramic SCAN 150 1 17 User s Guide Index 130 July 4 2013 Rev 1 3DHISTECH Ltd 4 130 ...

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

Page 6: ...Y 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 ...

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 ...

Page 8: ...tory 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 sa...

Page 9: ...ly 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 witho...

Page 10: ...d 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...

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: ...ical 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 July 4 2013 Rev 1 3DHISTECH Ltd 12 130 ...

Page 13: ...tstanding 0 2 µm pixel resolution is achieved with the 40 NA 0 95 equivalent to 50 magnification in BF and 62 magnification in FL Carl Zeiss Plan Apochromat objective Key features of the Pannoramic SCAN 150 Scanner are Up to 9 freely selectable color filters for fluorescence High end fluorescent illumination device Lumencor Spectra Light Engine 6 Multiband filter support FL scanning with a low noi...

Page 14: ...ality daily throughput granted by the loading capacity of 150 slides 1 1 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 illuminator Figure 1 Warning and information labels July 4 2013 Rev 1 3DHISTECH Ltd 14 130 ...

Page 15: ...Output stack for magazines 3 Input stack for magazines 4 Protective cover for magazine loader 5 Magazine feeder door cover 6 CIS VCC FC60FR19CL scan camera 7 Safety rails 8 HXP 120 fiber coupled illuminator optional use with AxioCam MRm Rev3 camera only 9 HXP 120 illumination adapter optional use with AxioCam MRm Rev3 camera only 10 Fiber optic cable July 4 2013 Rev 1 3DHISTECH Ltd 15 130 ...

Page 16: ...owing 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 1 HXP 120 fiber coupled illuminator option 2 24 V external power supply unit 3 Monitor 4 Mouse 5 Control computer July 4 2013 Rev 1 3DHISTECH Ltd 16 130 ...

Page 17: ...onochrome camera for high quality sensitive fluorescent applications CIS VCC FC60FR19CL CMOS camera for high quality brightfield applications allowing fast scanning pco edge Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast scanning and an outstanding low read out noise Cooled with Peltier element Stingray F146C IRF Medical camera 1 CCD camera for normal br...

Page 18: ...e and filters for fluorescence scanning Pannoramic SCAN 150 Advanced Fluorescence Option Base unit completely equipped with pco edge camera and Lumencor fluorescence illuminator trigger cable and filters for fluorescence scanning Pannoramic SCAN 150 Basic Mixed Option Base unit completely equipped with Stingray or CIS VCC FC60FR19CL cameras for Brightfield scanning with AxioCam camera and HXP 120 ...

Page 19: ...ollar settings on the 40 NA objective if you need it to be set contact customer service Fluorescent Options for Pannoramic SCAN 150 Fluorescent unit internal part HXP 120 Fluorescent illumination unit can be used with AxioCam MRm Rev3 and Stingray cameras only Lumencor Spectra Light Engine 6 illumination unit can be used with pco edge camera only July 4 2013 Rev 1 3DHISTECH Ltd 19 130 ...

Page 20: ...e Extended focus Z stack Barcode reader licensed feature Scan To Server Pannoramic Viewer software fully functional Optional CaseCenter Pannoramic Viewer TMA module 3D Reconstruction module HistoQuant NuclearQuant MembraneQuant FISHQuant and DensitoQuant modules ImmunoScreener module E School Encoder July 4 2013 Rev 1 3DHISTECH Ltd 20 130 ...

Page 21: ... by an installation carried 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 co...

Page 22: ...A for Stingray F146C and AxioCam MRm Rev3 cameras 2 2 Connectors and cables Caution It is not recommended to use USB and FireWire cables longer than 2 5 meters Control USB cable between scanner and control computer 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 c...

Page 23: ...t Power supply cable between 230V 110V and CIS camera Power supply cable between 230V 110V and pco edge camera Optical cable between HXP 120 fluorescent illuminator or Lumencor Spectra Light Engine 6 unit and scanner Trigger cable between AxioCam and HXP 120 fluorescent illuminator Trigger cable between pco edge and Lumencor fluorescent illuminator USB to RS232 serial communication cable between L...

Page 24: ...5 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 comp...

Page 25: ...ing 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 5 Slide with a barcode sticker The label area is recorded by the preview camera and can be displayed by the ...

Page 26: ...arcode sticker protrude from slide edges or stick on the coverslip surface 3 The thickness of the barcode sticker on the slide must not exceed 0 4 mm Do not stick more than 4 barcode stickers over each other and the overall thickness must must be kept below 1 65 mm including the barcodes and the slide 3 3 Inserting and Removing Slides To insert slides into a magazine Figure 6 Inserting slides into...

Page 27: ...lides Push slide 1 into the magazine 3 with its barcode end 2 first The symbols on 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 To insert or remove a filled magazine from the device or when transporting it without its cover 4 slightly tilt i...

Page 28: ...ile magazines are loaded unloaded The doors must be closed during operation The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader 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 prevents soiling and mechanical damage 2013 July 4 3DHIS...

Page 29: ...uide pins or magazines Caution Make sure that the magazines are not misplaced because it can cause serious damages in the feeding mechanism Figure 8 Misplaced magazine Note The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader Caution Do not place magazines into the output stack 3 or remove magazines with already digitized slides from there durin...

Page 30: ... initialized After successful initialization the program displays a Mode selection window Figure 9 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 31: ... 4 2 Options The Options menu can be activated from the main menu of the Mode selection window Figure 10 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 t...

Page 32: ...put 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 To display an image of the barcode area click You can redefine the barcode reading area by dragging the edges of the green square July 4 2013 Rev 1 3DHISTECH ...

Page 33: ... correctly or there is no barcode in the barcode area the software 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 July 4 2013 Rev 1...

Page 34: ...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 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 create a new compensation image when ...

Page 35: ...ompensation Figure 12 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 July 4 2013 Rev 1 3DHISTECH Ltd 35 130 ...

Page 36: ...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 37: ...ftware Description 4 2 3 Microscope Settings By moving the mouse cursor over the buttons the software displays information about the setting you are interested in Base Settings Figure 14 Base Settings tab July 4 2013 Rev 1 3DHISTECH Ltd 37 130 ...

Page 38: ...also available for you to define which filters occupy which turret positions Save settings by clicking Note If Lumencor is configured as illumination unit the corresponding Enable Lumencor hardware trigger option is 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 ca...

Page 39: ...Pannoramic SCAN 150 1 17 User s Guide 4 Software Description Figure 15 Camera Rotation tab July 4 2013 Rev 1 3DHISTECH Ltd 39 130 ...

Page 40: ... 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 16 Z Difference tab July 4 2013 Rev 1 3DHISTECH Ltd 40 130 ...

Page 41: ... 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 4 2 4 External Application Call Settings Figure 18 External Application Settings July 4 2013 Rev 1 3DHISTECH Ltd 41 130 ...

Page 42: ...ccurred 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 Error Occurred Call settings work by clicking By moving the mouse cursor over the buttons the software displays information about the setting you are interested in 4 3 Using Bright...

Page 43: ...indow of control software 1 Tab panel with scanner functions and settings 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 July 4 2013 Rev 1 3DHISTECH Ltd 43 130 ...

Page 44: ...n 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 July 4 2013 Rev 1 ...

Page 45: ...he button on this tab that you can start 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 Dele...

Page 46: ... You can choose the following image formats in the Image Encoding field JPEG The quality can be adjusted with the JPEG quality factor slider Greater values result in better quality but larger files The default setting is 80 PNG lossless compressed image format BMP lossless uncompressed image format but larger files due to less effective compression It is a raw data file July 4 2013 Rev 1 3DHISTECH...

Page 47: ... for all slides Use this function when the slide is completely covered by the specimen for example blood smear thereby making compensation image capture impossible For such slides use an empty slide with coverslip to grab a compensation image for more information see section 4 2 2 Image Compensation Brightfield Compensation If you select this the software will not create new compensation images fo...

Page 48: ...imen 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 July 4 2013 Rev 1 3D...

Page 49: ... 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 the sensitivity of the specimen detection inside...

Page 50: ... these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filtering specks and other uninteresting objects out Set the maximum size of specks not to be digitized by adjusting the Speck size slider Scan area dilation Adjust the slider To enlarge or decrease the scanned ...

Page 51: ...ou 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 enabled there is a black frame displayed in the image Figure 25 Preview image Colors used in preview image The followin...

Page 52: ...mple 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 tab 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 53: ...ck on the area of interest on the preview image This will define the Live image that you can access from the Focus tab 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 54: ...he selection settings on the following four tabs Select tab Figure 29 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 tab Figure 30 TMA tool Block July 4 2013 Rev 1 3DHISTECH Ltd 54 130 ...

Page 55: ...nce Y µm fields or select the appropriate values with the arrows 7 Enter the average diameter of the spots in the Side length of µm field or select the appropriate value with the arrows Grid tab The Grid tab displays the previously set grid settings Figure 31 TMA tool Grid Move tab The Move tab allows the rotation and moving of the TMA selection spots that are displayed on the preview image To mov...

Page 56: ...Pannoramic SCAN 150 1 17 User s Guide 4 Software Description Figure 32 TMA tool Move tab with preview July 4 2013 Rev 1 3DHISTECH Ltd 56 130 ...

Page 57: ...7 User s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degrees checkbox Figure 33 Label area 4 3 5 Focus tab Figure 34 Focus tab July 4 2013 Rev 1 3DHISTECH Ltd 57 130 ...

Page 58: ...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 59: ...acing 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 tab Figure 36 Service tab 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 pro...

Page 60: ...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 37 Display field and toolbar for live images July 4 2013 Rev 1 3DHISTECH Ltd 60 130 ...

Page 61: ...es 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 nois...

Page 62: ...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 tab Figure 3...

Page 63: ...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 64: ...amic SCAN 150 1 17 User s Guide 4 Software Description 4 4 2 Barcodes tab Figure 39 Barcodes tab Identification features and profiles for slides can be set on this panel July 4 2013 Rev 1 3DHISTECH Ltd 64 130 ...

Page 65: ... 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 You can create up to five subdirectories ...

Page 66: ...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 4 Generate name if no name was defined By choosing this option a name is generated automatically in the following format if ...

Page 67: ...fferent 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 information will be saved in a CSV format 1 slide position slide name profile name You can export this information int...

Page 68: ...ions 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 tab Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings July 4 2013 Rev 1 3DHISTECH Ltd 68 1...

Page 69: ... 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 of ...

Page 70: ...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 tab Figure 43 Service tab This tab 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 ...

Page 71: ... the Clear button or saved as a text file by selecting Save to file Figure 44 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 interrupted a digitization process the slide currently being digitized is placed back into its magazine With the start of the digitization process the u...

Page 72: ...de 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work tab Figure 45 Routine work tab The Routine work panel provides basic digitization functions To insert and remove slides July 4 2013 Rev 1 3DHISTECH Ltd 72 130 ...

Page 73: ...y 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 tab To administer profiles use the Scan Profiles field The current prof...

Page 74: ... 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 default selection is Foc...

Page 75: ...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 settings can be activated in this field accordingly y...

Page 76: ...s 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 47 Multilayer Settings window Set the focus level value under the Number of focus levels box and the Focus step size one step 0 2 µ...

Page 77: ...150 1 17 User s Guide 4 Software Description 4 5 2 Scan Options Figure 48 Scan options tab These settings determine the resulting quality and storage location of the virtual slide July 4 2013 Rev 1 3DHISTECH Ltd 77 130 ...

Page 78: ...requency This value determines how many field of views will pass before the sample is refocused This value should be selected depending on the unevenness and size of the specimen Maximum exposure time A limit value can be set to determine that the exposure time cannot be longer than the time of focusing and calculation of exposure This is necessary because the exposure time would be too long when ...

Page 79: ...asurements can be made on the slide Sharpening image contrast is increased the image may become noisier Note Do not use this option if you want to take quantitative measurements since it may minimally affect the results Exposure Time Calculate exposure time for each area Calculates exposure time that is specific to each area and that varies according to the different characteristics Calculate expo...

Page 80: ...on if using multi band filter for multi channel digitization Digital Slide Destination This field determines where to digitize the virtual slides To be able to choose the Scan to CaseCenter function you have to install the ScanToServer application For information on how to install and use the ScanToServer application see section 4 7 Scan To Server If you enable the Directory function the virtual s...

Page 81: ...imen 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 July 4 2013 Rev 1 3D...

Page 82: ...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 the Marker threshold level selection box in the range of 0 255 This sets t...

Page 83: ...igitized 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 m...

Page 84: ...Pannoramic SCAN 150 1 17 User s Guide 4 Software Description 4 5 4 Hardware tab Figure 51 Hardware tab selected mode User controlled July 4 2013 Rev 1 3DHISTECH Ltd 84 130 ...

Page 85: ...lter 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 tab 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 camera so i...

Page 86: ... 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 Search for the sharpest focus on the current field of view automatically by clicking Note If you want to speed up the process turn off the live image display because this red...

Page 87: ...re times The values are typically set on Auto meaning that the exposure times are determined automatically After selecting the corresponding filter and activating the live image you can preset an exposure time in the Exposure value field It is recommended to go to various positions in order to determine the intensity distribution throughout the specimen and define a representative value You can ac...

Page 88: ...ently scanned image field during scanning in the live image display field This slows down digitization process and should be activated only with purpose 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work tab Figure 53 Routine work tab The Routine work tab panel provides some basic digitization functions July 4 2013 Rev 1 3DHISTECH Ltd 88 130 ...

Page 89: ...click this button You also find the button on this tab that you can start scanning with but it 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 o...

Page 90: ...ime 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 previous...

Page 91: ...e 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 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...

Page 92: ...channel Figure 55 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 For more information about Extended Focus s...

Page 93: ... 1 17 User s Guide 4 Software Description 4 6 2 Barcodes tab Figure 56 Barcodes tab On this panel you can set identification features to the various slides and for assigning profiles July 4 2013 Rev 1 3DHISTECH Ltd 93 130 ...

Page 94: ...he 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 prof...

Page 95: ... 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 tab...

Page 96: ...he 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 tab panel Figure 57 Preview tab panel J...

Page 97: ...election box option the area cannot be set For more information see section 4 5 3 Preview tab panel Note It is recommended to use profiles because settings cannot be modified in Automatic mode 4 6 4 Focus tab panel Figure 58 Focus tab 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 selectio...

Page 98: ...nually 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 If you want to scan directly to a server first you have to install the ScanToServer which is an embedded application that can be run un...

Page 99: ... Guide 4 Software Description 2 Accept the License Agreement then click Install to continue 3 After checking the prerequisites click Install to start the installation of ScanToServer application July 4 2013 Rev 1 3DHISTECH Ltd 99 130 ...

Page 100: ...k Finish to finalize the installation process of the ScanToServer application To setup a connection with a designated server follow the steps below 1 Click Scan Options on the Routine Work tab panel Figure 60 Scan Options button July 4 2013 Rev 1 3DHISTECH Ltd 100 130 ...

Page 101: ...own menu and give the User name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 62 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 63 ...

Page 102: ...played in a form for each magazine If in Manual Mode only the data of the actually loaded slide can be set see Figure 64 When in Automatic Mode the form contains 25 rows for all the slots per magazine Figure 65 To additional magazines click Add tab next to the Magazine 01 tab Figure 64 CaseCenter window in Manual Mode Figure 65 CaseCenter window in Automatic Mode July 4 2013 Rev 1 3DHISTECH Ltd 10...

Page 103: ...l 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 c...

Page 104: ...adings 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 supp...

Page 105: ... be transferred to and used on another control computer 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 present in Fluorescent mode Interpolated Focus distance present in Brightfield mode Compressio...

Page 106: ...tion 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 Selected image bit depth Other settings Limitation of focus range ON OFF Enable disable Multilayer options Use of extended focus or Z stack step size a...

Page 107: ...h Decontaminate 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 t...

Page 108: ...easy 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 order a new...

Page 109: ... Exit 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 5 Removing the 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 ...

Page 110: ... 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 Poo...

Page 111: ...zine 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 112: ...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 113: ... 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 69 Removal of covers Five eccentric screws 3 are located on the bottom face of the base plate 4 They attach the...

Page 114: ...d 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 70 Replaci...

Page 115: ...to the hole 5 on the heat sink body 7 Remove the lamp mount with the lamp 8 Remove the defective lamp 4 from the lamp mount 9 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 10 Taking care that the two clamps 3 on the lamp mount are correctly aligned to the hole 5 on the heat sink...

Page 116: ...e 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 71 Figure 71 Removing the lateral cover of the HXP 120 3 Press plug securing latches in...

Page 117: ...the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 74 Figure 74 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 Re establish plug in connection 8 ...

Page 118: ... be easily removed by clicking the Emergency Manual Slide Removal Position button see section 4 3 6 Service tab 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 75...

Page 119: ...pieces completely from the device The edge of the broken area of the slide is sharp and it can lead to injury and contagion Broken slide can be removed only by a well trained person 6 Release clamping lever 4 and turn down the slide loader 2 back into the original position and pull it inwardly until the guiding pin connects with the motor block groove again 7 Press the slide loader down to mechani...

Page 120: ...rotective cover halves apart or remove the right part completely see section 5 3 1 Removing the protective covers 3 Select the desired filter in the corresponding software window see section 4 2 3 Microscope Settings Base Settings tab 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 inp...

Page 121: ...ounting position of the filters excitation filter 5 emission filter 4 7 To remove the filter module first slightly tilt it out of its upper spring loaded fixtures then pull it out of the bottom spring loaded components and take it off 8 Place the protective covers back again see 5 3 1 Removing the protective covers 9 Turn the HXP120 illuminator on again consider the cooling time possibly required ...

Page 122: ...ge from the driving worm gear 6 3 Push the magazine on the guide rails 2 3 to the left or to the right to remove it from the transporting system 4 If the 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 knurled wheel 4 by hand until the tappets are in their i...

Page 123: ...t has four carrying handles for transporting Two or four people can carry the base unit using these carrying handles To determine the appropriate number of transporter people observe the laws of your country regarding load carrying capacity 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...

Page 124: ...ce 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 5 After finishing transportation push carrying handles back into normal position C July 4 2013 Rev 1 3DHISTECH Ltd 124 130 ...

Page 125: ... 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 126: ...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 127: ...s 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 Numeric...

Page 128: ...388 x 1040 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...

Page 129: ...on type dual Camera Link full 10 taps Control computer minimum system requirements Operating System Microsoft Windows 7 SP1 64 bit EN HU CPU Intel Xeon E5630 2 53 GHz RAM 4 GB Hard disk 1 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 x 1024 True color Input devices keyboard mouse Ports 2 x Fire Wire 1394 A 1394 B 4 x USB 2 0 GB Ethernet 2013 July 4 3DHISTECH Ltd 129 130 ...

Page 130: ...5 76 78 79 85 86 87 90 91 92 97 105 106 110 111 H Halogen lamp 110 113 114 127 HXP 120 14 15 16 18 19 23 38 108 112 116 120 127 L Lumencor 13 18 19 23 85 107 112 127 M Marker 49 52 82 105 P Pannoramic SCAN 150 8 9 10 11 13 14 16 17 18 19 21 27 38 98 109 113 122 123 124 Pannoramic Viewer 20 59 70 111 Pco edge 13 Preview 22 25 30 36 42 43 48 50 51 52 53 55 56 58 68 71 81 83 86 87 96 97 127 R RGB 61 ...

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3DHISTECH Pannoramic SCAN 150, User Manual

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