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3DHISTECH Pannoramic 250, User Manual

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3DHISTECH Pannoramic 250 User Manual Download Page 113

Pannoramic 250 1.15 User’s Guide

4 Software Description

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

•

Brightfield

•

Fluorescent

Scan Options

•

Focus frequency (present in Fluorescent mode)

•

Interpolated Focus distance (present in Brightfield mode)

•

Compression procedure

•

Use of a fixed compensation image (ON/OFF)

•

Use of stitching (ON/OFF)

Determination of the area to be scanned

•

Use of automatic threshold specimen 

•

Use of specimen threshold value

•

Use of Brightfield/Darkfield preview image

•

Use of marker pen threshold and specimen threshold values

•

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

•

Remove coverslip function (ON/OFF)

•

Filling of holes (ON/OFF)

•

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

March 13, 2012 – Rev. 1

3DHISTECH Ltd.

113

(

135

)

Summary of Contents for Pannoramic 250

Page 1: ...Pannoramic 250 1 15 User s Guide March 13 2012 Rev 1 ...

Page 2: ...e 21 2 Installation 23 2 1 Control computer ports 23 2 2 Connectors and cables 24 2 3 Mounting the Lumencor Spectra unit 25 3 Operating Slides and Magazines 27 3 1 Preparing Slides and Magazines 27 3 2 Affixing Barcode Stickers to Slides 28 3 3 Inserting and Removing Slides 29 3 3 1 Insert slides into a magazine 29 3 3 2 Insert and remove magazines 30 3 3 3 Opening Closing the FL protective cover ...

Page 3: ...Mode 79 4 5 1 Routine work tab panel 79 4 5 2 Scan Options 84 4 5 3 Preview tab panel 88 4 5 4 Hardware tab panel 91 4 5 5 Service tab panel 94 4 6 Using Fluorescent Automatic Mode 96 4 6 1 Routine work tab panel 96 4 6 2 Barcodes tab panel 101 4 6 3 Preview tab panel 105 4 6 4 Focus tab panel 106 4 6 5 Service tab panel 106 4 7 Scan to Server 107 4 8 Using Profiles 113 5 Troubleshooting and Maint...

Page 4: ...Guide 5 3 5 Installing and Removing the Filter Module Fluorescent Option 126 5 3 6 Removing a Magazine from the Transporting System 127 5 3 7 Transporting 129 6 Technical Data 131 Index 135 March 13 2012 Rev 1 3DHISTECH Ltd 4 135 ...

Page 5: ...nsequential 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 associated with use of Product digitalized slides quality of staining quality of stained slides quality of used method of staining 3DHISTECH Ltd assumes no responsibility for the f...

Page 6: ...ND 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 ANY ...

Page 7: ...ple function keys such as F11 or the Ctrl M key combination Example Cross references within this document or to other documents Warning It might cause irreversible damage or harm to the user of the product or the product itself if this instruction is not followed Caution It might cause the product not to work properly if this instruction is not followed Note Calls attention to some important featu...

Page 8: ...ill be null and void in any such case Warning Insert the power cord plugs only into a grounding outlet The protective action must not be rendered ineffective by extension cables without protective conductor The Pannoramic 250 has a built in protection which must not be rendered ineffective by extension cables without protective earth ground conductor Warning The operation of the instrument in expl...

Page 9: ...note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the insert Warning Clogged or covered ventilation slots may result in a heat build up with a damaging effect for the Pannoramic 250 In extreme cases this may also cause fire Keep the ventilation slots always unobstructed and refrain from inserting or dropping objects into...

Page 10: ...cepted 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 claim for ...

Page 11: ...rtual 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 and comment send to a colleague electronically for co operation or advice and so on March 13 2012 Rev 1 3DHISTECH Ltd 11 135 ...

Page 12: ...0 16 µm pixel resolution is achieved with a 40 0 95 NA equivalent to 62 magnification Carl Zeiss Plan Apochromat objective Key features of the Pannoramic 250 Scanner Extreme fast brightfield scanning mode Continuously moving stage during scanning The new brightfield camera sees 30 larger field of view with better pixel resolution and has double frame rate Light source is a Xenon flash lamp Improve...

Page 13: ... fluorescence Motorized Objective changer for two objectives 10 times higher resolution for barcode reading and preview image Compact design Cameras are placed inside the unit Built in power supply 250 slide automatic loading and scanning This device is recommended for customers who need high quality daily throughput granted by the biggest loading capacity of 250 slides The device has many advance...

Page 14: ...escription 1 1 3 Warning and Information Labels The following figure contains the labels used on the Pannoramic 250 main unit and the HXP 120 fluorescent illuminator Figure 1 Warning and information labels March 13 2012 Rev 1 3DHISTECH Ltd 14 135 ...

Page 15: ... 2 Main parts of base unit 1 Protective FL cover 2 Input and output stack for magazines 3 Cover release hole 4 Power supply switch 5 USB port 6 Main power switch 7 Power supply cable connector 1 2 System Overview The standard scope of delivery of the product includes the following hardware and software components March 13 2012 Rev 1 3DHISTECH Ltd 15 135 ...

Page 16: ...0 base unit 2 Monitor 3 Mouse 4 Control computer 5 Keyboard 6 Slide magazine with cover 7 HXP 120 fiber coupled fluorescent illuminator optional used with AxioCam MRm Rev3 8 Lumencor Spectra 7 Light Engine illuminator optional used with pco edge camera 1 2 2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order March 13 2012 Rev 1 3DHISTECH ...

Page 17: ...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 Camera adapters 0 63x adapter 1x adapter March 13 2012 Rev 1 3DHISTECH Ltd 17 135 ...

Page 18: ...and switched by the software automatically without any human assistance This system also enables switching between brightfield and fluorescent scanning by one click Warning The installation of the cameras in Pannoramic 250 must be carried out by trained professionals In any other case the warranty will be automatically voided Supplier Distributor is not liable for any damages caused by an installa...

Page 19: ...ective 2 20x NA 0 80 and 40x NA 0 95 objectives can be used the 40x objective cannot be used in Brightfield mode but only in Fluorescent You can change between the objectives with one click This helps you to select the magnification and resolution that is the most suitable for your requirements Important Note that higher resolution results in slower digitization process March 13 2012 Rev 1 3DHISTE...

Page 20: ...rescent accessories included Pannoramic 250 Basic Fluorescence Option base unit completely equipped with CIS VCC F52U25CL camera for Brightfield scanning with AxioCam camera and HXP 120 illuminator trigger cable and filters for fluorescence scanning Pannoramic 250 Advanced Fluorescence Option base unit completely equipped with CIS VCC F52U25CL camera for Brightfield scanning and with pco edge came...

Page 21: ...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 Z stack Barcode reader licensed feature ScanToServer March 13 2012 Rev 1 3DHISTECH Ltd 21 135 ...

Page 22: ...mic 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 22 135 ...

Page 23: ...hat is not carried out by a professional person Only qualified service assistants are allowed to install the hardware and software The product is ready for use after installation 2 1 Control computer ports The following figure shows the location of the connectors in order to enable easier transportation of the product for a short distance by disconnecting cables and detaching hardware components f...

Page 24: ...am camera and control computer CIS a pair of CameraLink cables between CIS camera and control computer pco edge a pair of CameraLink cables between pco edge camera and control computer Video cable between monitor and control computer Power supply cable between 230V 110V and monitor Power supply cable between 230V 110V and control computer Power supply cable between 230V 110V and Pannoramic 250 mai...

Page 25: ...it has to be attached to the Pannoramic 250 base unit 1 Switch off the main power supply on the rear panel of the Pannoramic 250 and disconnect the power cables see section 1 1 3 Main parts of the Base Unit 2 Open protective cover see section 5 3 1 Opening the protective cover 3 Find the mounting hole 1 at the back side of the Pannoramic 250 unit and rotate the Lumencor unit 2 upside down Figure 8...

Page 26: ...e Lumencor unit so the contact surfaces at the mounting point are tightly compressed see Figure 10 Step 1 6 Secure the locking lever by moving it to the left see Figure 10 Step 2 If the lever stucks at around the center position apply a bit more pressure to the Lumencor unit Figure 10 Mounting the Lumencor unit 7 Close the protective cover of the Pannoramic 250 March 13 2012 Rev 1 3DHISTECH Ltd 26...

Page 27: ...H 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 protocol For further information se...

Page 28: ... change correction collar settings on 40x objective if you need it to be set contact customer service 3 2 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides Barcodes enable virtual slide identification Figure 11 Slide with a barcode sticker The label area 1 is recorded by the preview camera and can be displayed by the control and viewer software To a...

Page 29: ...ification Caution Do not let barcode sticker protrude from slide edges or stick on the coverslip surface 3 Do not stick more than 4 barcode stickers over each other and the overall thickness must must be kept below 1 65 mm including the barcodes and the slide 3 3 Inserting and Removing Slides 3 3 1 Insert slides into a magazine Figure 12 Inserting slides into a magazine March 13 2012 Rev 1 3DHISTE...

Page 30: ... it by the magnet in the side of the magazine 4 Note You should insert several slides into a magazine without empty slots Begin the insertion on position 1 of the magazine Caution To insert or remove a filled magazine from the device or when transporting it without its cover 5 slightly tilt it to its closed side to prevent the slides from accidentally falling out Magazines should always be kept cl...

Page 31: ...em does not detect the inserted magazine in the input stack check whether you have inserted it correctly If the magazine is placed correctly there may be a problem with the sensor In this case contact 3DHISTECH Service Support 1 Remove magazine cover before you insert magazines Caution Replace magazine cover when magazine is not currently used or is stored for a longer period The cover prevents so...

Page 32: ...r wheels 6 or magazines Figure 14 Gear wheels Caution Make sure that the magazines are not misplaced because it can cause serious damages in the feeding mechanism Figure 15 Misplaced magazine Note The input stack can be filled with a maximum of 9 magazines in addition to the one in the magazine loader March 13 2012 Rev 1 3DHISTECH Ltd 32 135 ...

Page 33: ...the FL protective cover Figure 16 Opening the FL protective cover Open the protective cover by moving it upwards and lay it down to the upper cover of the unit then insert magazines When scanning slides close the FL protective cover 1 of the base unit after inserting the magazine s into the input stack 1 Mount the protective cover properly 2 After finishing the digitization process open the protec...

Page 34: ...canner 2 During start up all motors the preview camera and the scan camera are initialized After successful initialization the program displays a Mode selection window Figure 17 Mode selection window The selection window displays two Brightfield and Fluorescent scan modes Automatic for digitizing multiple slides Manual for digitizing individual slides where contrast ratio is critical due to specim...

Page 35: ...n mode is selected Note It is recommended to use specimens with identical staining for a given batch of magazines in Automatic mode 4 1 2 Exiting the software If you close a mode or one of the options window the Mode selection window turns active again To exit the software click X in the title bar of the Mode selection window and the magazine s on the input stack will automatically be unloaded to ...

Page 36: ...predefining the barcode type foreground color black or white the color of the barcode and other settings you enable the Read Barcode option when using the control software Note You can only scan the barcode type that you have previously set If you want to read several barcode types you always have to set the current barcode type before reading it March 13 2012 Rev 1 3DHISTECH Ltd 36 135 ...

Page 37: ...ck click To display an image of the barcode area click You can redefine the barcode reading area by dragging the edges of the green square To check whether the barcode reading settings are correct display the barcode digits in the Barcode field by clicking Note If you did not set the barcode type correctly or there is no barcode in the barcode area the software will display the following error mes...

Page 38: ...t Exclude check digit then the check digit number will also be analyzed as a barcode number Foreground Color You can select the following foreground color of the barcode area Black White Barcode Image Compensation Click Use barcode compensation image to use the previously created compensation image for scanning the label area You can take a new compensation image from a slide with blank barcode st...

Page 39: ...ation errors deriving from the slide illumination staining or embedding medium irregularities from an empty slide by setting these options By moving the mouse over the buttons the software displays information about the setting you are interested in Brightfield compensation Figure 20 Image compensation March 13 2012 Rev 1 3DHISTECH Ltd 39 135 ...

Page 40: ...ation of the compensation images Current threshold To modify the threshold settings set the desired threshold 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 cli...

Page 41: ...Pannoramic 250 1 15 User s Guide 4 Software Description Figure 21 Image compensation March 13 2012 Rev 1 3DHISTECH Ltd 41 135 ...

Page 42: ... the current specimen in the Live image display field by clicking The cross hair on the slide has to be focused to create the best quality compensation image s The edge of the cross hair has to be visible approximately in the middle of the image either horizontally or vertically Exposure and Focus Both the focus on the sample and the exposure time can be set either manually or automatically NOTE D...

Page 43: ... selection box by selecting Use Selection Box By clicking Advanced Options button you can set the maximum exposition time used for creating the compensation image 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 Image Browser This function displays the create...

Page 44: ...ngs You can define for the software which filters occupy which turret positions By moving the mouse over the buttons the software displays information about the setting you are interested in Base Settings Figure 23 Base Settings tab panel March 13 2012 Rev 1 3DHISTECH Ltd 44 135 ...

Page 45: ...can save the 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 there is a possibility that the camera does not display the images properly If you experi...

Page 46: ...Pannoramic 250 1 15 User s Guide 4 Software Description Figure 24 Camera Rotation tab panel March 13 2012 Rev 1 3DHISTECH Ltd 46 135 ...

Page 47: ...erence 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 25 Z Difference tab panel March 13 2012 Rev 1 3DHISTECH Ltd 47 135 ...

Page 48: ...ved Manually Click this button to notify the software that you have removed the slide manually New Compensation Image for Preview Camera By clicking this button you can create a new compensation image if the preview camera fails to display a satisfactory preview image It is important to check that there is no slide in the device during this process Note The software asks you to remove the slide be...

Page 49: ... call settings for the following cases Scan Finished Call Error Occurred Call You can define the external software by entering the file path in the Application box or by browsing for it by clicking If you define parameters in the Parameters box it will pass them to the software that it starts If no parameter is defined then the parameter will not be passed The default parameters are the following ...

Page 50: ...sing Brightfield Manual Mode You can use Brightfield Manual mode to set the scanning preview and image quality settings You can also set profile settings here and start scanning in Brightfield Manual mode This Manual mode is perfect for digitizing slides that require unique settings or single slides You can also define profiles here which can be used in the Automatic mode For more information on p...

Page 51: ...he Routine work tab panel provides basic digitization functions Features are described in the forthcoming section To insert and remove slides To move the lowest magazine in the input stack to the loading position click To move the magazine into the output stack click To move a selected slide from its magazine to the specimen holder either enter its position number to the Current slide field and cl...

Page 52: ...ton on this tab panel 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 53: ...u 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 March 13 2012 Rev 1 3DHISTECH ...

Page 54: ...ge Compensation Brightfield If you select this option the software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading The Scanned slide destination field determines where to digitize the virtual slides To be able to choose the Scan To CaseCenter function you have to install the ScanToServer application For informatio...

Page 55: ...ou to choose in case the sample is not correctly stained for example the specimen is lacking contrast when using Brightfield illumination The image is created within a minute Scan specimen with auto threshold This automatically detects the specimen in the preview image Important Make sure that the detection result is acceptable for you Otherwise set the threshold value manually or append missing a...

Page 56: ... 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 the mark...

Page 57: ...se 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 area...

Page 58: ...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 34 Preview image Colors used in preview image The following f...

Page 59: ...reas 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 panel the preview camera detects the marker pen The inside areas appear in red color and will be digitized Areas scanned in This color is only d...

Page 60: ...on the area of interest on the preview image This will define the Live image that you can access from the Focus tab panel To display the original image created by the preview camera Brightfield or Darkfield click To shrink or enlarge the preview image set the zoom level at the left Size selection box 50 400 To fit the preview image to the preview area click Fit Choose from the Scanned or the Not s...

Page 61: ...on TMA slides You can set the selection settings on the following four tabs Select tab panel Figure 38 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 March 13 2012 Rev 1 3DHISTECH Ltd 61 135 ...

Page 62: ...select the appropriate values with the arrows 3 Enter the distance between two spots on the X and the Y axis in μm in the Spot distance X μm and Spot distance Y μm fields or select the appropriate values with the arrows 4 Enter the average diameter of the spots in the Side length of μm field or select the appropriate value with the arrows Grid tab panel The Grid tab panel displays the previously s...

Page 63: ... 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 41 TMA tool Move tab panel with preview March 13 2012 Rev 1 3DHISTECH Ltd 63 135 ...

Page 64: ...Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degree checkbox Figure 42 Label area 4 3 5 Focus tab panel Figure 43 Focus tab panel March 13 2012 Rev 1 3DHISTECH Ltd 64 135 ...

Page 65: ... 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 Step size slider or search for the sharpest focus on the current fiel...

Page 66: ...ls 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 panel Figure 45 Service tab panel This tab panel contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective ...

Page 67: ...Toolbar for live images The toolbar is only available for the displayed live image but not available for camera images during digitization Zoom in Zoom out One pixel on the monitor corresponds to one pixel on the camera The live image completely fills the display area March 13 2012 Rev 1 3DHISTECH Ltd 67 135 ...

Page 68: ... resulting images will have a higher noise level This function is useful only in fluorescent scanning mode where in spite of the higher noise level the resulting image will refresh like in normal live mode Normal live mode images are taken with an auto specified exposure time Status bar Current position of the cursor related to the live image RGB value of current pixel Zoom level of the current li...

Page 69: ...l number of magazines 1 10 to be loaded If a magazine is present in the input feed the button turns active Click this button to load the magazine If you do not want to load all slides you can specify the first and last slide to be loaded in the Scan Range by entering the appropriate slide numbers in the selection boxes of First slide and Last slide To move all magazines to the output stack click Y...

Page 70: ...isting profile from the selection menu click Load You can delete the current profile by clicking Delete To access the Scan Options window click Note These settings are only applicable if you do not use profiles If you use profiles the settings stored in them are used The used profile name is indicated at the bottom left of the main window For more information see section 4 3 2 Scan Options window ...

Page 71: ...Pannoramic 250 1 15 User s Guide 4 Software Description 4 4 2 Barcodes tab panel Figure 48 Barcodes tab panel March 13 2012 Rev 1 3DHISTECH Ltd 71 135 ...

Page 72: ...output directory the name and the profile to be used by barcodes The positions of the characters in the barcode are defined in the mask fields It is possible to define areas using the character Characters located at different places of the barcode may be combined by using a comma Mainly 2D barcodes are used for this purpose It is possible to use 1D barcodes however it can contain less information ...

Page 73: ...ode 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 no n...

Page 74: ... in column Profiles if you intend to use different profiles for slides Current Profile is the profile loaded in Routine Work Scan Profiles Save entered names and assigned profiles by clicking You can define a name before saving The information will be saved in a CSV format 1 slide position slide name profile name You can export this information into Excel where you can change the data and save it ...

Page 75: ...me as described in Manual mode In Automatic mode you cannot change the threshold values it will use the threshold values that were set previously in the Manual mode and when activating the Use selection box option the area cannot be set For more information see section 4 3 3 Preview tab panel Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check ...

Page 76: ... 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 ...

Page 77: ...ed this way and can be opened with Pannoramic Viewer The Z stack slide contains the extended focus layer Focus step size determines the spacing between focus levels One step is around 0 2 µm The default settings are Number of focus levels 7 Focus step size 5 4 4 5 Service tab panel Figure 52 Service tab panel This tab panel contains the following control and maintenance functions Emergency Manual ...

Page 78: ...of the scanning process The logs can be erased by clicking the Clear button or saved as a text file by selecting Save to file Figure 53 Information on scan progress You can interrupt a running digitization process by clicking This button is only enabled if a digitization process is in progress If you have interrupted a digitization process the slide currently being digitized is placed back into it...

Page 79: ...Pannoramic 250 1 15 User s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work tab panel Figure 54 Routine work tab panel March 13 2012 Rev 1 3DHISTECH Ltd 79 135 ...

Page 80: ...s the Scan Options window click Note These settings are only applicable if you do not use profiles If you use profiles the profile settings are used Scanning Mode Full automatic focus and exposure time are automatically determined by the software User controlled you can define focus and exposure time manually The selection of scanning mode influences the number of options on the Focus tab panel To...

Page 81: ...el Settings field Stitching channel This is done on one channel You can choose whether you want to do stitching on the focus channel or on another channel It is recommended to choose another channel if the focus channel was determined on the basis of exposition time and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of t...

Page 82: ...s the Filter Properties window Figure 55 Filter properties window Filter name The name of the filter is displayed here Exposure Settings You can set the Exposure time weight here displayed under TW in the Channel Settings frame In full automatic mode the system automatically calculates the exposition time to the given channel You can increase or decrease this amount here in a range of 50 200 Multi...

Page 83: ... are created previously To create compensation image see section 4 2 2 Image Compensation Fluorescent 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 56 ...

Page 84: ...Pannoramic 250 1 15 User s Guide 4 Software Description 4 5 2 Scan Options Figure 57 Scan options tab panel March 13 2012 Rev 1 3DHISTECH Ltd 84 135 ...

Page 85: ...s image compression checkbox Image Bit Depth You can choose 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...

Page 86: ...unction is used for defining time length used for determination of focus but is inactive when using AxioCam and pco edge cameras 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 exposure time for full slide After analyzing the slide the program uses the same smallest expos...

Page 87: ...ores the swap files necessary for scanning Scanned 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 slides will be digi...

Page 88: ...o be scanned Figure 58 Preview tab panel Use threshold Brightfield preview a normal type of illumination in the microscope for scanning the slide This option is not recommended in Fluorescent manual mode Darkfield preview the preview image is created with transmitted Darkfield illumination The image is created within a minute March 13 2012 Rev 1 3DHISTECH Ltd 88 135 ...

Page 89: ...t be digitized Scan area inside the marker If the specimen cannot be identified as required for digitization for example weak contrast it can help to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area If this option is selected only the are...

Page 90: ...s out Set the maximum size of specks not to be digitized 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 sav...

Page 91: ...Software Description 4 5 4 Hardware tab panel Figure 61 Hardware tab panel selected mode User controlled Live Click to display a live image of the current specimen in the Live image display field March 13 2012 Rev 1 3DHISTECH Ltd 91 135 ...

Page 92: ... section 4 5 1 Routine work tab panel Note After 10 seconds an empty position is rotated into position instead of the filter However the last snapshot is still displayed In case Lumencor illumination unit is used it is triggered by the pco edge camera so it will not emit light Exposure You can automatically detect the appropriate exposure time by clicking You can also enter the exposure time manua...

Page 93: ...s 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 reduces the processing spee...

Page 94: ...rts scanning on the basis of the interpolated values without pre fine focusing Manual Exposure By selecting the Use manual exposure times you can determine the exposure times The values are typically set to Auto meaning that the exposure times are determined automatically After selecting the corresponding filter and activating the live image you can preset the Exposure value It is recommended to g...

Page 95: ...ing scanning in the live image display field This slows down digitization process and should be activated only with purpose New Compensation Image for Preview Camera By clicking this button you can create compensation image for the preview camera if it fails to display a satisfactory preview image It is important that there is no slide in the device during this process Note The software asks you t...

Page 96: ... 4 Software Description 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work tab panel Figure 63 Routine work tab panel The Routine work tab panel provides some basic digitization functions March 13 2012 Rev 1 3DHISTECH Ltd 96 135 ...

Page 97: ... button You also find the button on this tab panel that you can start scanning with but it is recommended to go through all the settings before clicking it Slide Range You can select a range of slides to be scanned here by entering the first and last slides in the selection boxes To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of t...

Page 98: ...ose a filter that is related to the staining that stained the most of the specimen The default selection is Focus channel Objective position Set the objective changer to the appropriate position in this field To set the objectives see section 4 2 3 Microscope Settings Base Settings Channel Settings Select what types of filters you want to use during scanning You can select the filter types and the...

Page 99: ...tion is set the Exposure time weight value is not valid You can set the Exposure time weight here displayed under TW in the Filter Selection frame In full automatic mode the system automatically 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 activat...

Page 100: ...ction 4 2 2 Image Compensation Fluorescent Compensation You can move between the filters by clicking Previous Filter or Next Filter Multilayer Settings By clicking the 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 65 Filter properties window Set the focus lev...

Page 101: ... Guide 4 Software Description 4 6 2 Barcodes tab panel Figure 66 Barcodes tab panel On this tab panel you can set identification features to the various slides and for assigning profiles March 13 2012 Rev 1 3DHISTECH Ltd 101 135 ...

Page 102: ... 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 by the...

Page 103: ...Folder mask 3 empty Folder mask 4 empty Folder mask 5 empty Name mask 8 10 Profile mask 12 21 Note The Profile mask row is inactive if the option Apply one profile to all slides is active Generate name if no name was defined By choosing this option a name is generated automatically in the following format if no name was defined and there is no barcode magazine number M slide position for example 1...

Page 104: ...ames and Profiles to File By clicking the button you can 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 Load Names and Profiles from File You can import previously saved name...

Page 105: ...e as described in Manual mode In Automatic mode you cannot change the threshold values it will use the threshold values that were set previously in the Manual mode and when activating the Use selection box option the area cannot be set For more information see section 4 5 3 Preview tab panel Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check s...

Page 106: ...l contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective cover Slide Removed Manually Click this button to notify the software that you have removed the slide manually Show images during scanning If you select this opti...

Page 107: ...l the ScanToServer which is an embedded application that can be run under the Pannoramic 250 scanner software Follow these steps to install the ScanToServer application 1 Run the ScanToServer_1_15_xx exe to launch the installation wizard 2 Accept the License Agreement then click Install to continue March 13 2012 Rev 1 3DHISTECH Ltd 107 135 ...

Page 108: ...inish 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 70 Scan Options button March 13 2012 Rev 1 3DHISTECH Ltd 108 135 ...

Page 109: ...drop down menu and give the User name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 72 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 Marc...

Page 110: ...played in a form If in Manual Mode only the data of the actually loaded slide can be set see Figure 73 When in Automatic Mode the form contains 25 rows for all the slots per magazine Figure 74 To additional magazines click Add tab panel next to the Magazine 01 tab panel Figure 73 CaseCenter window in Manual Mode Figure 74 CaseCenter window in Automatic Mode March 13 2012 Rev 1 3DHISTECH Ltd 110 13...

Page 111: ...read and set in the Barcode field Use masks for automatic fills Activate the Use mask option and the mask fields become fillable To save masks click the Save Mask button Click Set Mask to modify masks 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 three cha...

Page 112: ...dow Rows can be selected one by one clicking the row headings 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 of the CaseCenter server while the CaseCenter window is open click Update Tree to refresh the tree view ...

Page 113: ...Focus frequency present in Fluorescent mode Interpolated Focus distance present in Brightfield mode Compression procedure Use of a fixed compensation image ON OFF Use of stitching ON OFF Determination of the area to be scanned Use of automatic threshold specimen Use of specimen threshold value Use of Brightfield Darkfield preview image Use of marker pen threshold and specimen threshold values Use ...

Page 114: ...titching 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 and focus level Use of objective position Enable disable Multilayer options present in Fluorescent mode March 13 2012 Rev 1 3DHISTECH Ltd 114 135 ...

Page 115: ...y of the device Protect it with dust cover when not in use Switch the power off before covering it There is crush hazard during operation in the area of input or output Inserts magazines should be moved through software The protective shield of the magazine feed unit can be unmounted when slide scanning has stopped The device can be opened for service reasons only when switched off and in cases st...

Page 116: ...ton cloth and gently rub the surface 5 1 2 Cleaning the magazine Do not clean the magazines with xylene because it might harm the plastic We recommend to apply Isopropanol or Ethanol on a piece of lint free cotton cloth and gently rub the surface instead In case the magazine is damaged use either order a new one as inserting a deteriorated magazine could lead into unsafe loading of slides 5 1 3 Pr...

Page 117: ...ect power supply cable see section 1 1 4 Main parts of the Base Unit 3 Remove protective covers see section 5 3 1 Opening the protective cover 4 Remove magazine manually see section 5 3 6 Removing a Magazine from the Transporting System If a jammed magazine cannot be removed contact service personnel 5 Reattach protective covers 6 Reconnect power supply cable of the base unit and the control compu...

Page 118: ...noramic Viewer Scan camera is not properly adjusted for example due to loose fixture Contact 3DHISTECH Service for support Preview image is too dark too bright Invalid compensation image for preview camera Capture a new compensation image for the preview camera see section 4 3 6 Service tab panel Digitization process is extremely slow Extended focusing option is activated Deactivate the Extended f...

Page 119: ...trol with the button at the front of the HXP 120 The switching of the Lumencor cannot be triggered in spite of trigger connection through the camera Contact 3DHISTECH Service for support No suitable exposure time can be found Signal is too weak HXP 120 Shutter is closed The opening of the iris contained in the lamp module for fluorescent applications can be varied by means of the wheel located at ...

Page 120: ...bles see section 1 1 4 Main parts of the Base Unit Warning The opening mechanism is operated by a pre tensioned hinge Be sure that before opening the protective cover open the FL cover first so it will not lash to the cover during opening For information on how to open the FL cover see section 3 3 3 Opening Closing the FL protective cover Figure 77 Opening the cover To open the cover you will need...

Page 121: ...located next to the main power supply switch at the back side of the Pannoramic 250 3 Release lock 1 by pushing the lever to the left so the insert 2 can be pulled out Figure 78 Fuse compartment 4 Remove insert from the compartment Figure 79 Removing the fuse insert 5 Replace fuses put the insert back into its mounting and push it inwards until you hear a snap so the lever locks Figure 80 Replacin...

Page 122: ... 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 81 Figure 81 Removing the lateral cover of the HXP 120 3 Press plug securing latches inw...

Page 123: ... sure that the groove 1 in the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 84 Figure 84 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 8 Re esta...

Page 124: ...tion where the slide can be easily removed by clicking the Emergency Manual Slide Removal Position button see section 4 3 6 Service tab panel Warning Crush hazard Before you remove a jammed slide cancel the running digitization process terminate the software session and turn the power off Any manipulation performed on a mechanical component must be followed by a complete device initialization rout...

Page 125: ...n lock releases 5 Retrieve slide 3 from the holder 6 Release clamping lever 7 Turn down the slide loader back into the original position and pull it inwardly to the Pannoramic 250 until the guiding pin connects with the motor block groove again 8 Press the slide loader down to mechanical stop position in which the locking lever must engage 1 Use moderate force to press the loader part opposite the...

Page 126: ... 1 Opening the protective cover 3 Select the desired filter in the corresponding software window see section 4 2 3 Microscope Settings Base Settings panel The filter will be positioned in such a way that the user can access it without having to turn the filter wheel manually 4 Enter the respective parameters in the input fields 5 Hold the filter module 3 by its handling pads one on the right one o...

Page 127: ...es then pull it out of the bottom spring loaded components and take it off 8 Close the protective cover see section 5 3 1 Opening the protective cover 9 Switch the HXP 120 illuminator on again consider the cooling time possibly required 5 3 6 Removing a Magazine from the Transporting System Figure 88 Removing a magazine 1 Open the protective cover see section 5 3 1 Opening the protective cover War...

Page 128: ...f the camera is not in the way The base unit is shipped with two cameras that are positioned upwards 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 gear 5 by hand until the tappets are in their initial position again and the magazine flatly rests o...

Page 129: ...nd Maintenance 5 3 7 Transporting The following procedure shows how to transport Pannoramic 250 Figure 89 Transporting handles Caution Do not use the protective cover 2 to raise shift or transport Pannoramic 250 March 13 2012 Rev 1 3DHISTECH Ltd 129 135 ...

Page 130: ...can find the weight data of the base unit in section 6 Technical Data To transport Pannoramic 250 do the following 1 Switch power supply off see section 1 1 4 Main parts of the Base Unit and detach all other cables 2 Pull carrying handles out 1 until mechanical stop position A 3 Turn carrying handles by 90 B towards the base unit to secure them 4 Now you can transport Pannoramic 250 with the help ...

Page 131: ...approx 49 kg Ambient conditions Transportation shipment packed Permissible ambient temperature 40 C to 70 C Storage Permissible ambient temperature 0 C to 60 C Permissible relative air humidity non condensing 75 Operation Permissible ambient temperature 10 C to 35 C Permissible relative air humidity 75 Altitude at installation site max 2000 m Atmospheric pressure 500 hPa to 1060 hPa Degree of poll...

Page 132: ... Source Average service life of halogen lamp 2 x 109 flashes Lamp module for HXP 120 fluorescent option 120 W Average service life of Mercury short arc reflector lamp 2000h Lumencor light source SPECTRA 7 Light Engine Average service life of the Lumencor s light source 10 000 h This User s Guide describes Lumencor SPECTRA 7 and HXP 120 as light sources The X Cite 120 illuminator may also be used a...

Page 133: ...S2051 Pixel size 6 5 µm x 6 5 µm Camera resolution 2560 x2160 pixel Camera max speed 100 fps at full resolution 2560 2160 pixel Bit depth 16 bit Pixel resolution with 20x objective and 1x C mount adapter 0 22µm Cooling Peltier with forced air fan Connection type dual Camera Link full 10 taps AxioCam MRm Rev 3 2 3 progressive scan CCD Pixel size 6 45 6 45 µm Camera resolution 1388 1040 pixel Camera...

Page 134: ... 0 22µm Connection type CameraLink Control computer minimum system requirements Operating System Microsoft Windows 7 Professional SP1 64 bit EN HU CPU Intel Quad core processor 12 MB l2 cache RAM Min 8 GB DDR2 or DDR3 Recommended 12 GB DDR3 Hard disk Min 1 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices Keyboard mouse Ports 2xDouble CameraLink port 1 FireWir...

Page 135: ...Focus 3 13 21 42 47 54 57 60 64 65 66 76 77 81 82 83 84 86 87 93 94 95 99 100 101 107 116 117 121 122 H Halogen lamp 135 HXP 120 14 16 20 21 24 25 45 118 119 122 125 129 130 135 L Lumencor 2 12 16 20 21 24 25 26 93 118 122 135 M Marker 56 59 90 116 P Pannoramic 250 2 8 9 10 12 14 16 18 19 20 21 23 24 25 26 30 31 108 120 123 124 128 131 132 133 Pannoramic Viewer 22 66 77 120 121 Preview 3 13 20 24 ...

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