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PANNORAMIC® DESK DW II 3.0.4

SCANNING MODES AND SETTINGS

MARCH 30, 2021

Threshold options

This section is located at right side of the preview window.

Scanmap Source

is designed to

set which type of scanmap is used on the preview image. This scanmap is displayed
automatically in the

Profile Scanmap Source

setting. Selectable scanmap types are the

following:

•

Use threshold

•

Load previously saved Scanmap from file

•

Custom Scanmap

Preview Type

setting determines the type of illumination. In Brightfield mode the following

preview types are available:

•

Brightfield preview

–

a normal type of illumination in the microscope for scanning

the slide. This option is recommended when scanning in Brightfield mode.

Remove Coverslip

–

If selected, the edges of the coverslip are not detected as

specimen to be scanned. Depending on the threshold level, it is possible that the edges of
the coverslip are detected as areas to be digitized.

Figure 44 – Preview image with and without coverslip edge

Содержание PANNORAMIC DESK DW II 3.0.4

Страница 1: ...PANNORAMIC DESK DW II 3 0 4 USER S GUIDE December 8 2021 Rev 1...

Страница 2: ...System overview 16 1 2 1 Pannoramic DESK DW II system 16 1 2 2 Hardware options 18 1 2 3 Control software 19 2 Installation 20 2 1 Operation system of the control computer 21 2 2 Control computer por...

Страница 3: ...5 2 3 Table view mode 78 5 2 4 Card collection view mode 79 5 3 Profile and preview overview on the planner 80 5 4 Progress features 81 6 Settings and Service 82 6 1 Settings 82 6 2 Service 91 6 3 Ho...

Страница 4: ...78 P0301911 PCT HU04 00019 EP 1644767 US 7327515 The above mentioned granted patents granted utility model registered trademarks pending international and national patent applications and the other co...

Страница 5: ...t damage consequential damage or incidental damage including damage resulting from lost profits interruption of business loss of business information pecuniary loss or similar damage that stems from o...

Страница 6: ...for Measurement Control and Laboratory Use Part 2 101 Particular requirements for in vitro diagnostic IVD medical equipment IEC 61010 2 081 2015 Safety requirements for electrical equipment for measur...

Страница 7: ...ully read this instruction manual and adhere to all WARNING and CAUTION notices refer to chapter Notes Regarding Operational Safety for more information and a copy should be kept in the close to the s...

Страница 8: ...ey combination Example text in bold and italics Cross references within this document or to other documents Warning Can cause irreversible damage or harm to the user of the product or the product itse...

Страница 9: ...Crush hazard The Pannoramic DESK DW II including any of its original accessory components should not be operated in any other way than described in chapter Intended use Any of the following notes shou...

Страница 10: ...bles without protective earth ground conductor Warning The operation of the instrument in explosion risk environments is not allowed Warning If protective devices are found to be ineffective the Panno...

Страница 11: ...DESK DW II does not include any special facilities to protect from samples with an etching potentially infectious toxic radioactive or other health damaging effect You are under obligation to comply...

Страница 12: ...switch If the door is opened while a digitization process is running the process will be stopped instantly Warning A defective Pannoramic DESK DW II is not classified as domestic waste It must be pro...

Страница 13: ...eplacement No warranty will be accepted in cases of natural wear notably wear and tear parts or improper product handling The Product Manufacturer will refuse any liability in the event of damage resu...

Страница 14: ...Field of View NA Numerical 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...

Страница 15: ...the PC will highly affect the functionality of the scanner program 1 1 2 Features and benefits The Pannoramic DESK DW II offers world class brightfield whole slide scanning An outstanding 0 12 m pixel...

Страница 16: ...g and information labels The following figure contains the labels used on the Pannoramic DESK DW II main unit and the external mains power supply unit Figure 1 Warning and information labels Notice Th...

Страница 17: ...t Figure 2 Main parts of the base unit 1 Protective cover 2 Sliding door 3 PointGreyGrasshopper3camera 1 2 System overview The standard scope of delivery of the product includes the following hardware...

Страница 18: ...SK DW II 3 0 4 PRODUCT DESCRIPTION MARCH 30 2021 17 Figure 3 Pannoramic DESK DW II system overview 1 24V external power supply unit 2 Pannoramic DESK DW II base unit 3 Monitor 4 Mouse 5 Control comput...

Страница 19: ...omputer and monitor can vary depending on the product order Camera Camera Description Point Grey Grasshopper 3 Monochrome 1 CCD monochrome camera for normal brightfield scanning Table 2 Camera Camera...

Страница 20: ...ption Base unit equipped with Point Grey Grasshopper 3 camera for Brightfield scanning Objectives Plan Apochromat 20 NA 0 8 Plan Apochromat 40 Corr NA 0 95 Warning Do not change correction collar sett...

Страница 21: ...stants are allowed to install the hardware and software The product is ready for use after installation Caution Make sure that the device is placed so that there is enough space for ventilation and fo...

Страница 22: ...exceptions of the antivirus program C Program Files 3DHISTECH C ProgramData 3DHISTECH C Program Files x86 3DHISTECH E ScannerSwap as the SWAP folder by default We recommend that you use the SWAP part...

Страница 23: ...tion of the product for a short distance by disconnecting cables and detaching hardware components from each other Figure 4 Ports on control computer 1 Status display 2 DVD drive RW 3 Power on off but...

Страница 24: ...ion Contact 3DHISTECH Service for support in such cases Control USB cable between scanner and control computer Preview camera USB cable between scanner and control computer Video cable between monitor...

Страница 25: ...s power and the device Front panel 1 main power switch 2 power supply connector Back panel 3 detachable power cord to connect the external power supply unit with the main unit Figure 5 24V external po...

Страница 26: ...pecifications of slides and coverslips Warning Always wear personal protective equipment safety goggles gloves and coat when working with biohazardous material or slides Warning Do not use a slide whe...

Страница 27: ...ware To affix barcode stickers to slides do the following 1 Peel off the barcode sticker 2 from the roll 2 Stick it on the colored label area 1 of the slide on the specimen side For large slides the l...

Страница 28: ...ain that the adapter is applied or not How to place and remove the adapter For the placement and removal of the adapter a special tool is needed This applicator has a magnet at its head thus allowing...

Страница 29: ...e applicator 3 Put both the applicator and the adapter in a safe place 4 The specimen holder is now capable to receive a large slide Figure 10 Specimen holder with the adapter removed If you want to l...

Страница 30: ...onto the specimen holder Figure 11 Placing the adapter onto the specimen holder 4 After the adapter is placed on its location lift the applicator and make sure the adapter stays at its place Figure 12...

Страница 31: ...ell trained person Figure 13 Inserting and removing a slide 1 Click in Pannoramic Scanner 3 0 3control software The specimen holder moves to the load unload position 2 Open the slide insert door 1 by...

Страница 32: ...d person 5 Close the fixing lever by pushing it to the right so that it touches and therefore fixes the slide 6 Close the slide insert door 1 by pushing it to the right Caution When closing the slide...

Страница 33: ...older moves to the load unload position when selecting any of these two options and click Cancel to exit the window without ejecting the slide 2 Open the slide insert door 1 by pushing it to the left...

Страница 34: ...nnoramic Scanner Before software initialization the user interface is opened and the mode selection icons are displayed Figure 14 Mode selection window These three mode buttons represent Microscope an...

Страница 35: ...owing functions are available for you to select from at the main menu bar Switch between Microscope and Planner modes Microscope initialization All motors and the preview camera during start up Bright...

Страница 36: ...images during digitization One pixel on the monitor corresponds to one pixel on the camera The live image completely fills the display area Displays or hides the vertical and horizontal scale bars Di...

Страница 37: ...Image Processor Plugins o Convolute gray scale image by custom kernel o Multi channel histogram with normalization o Invert image for testing purposes o Mark overexposed pixels Scan Properties Unique...

Страница 38: ...me based on the corresponding settings set in Preferences activate Generate function Barcode parsing Select the type of barcode profile from the drop down list for slide naming though parsing the barc...

Страница 39: ...ist blank input fields will be displayed Figure 18 Create new barcode Define modify profile name in the Name input field select barcode type from the Type drop down list Define modify ranges within th...

Страница 40: ...and click Create new at the top of the panel to create a new profile item Slide save path Set destination folder in the input field by typing in the path or clicking to browse for the folder Free spac...

Страница 41: ...erlapping o Tiled TIFF settings Click Reset to set everything to default Zero based index in names Z Stack layers of the generated TIFF files will be indexed starting with 0 and the focus distance of...

Страница 42: ...00 Zoom scale set the level of zoom at which the TIFF image is created to get the smallest file size possible o DICOM settings Click Reset to set everything to default Frame number maximum default 0 O...

Страница 43: ...is displayed in the Converter queue window of the converter Figure 20 Conversion window o Other settings Scan separately The FOV areas of the preview image will be scanned and saved separately as dis...

Страница 44: ...ndow Display Name Host Name Protocol Figure 22 Window of server editor Server Editor stores each of the created server in a list List entries can be removed or a new entry can be added if required Wit...

Страница 45: ...rcode settings for parsing can be modified in the Barcode Editor window Figure 24 Barcode Editor If using MIL for barcode reading you can select the following barcode types 1D barcode types Code 39 Co...

Страница 46: ...in CaseCenter is automatically selected as scanning destination based on the CaseID containing slide and patient data stored on HIS LIS Therefore Folder Case Block and Slide name field data cannot be...

Страница 47: ...want to scan from the Server drop down list Click the arrow to show the list of saved server profiles or click Add new item at the bottom of the list to create another server connection When creating...

Страница 48: ...panel After loading server data User name and Password are required to be added for authentication and accessing the server If connection is successful a green checkmark is displayed in the window Fi...

Страница 49: ...ettings for more information HIS Integrated output This folder contains converted slides where barcode reading was successful and they can be connected to a HIS case Unidentified output This folder co...

Страница 50: ...ntaining a list of previously saved profiles is opened Additional profiles can be created after clicking Create After expanding the Filter section of the panel search for a specific profile can be ini...

Страница 51: ...Profile The selected profile can be saved in this window after typing the profile name into the text field and clicking Save as Note that this function is not available in Planner mode Figure 32 Save...

Страница 52: ...e information In accordance with the selected mode the Profile Settings Panel and the Microscope Control Panel views are modified 5 1 Brightfield scanning mode Microscope View consist of three differe...

Страница 53: ...for scan profile Limits of the range You can define focus limits by defining the upper and lower limits by selecting the desired value in the selection boxes This is useful if focusing was not target...

Страница 54: ...roscope for scanning the slide This option is recommended when scanning in Brightfield mode Thresholding The manually specified value is used for thresholding during scanning Preview image of the load...

Страница 55: ...hreshold value manually or append missing areas with the help of appropriate functions in the Preview window o Use marker with threshold If the specimen cannot be identified as required for digitizati...

Страница 56: ...a selected not selected Threshold enhancement o Remove coverslip If selected the edges of the coverslip are not detected as specimen to be scanned Depending on the threshold level it is possible that...

Страница 57: ...e maximum size of specks not to be digitized by adjusting the slider o Dilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by 100 m each time Scanmap...

Страница 58: ...vels with the Levels selection box The current focus value is the initial level If you set 5 for example then the initial level plus four two focus levels above and below the FOVs are captured Therefo...

Страница 59: ...the following predefined image formats and a subsequent custom option from the Image Quality drop down list in the Image Encoding section of the window Excellent JPEG 90 Good JPEG 80 Medium JPEG 60 L...

Страница 60: ...software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading With Save focus quality the measurement of focus quality c...

Страница 61: ...y saved Scanmap from file Custom Scanmap Preview Type setting determines the type of illumination In Brightfield mode the following preview types are available Brightfield preview a normal type of ill...

Страница 62: ...d smear the Remove Coverslip function cannot be activated and focusing on the coverslip area is not available If you want to use the Remove Coverslip function first switch to Custom Scanmap Fill holes...

Страница 63: ...areas will be digitized however this may also include specks or other imperfections of the slide Greater values result in a less sensitive scanning but it is possible that some of the smaller specime...

Страница 64: ...everything within the marked area check the Scan everything within marker selection box Figure 45 Scan everything within the marker selected not selected Dilate mask Adjust the slider to enlarge or de...

Страница 65: ...ide click Position sample and then click on the area of interest on the preview image This will define the Live image that you can access from the Live view Union Add the selected areas to the preview...

Страница 66: ...scanned with the different tools on the Preview toolbar Place focus point You can add manual focus points on the preview image the coordinates of the manual focus points you add are listed on the Focu...

Страница 67: ...MA tool Grid selector Delete TMA grid by clicking the X at the top right corner and rotate grid by clicking the icon at the bottom right corner Enter the number of rows and columns in the Rows and Col...

Страница 68: ...selected a black frame displayed in the image and only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external...

Страница 69: ...ew 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 displayed during scanning Hide all layers All the laye...

Страница 70: ...t the upper and lower limits by selecting the desired value in the selection boxes By using Set Range the Lower limit value is set to 32 of the current focus value and the Upper limit value is set to...

Страница 71: ...s window An image is defined as a two dimensional function f x y the amplitude of at any pair of coordinates x y is called the intensity or gray level of the image at that point The pixel intensity at...

Страница 72: ...e to the required direction with the set step size 5 1 3 Quick preview functions Use Ctrl mouse wheel to zoom in or out to the preview area or the Live image A quick preview function tool pops up by r...

Страница 73: ...unctions tool can be displayed upon right clicking on the background of the main window outside the preview window It includes quick access buttons to main functions for DESK DW II Figure 58 Quick too...

Страница 74: ...nked in a row displayed at the bottom left corner of the main window Figure 59 Progress of the profile modification history Once you are moving the mouse cursor over a unit all the parameters will bec...

Страница 75: ...SETTINGS MARCH 30 2021 74 Figure 61 Profile history tree 5 2 Planner mode The whole scanning procedure of the loaded slide can be planned in this mode Virtual slides can be created and stored in diff...

Страница 76: ...lide view with card mode Load slide Available after initialization upon clicking the slide icon the slide can be loaded Remove Change slide Available only if a slide is loaded into the scanner Click t...

Страница 77: ...e view with card Click in the Preferences window Planner layout selector to activate this view in which the slide position and its card can have a horizontal or vertical layout Slide preview and the l...

Страница 78: ...ntal Slide view with card The parameters of the assigned profile are displayed in a card Figure 65 Brightfield profile card The following information are included in a profile card Profile name in the...

Страница 79: ...le editor for Scheduler Notice Once scanning has finished the thumbnail of the digital slide is added to the card at the bottom Double click the thumbnail image of the digital slide to open it in View...

Страница 80: ...ed profile Profile name Illumination Objective type Filters N A Progress Properties The location of the virtual slide with the selected profile can be defined Scan result Scan duration Scanned FOVs To...

Страница 81: ...s can be checked here The expanding panel at the right side includes all the profile settings in coherence with the view type of the Profile Setting panel Slide preview is displayed in the Preview win...

Страница 82: ...and Planner modes whenever there is a running hardware operation or scanning procedure Progress content can be therefore different depending on the type of the running procedure Figure 69 Progress da...

Страница 83: ...te Services by clicking and Settings by clicking at the right side of the main menu bar 6 1 Settings Activate Settings by clicking at the right side of the main menu bar Preferences This panel contain...

Страница 84: ...SlideScanner Globalization contains another language file that language can be set in this drop down menu too Appearance settings o View Mode Selector Text mode Icon mode Float Text mode Float Icon mo...

Страница 85: ...creenshot folder Set the folder for storing screenshots by clicking Browse Otherwise the C Users Username Pictures folder is used by default Slide settings o Unload slide after FL grabbing N A o Slide...

Страница 86: ...TECH SlideScanner HWLogDataBase The following motor movements are recorded in the log list General Microscope Part Objective Changer Preview Light Relay Scan Loader Service Slide Scanner Stage o Softw...

Страница 87: ...settings o On this panel you can define the Swap file location and set the Number of compensation images for preview camera if needed o If a certain time is set for Watchdog timeout the scanning proc...

Страница 88: ...ure 73 Profile behavior settings o Use profile history save With this function each profile modification is saved in Profile History from which the different stages can be reloaded o Save interval Pro...

Страница 89: ...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 field it will pass them to the software t...

Страница 90: ...d set the message body in the Message subject field by entering a text for example to inform recipients on the location of the scanner or the slide set you are working with Click to test settings by s...

Страница 91: ...on Click Delete user if you want to remove a user from the list after selection Report sender settings Figure 76 Report sender settings Add new recipients to the list by clicking or remove selected fr...

Страница 92: ...RCH 30 2021 91 6 2 Service Activate Service by clicking at the right side of the main menu bar Service password Enter password first to enable service settings for modification Figure 77 Enter service...

Страница 93: ...profile has effect on the color set color temperature and gamma value of the scanned image Preset profiles are the following Calibrated Linear Color scheme is defined by calibration Gamma value is not...

Страница 94: ...x o Reset all camera rotation Click this button to set camera rotation values to default Save settings by clicking Image compensation You can use a saved compensation image whenever compensation relat...

Страница 95: ...utton to interrupt the process The progress bar at the bottom of the window displays the progress of the compensation image creation o Export image Save compensation image Barcode settings By predefin...

Страница 96: ...figure correctly or there is no barcode in the barcode area the software will display the following error message Barcode detection unsuccessful There might be no barcode present o Barcode reader lib...

Страница 97: ...xclude check digit Checksum value is ignored when reading Interleaved2of5 and Code39 barcode types 6 3 Hosting Hosting a live teleconsultation session gives specialists the opportunity to examine the...

Страница 98: ...ting a teleconsultation session 1 Select Hosting from the microscope mode menu 2 Type in your nickname used during the session 3 Click to start hosting the session 4 The software displays the hosting...

Страница 99: ...quality 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 marker pen threshold and specimen threshold v...

Страница 100: ...sure click No For more comfortable and safer use the Planner autosave function allows the taking of automatic backups while creating a scan plan The backups are placed in the default document folder o...

Страница 101: ...nnect the power plug before changing the bulbs Defective devices do not classify as domestic waste Dispose of the device in compliance with the currently valid legal requirements 8 2 1 Cleaning the de...

Страница 102: ...ts and is open in Pannoramic Viewer Close virtual slide in Pannoramic Viewer Slide jammed 1 Exit the Pannoramic Scanner 3 0 4 control software 2 Switch off the power supply and disconnect the power ca...

Страница 103: ...correctly Guiding fault in transport system Contact 3DHISTECH Service for support Digitization process is extremely slow Extended focusing option is activated Deactivate the Extended focusing option i...

Страница 104: ...e cover To perform maintenance work and because of slide jamming the protective cover of the Pannoramic DESK DW II need to be removed to eliminate the problem First make sure that the running digitiza...

Страница 105: ...Note that the rear part of the cover must be pushed over the top part of the blue basic unit 7 5 To lock the cover in place insert the screws again and fasten them Caution Make sure that no cables ar...

Страница 106: ...move the slide 1 from the holder 2 Warning If the slide is broken make sure to remove all pieces completely from the device The edge of the broken area of the slide is sharp and it can lead to injury...

Страница 107: ...transporting One or two persons can carry the base unit by holding it by its base plate You can find the weight data of the base unit in chapter Technical Data Caution Be sure that the scan camera is...

Страница 108: ...4 3 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...

Страница 109: ...with EN 61326 2 6 2012 Base unit input voltage 24V DC 1V Power consumption of the complete device 60 VA SINPRO MPU101 108 24V external mains power supply unit Intended site closed room facilities Ele...

Страница 110: ...3 2 um x 3 2 um Max frame rate 13 Hz Bit depth 8 10 bit Scan camera Point Grey Grasshopper 3 GS3 U3 51S5M C Global Shutter Type CMOS Sony IMX250 Pixel size 3 45 m 3 45 m Camera resolution 2448 H 2048...

Страница 111: ...requirements Operating System Microsoft Windows 10 Professional 64 bit EN CPU Intel Core i5 8600 RAM 32GB DDR3 1600 Hard disk 500 GB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True c...

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