3D Histech Pannoramic SCAN 150 User Manual Download Page 76

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Pannoramic SCAN 150 1.15 User’s Guide

4 Software Description

4.5 Using Fluorescent Manual Mode

4.5.1 Routine work tab

Figure 46 – Routine work tab

The Routine work panel provides basic digitization functions.

2012. March 13.

3DHISTECH Ltd.

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132

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Summary of Contents for Pannoramic SCAN 150

Page 1: ...Pannoramic SCAN 150 1 15 User s Guide March 13 2012 Rev 1 ...

Page 2: ...ns 17 1 2 3 Control Software 19 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 27 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 3...

Page 3: ...91 4 6 1 Routine work tab 91 4 6 2 Barcodes tab 96 4 6 3 Preview tab 99 4 6 4 Focus tab 100 4 6 5 Service tab 100 4 7 Scan To Server 101 4 8 Using Profiles 107 5 Troubleshooting and Maintenance 109 5 1 Safety Information 109 5 1 1 Cleaning the device 110 5 1 2 Cleaning the magazine 110 5 1 3 Preventive maintenance 110 5 2 Troubleshooting 111 5 2 1 Fluorescent Applications optional 114 5 3 Maintena...

Page 4: ...Pannoramic SCAN 150 1 15 User s Guide Index 132 March 13 2012 Rev 1 3DHISTECH Ltd 4 132 ...

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 AN...

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: ...ry 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 same...

Page 9: ... 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 protective...

Page 10: ...e Pannoramic SCAN 150 must be protected with a dust cover Check that power is turned 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 ...

Page 11: ... 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 s...

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 March 13 2012 Rev 1 3DHISTECH Ltd 12 132 ...

Page 13: ... to 9 channels An outstanding 0 12 µm pixel resolution is achieved with the 40 NA 0 95 Carl Zeiss Plan Apochromat objective Key features of the Pannoramic SCAN 150 Scanner Up to 9 freely selectable color filters for fluorescence High end fluorescent illumination device Lumencor Spectra 7 Light Engine Multiband filter support Noiseless FL scanning with the best FL camera available pco edge 150 slid...

Page 14: ...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 March 13 2012 Rev 1 3DHISTECH Ltd 14 132 ...

Page 15: ...parts of base unit 1 Protective cover 2 Output stack for magazines 3 Input stack for magazines 4 Protective cover for magazine loader 5 Magazine feeder door cover 6 CIS VCC F52U25CL scan camera 7 Safety rails 8 HXP 120 fiber coupled illuminator option 9 HXP 120 illumination adapter option 10 Fiber optic cable March 13 2012 Rev 1 3DHISTECH Ltd 15 132 ...

Page 16: ...wing 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 March 13 2012 Rev 1 3DHISTECH Ltd 16 132 ...

Page 17: ...nochrome camera for high quality sensitive fluorescent applications CIS VCC F52U25CL 3 CCD 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 brig...

Page 18: ...canning no fluorescent accessories included Pannoramic SCAN 150 Basic Fluorescence Option Base unit completely equipped with Stingray or CIS cameras for Brightfield scanning with AxioCam camera and HXP 120 illuminator trigger cable and filters for fluorescence scanning Pannoramic SCAN 150 Advanced Fluorescence Option Base unit completely equipped with CIS VCC F52U25CL camera for Brightfield scanni...

Page 19: ...Options for Pannoramic SCAN 150 Fluorescent unit internal part HXP 120 Fluorescent illumination unit can be used with AxioCam MRm Rev3 only Lumencor Spectra 7 Light Engine illumination unit can be used with pco edge camera only 1 2 3 Control Software Pannoramic Scanner control software Optional Fluorescence Extended focus March 13 2012 Rev 1 3DHISTECH Ltd 19 132 ...

Page 20: ...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 March 13 2012 Rev 1 3DHISTECH Ltd 20 132 ...

Page 21: ...d 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 c...

Page 22: ...era 14 2x FireWire port IEEE 1394 A B for Stingray F146C or AxioCam MRm Rev3 and DFK preview camera 2 2 Connectors and cables Caution It is not recommended to use USB and FireWire cables longer than 2 5 meters Control USB between scanner and control computer Preview camera FireWire 1394 A cable between scanner and control computer Stingray FireWire 1394 B cable between Stingray camera and control ...

Page 23: ...V and HXP 120 fluorescent illuminator Power supply cable between 230V 110V and CIS camera Optical cable between HXP 120 fluorescent illuminator or Lumencor Spectra 7 LE 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 Lumencor fluorescent illuminator...

Page 24: ...rs Edges Grounded or cut Note FISH fluorescent signals become more easily detectable for the scanner therefore resulting in a brighter and better image by treating the slide with a formula that prevents rapid photobleaching of fluorescent reagents e g VECTASHIELD Fluorescent Mounting Medium by Vector Laboratories and ProLong Gold and SlowFade Gold antifade reagents by Invitrogen during the FISH pr...

Page 25: ...embedding medium If not so the coverslip can be shifted that makes slide loading less reliable Not completely dried embedding might also influence the operation of objectives and other device parts Warning Do not change correction collar settings on the 40 NA objective if you need it to be set contact customer service 3 2 Affixing Barcode Stickers to Slides This section describes how to affix barc...

Page 26: ... the specimen side Note Ensure that a marginal space of 1 2 mm remains on all sides between the sticker and the label area outer limits It is vital for barcode identification Caution 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 oth...

Page 27: ...d in the magazine The edge of the broken area of the slide is sharp and its removal can lead to injury and contagion Broken slide can be removed only by a well trained person Only original 3DHISTECH magazines are allowed for use with Pannoramic SCAN 150 The magazines can contain a maximum of 25 slides Push slide 1 into the magazine 3 with its barcode end 2 first The symbols on the side of the maga...

Page 28: ...illed magazine from the device or when transporting it without its cover 4 slightly tilt it to its closed side to prevent the slides from accidentally falling out Magazines should always be kept clean from dust broken glass and other mounting media residues Slide loader will only operate safely and properly if magazines are clean To insert and remove magazines Figure 7 Inserting a magazine 2012 Ma...

Page 29: ...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 magazine on the input guide rails un...

Page 30: ...s from there during the digitization process Only remove magazines from the output stack when you have finished digitization of all slides 4 Software Description 4 1 Starting Exiting Pannoramic Scanner Software 4 1 1 Starting the software For the scanning software you can choose from different scanning modes at the startup of the program 1 To start the program double click on the program icon on t...

Page 31: ...ng multiple slides Manual for digitizing individual slides where contrast ratio is critical due to specimen staining and where ideal parameters need to be determined for subsequent use in Automatic mode if profiles need to be defined for the Automatic mode Note It is recommended to use specimens with identical staining for a given batch of magazines in Automatic mode 4 1 2 Exiting the software If ...

Page 32: ...ide When closing the Mode selection window it automatically unloads magazine Scanning process ends with the slide out 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 Figure 11 Barcode settings 2012 March 13 3DHISTECH Ltd 32 132 ...

Page 33: ...lick 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 To display an image of the barcode area click You can redefine the barcode reading area by dragging the edges of the gre...

Page 34: ...rcode types Data Matrix PDF417 MicroPDF417 Maxicode QR code 1D barcodes with check digit CDV You can select the following 1D barcodes with check digit CDV Code 39 Interleaved 2 of 5 The check digit is always the last digit of the barcode It is an additional checking number If you select Exclude check digit then the check digit number will also be analyzed as a barcode number 2012 March 13 3DHISTEC...

Page 35: ...th 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 there are compensation errors deriving from the slide illumination staining or embedding medium irregularities from an empty slide by setting these options B...

Page 36: ...ion Brightfield Compensation Figure 12 Brightfield compensation Camera Selection This field displays the active camera Currently there is only one active camera for Brightfield mode and one active camera for Fluorescent mode 2012 March 13 3DHISTECH Ltd 36 132 ...

Page 37: ...hat 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 progress of the compensation image creation Fluorescent Compensation You have recei...

Page 38: ...Pannoramic SCAN 150 1 15 User s Guide 4 Software Description Figure 13 Fluorescent compensation 2012 March 13 3DHISTECH Ltd 38 132 ...

Page 39: ...sure and Focus Both the focus on the sample and the exposure time can be set either manually or automatically NOTE Different filters usually require different exposure settings Filter Selection for Compensation If you have selected a filter for a position in the Microscope Settings window the filters for each position are displayed in this field Tick the check boxes of the desired filters to be us...

Page 40: ... Click the Stop button to interrupt the process The Progress bar at the bottom of the window displays the progress of the compensation image creation Image Browser This function displays the created compensation image Figure 14 Image Browser 4 2 3 Microscope Settings By moving the mouse cursor over the buttons the software displays information about the setting you are interested in 2012 March 13 ...

Page 41: ... SCAN 150 1 15 User s Guide 4 Software Description Base Settings Figure 15 Base Settings tab Objective type You can select the type and the magnification level of the objectives 2012 March 13 3DHISTECH Ltd 41 132 ...

Page 42: ...nning modes It is also available for you to define which filters occupy which turret positions Save settings by clicking Note 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 Camera Rotation Caution If you have transported the product or changed the camera th...

Page 43: ...Pannoramic SCAN 150 1 15 User s Guide 4 Software Description Figure 16 Camera Rotation tab 2012 March 13 3DHISTECH Ltd 43 132 ...

Page 44: ...on Z Difference This function is available only for fluorescence settings it enables you to set the basic focus differences between the filters This facilitates more precise focusing during scanning Figure 17 Z Difference tab 2012 March 13 3DHISTECH Ltd 44 132 ...

Page 45: ...on 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 19 External Application Settings 2012 March 13 3DHISTECH Ltd 45 132 ...

Page 46: ... 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 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 Brig...

Page 47: ... window 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 2012 March 13 3DHISTECH Ltd 47 132 ...

Page 48: ...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 2012 March 13 3D...

Page 49: ... the 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 De...

Page 50: ...de 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 2012 March 13 3DHISTECH L...

Page 51: ... images 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 im...

Page 52: ...ned Figure 23 Preview tab Use threshold Scan specimen 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 2012 March 13 3DHISTECH Ltd 52 132 ...

Page 53: ...le 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 insi...

Page 54: ...en 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 scanne...

Page 55: ... 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 enabled there is a black frame displayed in the image Figure 26 Preview image Colors used in preview image The follow...

Page 56: ...sample areas that will not be scanned These areas are not digitized on the basis of their position for example they are outside the selection box They are detected by the selected threshold value Marker If Scan marker specified area is selected in the Preview 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 57: ...ample and then click 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 25 400 To fit the preview image to the preview area click Fit Choose from the Scanned or the Not scanned opt...

Page 58: ...A spots on TMA slides You can set the selection settings on the following four tabs Select tab Figure 30 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 2012 March 13 3DHISTECH Ltd 58 132 ...

Page 59: ...s or select the appropriate values with the arrows 6 Enter the distance between two spots on the X and the Y axis in µm in the Spot distance X µm and Spot distance Y µm fields or select the appropriate values with the arrows 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...

Page 60: ...ing of the TMA selection spots that are displayed on the preview image To move the spots enter the pixel value in the Move field or use the arrows To rotate the spots enter the degree value in the Rotate field or use the rotation arrows Figure 33 TMA tool Move tab with preview 2012 March 13 3DHISTECH Ltd 60 132 ...

Page 61: ...1 15 User s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degree checkbox Figure 34 Label area 4 3 5 Focus tab Figure 35 Focus tab 2012 March 13 3DHISTECH Ltd 61 132 ...

Page 62: ...t focus value Use the two arrow buttons to focus manually This is useful when you are interested in an area that remained blurry with Auto Focus for example the specimen is thicker in that area This does not influence the way slides are digitized in 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 b...

Page 63: ...spacing between focus levels One step is around 0 2 µm The default settings are Number of focus levels 7 Focus step size 5 4 3 6 Service tab Figure 37 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 p...

Page 64: ...for live images The display field for live images displays images of the scan camera The live image is displayed if no current digitization process is running or Show images during scanning option is enabled Figure 38 Display field and toolbar for live images 2012 March 13 3DHISTECH Ltd 64 132 ...

Page 65: ...aves 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 no...

Page 66: ...e 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...

Page 67: ...lide and Last slide To move all magazines to the output stack click You can save time if you remove all magazines from the input stack before you 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 To administer profiles use the Scan Profiles field The current profile name is displayed at th...

Page 68: ...oramic SCAN 150 1 15 User s Guide 4 Software Description 4 4 2 Barcodes tab Figure 40 Barcodes tab Identification features and profiles for slides can be set on this panel 2012 March 13 3DHISTECH Ltd 68 132 ...

Page 69: ...le 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 subdirectorie...

Page 70: ...e 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 i...

Page 71: ... in column Profiles if you intend to use different profiles for slides 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 into Excel where you can change the data ...

Page 72: ...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 tab Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings 2012 March 13 3DHISTECH Ltd 72 132...

Page 73: ...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 74: ...g 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 44 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 protectiv...

Page 75: ...ng the Clear button or saved as a text file by selecting Save to file Figure 45 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...

Page 76: ... 1 15 User s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work tab Figure 46 Routine work tab The Routine work panel provides basic digitization functions 2012 March 13 3DHISTECH Ltd 76 132 ...

Page 77: ... Note These settings are only applicable if you do not use profiles If you use profiles the profile settings are used Scanning Mode Full automatic focus and exposure time are automatically determined by the software User controlled you can define focus and exposure time manually The selection of scanning mode influences the number of options on the Focus tab To administer profiles use the Scan Pro...

Page 78: ... This is done on one channel You can choose whether you want to do stitching on the focus channel or on another channel It is recommended to choose another channel if the focus channel was determined on the basis of exposition time and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of the specimen The default selection i...

Page 79: ...d 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...

Page 80: ... To create compensation image see section 4 2 2 Image Compensation Fluorescent compensation To move between the filters click Previous Filter or Next Filter Multilayer Settings By clicking the button the Multilayer Settings window is displayed The containing settings are the same as in Brightfield mode but you can select Extended focus or Z stack value for the specific channel Figure 48 Multilayer...

Page 81: ...Pannoramic SCAN 150 1 15 User s Guide 4 Software Description 4 5 2 Scan Options Figure 49 Scan options tab 2012 March 13 3DHISTECH Ltd 81 132 ...

Page 82: ...hoose between 8 and 12 bit depths when using AxioCam MRm Rev 3 and between 8 and 16 when using pco edge camera Scan Settings Focus frequency 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...

Page 83: ...hat varies according to the different characteristics Calculate exposure time for full slide After analyzing the slide the program uses the same smallest exposition time for each area to omit over exposition Note This option is used only if no exposure times were manually predefined It is recommended to use the second option Multi Filter Change Mode This is for a multi channel digitization To opti...

Page 84: ...ToServer application see section 4 7 Scan To Server If you enable the Directory function the virtual slides will be digitized 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 creates it All parameter inputs are saved for the next software session 4 5 3 Preview tab The Preview tab offers options for threshold setti...

Page 85: ... it can help to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area If this option is selected only the area encircled with a marker pen will be scanned You can define the threshold level by changing the threshold value in the Marker thresho...

Page 86: ...tion 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 most adequate settings To save a new mask click Save It wil...

Page 87: ...Pannoramic SCAN 150 1 15 User s Guide 4 Software Description 4 5 4 Hardware tab Figure 52 Hardware tab selected mode User controlled 2012 March 13 3DHISTECH Ltd 87 132 ...

Page 88: ...age by clicking The Filter properties window can be displayed by clicking 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 it will not emit light Exposure You can automatically...

Page 89: ...hicker in that area This does not influence the way slides are digitized in Automatic mode The manual focus is mainly for setup purposes not for using the product as a traditional microscope Define the manual focus step size by adjusting the Step size slider 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 li...

Page 90: ...ut pre fine focusing Manual Exposure By selecting the Use manual exposure times you can determine the exposure 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 ...

Page 91: ...tion 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 54 Routine work tab 2012 March 13 3DHISTECH Ltd 91 132 ...

Page 92: ...magazines from the input stack before you 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 nam...

Page 93: ... 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 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 previo...

Page 94: ...ally calculates the exposition time to the given channel You can increase decrease this amount here in a range of 50 200 Multilayer Settings Enable Multilayer function and the concerning settings can be activated in this field accordingly you can set the Extended focus and Z stack values for each channel separately Digital Gain Note This function is camera dependent works with AxioCam MRm Rev 3 ca...

Page 95: ...tilayer 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 56 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 ...

Page 96: ...150 1 15 User s Guide 4 Software Description 4 6 2 Barcodes tab Figure 57 Barcodes tab On this tab you can set identification features to the various slides and for assigning profiles 2012 March 13 3DHISTECH Ltd 96 132 ...

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 pr...

Page 98: ...ed 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 t...

Page 99: ...n save 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 tab Figure 58 Preview tab 2012 ...

Page 100: ...e selection box option the area cannot be set For more information see section 4 5 3 Preview tab Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings 4 6 4 Focus tab Figure 59 Focus tab 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 s...

Page 101: ... 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 If you want to scan directly to a server first you have to install the ScanToServer which is an embedded application that can ...

Page 102: ...1 15 User s Guide 4 Software Description 2 Accept the License Agreement then click Install to continue 3 Click Finish to finalize the installation process of the ScanToServer application 2012 March 13 3DHISTECH Ltd 102 132 ...

Page 103: ...a designated server follow the steps below 1 Click Scan Options on the Routine Work tab panel Figure 61 Scan Options button 2 Select the Scan to CaseCenter option in the Scan Option window then click the Connect button Figure 62 Scan to CaseCenter option 2012 March 13 3DHISTECH Ltd 103 132 ...

Page 104: ...d from Not connected to Connected Click OK to close the Scan Options window Slide settings in the CaseCenter window 1 In the Routine work tab panel click the button 2 The CaseCenter window is displayed Slide data is displayed in a form for each magazine Slide data is displayed in a form for the slides loaded in the tray If in Manual Mode only the data of the actually loaded slide can be set see Fi...

Page 105: ...the Read barcode if no name is defined on the list option the slide barcode will 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 ...

Page 106: ...you do not use masks or select an item from the drop down list With the Multi fill option the selected slides will be given the same input data to their specific fields Profile Folder Case and Block fields can be auto filled this way by clicking the drop down lists at the Multi fill section at the bottom of the window Rows can be selected one by one clicking the row headings while the Ctrl button ...

Page 107: ...formed previously Click Yes to use the last used server or No to define a different one 4 8 Using Profiles Note Saved profile settings cannot 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 Bright...

Page 108: ...of removing specks according to the set value ON OFF Use saved scan area Use selection box ON OFF Fluorescent settings Filter position s Selected focus channel Selected stitching channel 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 Use of extended focus or Z stack step size ...

Page 109: ... 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 th...

Page 110: ...asy 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 111: ...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 c...

Page 112: ...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 Poor...

Page 113: ...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 114: ...e 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 rot...

Page 115: ... 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 68 Removal of covers Five eccentric screws 3 are located on the bottom face of the baseplate 4 They attach the ...

Page 116: ... 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 69 Replacin...

Page 117: ...o 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 118: ...le 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 70 Figure 70 Removing the lateral cover of the HXP 120 3 Press plug securing latches i...

Page 119: ...he contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 73 Figure 73 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 T...

Page 120: ...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 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 mechani...

Page 121: ...ieces 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 mechanic...

Page 122: ...otective 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 inpu...

Page 123: ...unting 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 5...

Page 124: ...e 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 in...

Page 125: ... 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 126: ...e 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 March 13 2012 Rev 1 3DHISTECH Ltd 126 132 ...

Page 127: ...g 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 ...

Page 128: ...ce 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 C...

Page 129: ... a substitute light source Slide identification Slides are identified by preview camera TIS DFK21F04 Barcode area is saved as image and label 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 encoding...

Page 130: ...m Camera resolution 1388 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 F52U25CL camera 1 1 8 PS IT CCD Pixel size 4 40 4 40 µm Camera resolution 1624 H 1224 V pixel Camera max speed up to 30 frames per second Bit depth 10 bit Pixel resolution with 20x...

Page 131: ...ion 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 2012 March 13 3DHISTECH Ltd 131 132 ...

Page 132: ... 79 80 82 83 88 89 90 93 94 95 100 107 108 112 113 H Halogen lamp 3 112 115 116 129 HXP 120 14 15 16 18 19 23 42 110 114 118 120 122 129 L Lumencor 13 18 19 23 88 109 114 129 M Marker 53 56 85 108 P Pannoramic MIDI 8 Pannoramic SCAN 150 2 3 9 10 11 13 14 16 17 18 19 21 27 42 101 111 115 124 125 126 Pannoramic Viewer 20 63 74 113 Preview 3 22 26 31 37 39 46 47 52 54 55 56 57 60 62 72 75 84 85 86 90...

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3D Histech Pannoramic SCAN 150, User Manual

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