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3D Histech Pannoramic MIDI II 2.0.5 User Manual Download Page 122

Pannoramic MIDI II 2.0.5 User’s Guide

6 Using Profiles

Fluorescent settings

•

Filter position(s)

•

Selected focus channel

•

Selected stitching channel

•

Flat field correction (ON/OFF)

•

Intensity statistics

•

Intensity reducing

•

Intensity equalization

•

Sharpening (ON/OFF)

•

Use of skip empty field-of-views (ON/OFF)

•

Do not use extended focus on empty field-of-views (ON/OFF)

•

Custom extended focus

Other settings

•

Limitation of focus range (ON/OFF)

•

Focus quality (ON/OFF)

•

Enable/disable Multilayer options

•

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

•

Output resolution

December 7, 2018 – Rev. 1

3DHISTECH Ltd.

122(144)

Summary of Contents for Pannoramic MIDI II 2.0.5

Page 1: ...PMII205 Rev1 Pannoramic MIDI II 2 0 5 User s Guide December 7 2018 Rev 1 ...

Page 2: ...re 20 2 Installation 22 2 1 Control computer ports 23 2 2 Connectors and cables 24 2 3 Coupling the Lumencor SOLA SM II unit with the scanner 24 2 4 Coupling the Lumencor Spectra 6 unit with the scanner 25 2 5 External power supply unit 25 2 6 Power the scanner on off 26 3 Preparing Slides and Trays 27 3 1 Affixing Barcode Stickers to Slides 29 3 2 Inserting and Removing Slides 30 4 Software Descr...

Page 3: ...ew overview on the Planner 100 5 5 Progress features 101 5 6 Settings and Service 102 5 6 1 Settings 102 5 6 2 Services 111 5 7 Hosting 119 6 Using Profiles 121 7 Troubleshooting and Maintenance 123 7 1 Safety Information 123 7 1 1 Cleaning the device 124 7 1 2 Cleaning the trays 124 7 1 3 Preventive maintenance 124 7 2 Troubleshooting 125 7 2 1 Fluorescent Applications optional 127 7 3 Maintenanc...

Page 4: ...Pannoramic MIDI II 2 0 5 User s Guide Packing the accessories 142 Closing the package 142 Handling of the package 143 Index 144 December 7 2018 Rev 1 3DHISTECH Ltd 4 144 ...

Page 5: ...er 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 digitized slide s that stems from or is associated with use of Product digitized slides quality of staining quality of stained slides qual...

Page 6: ...urther Information For the latest information on 3DHISTECH products and services please visit our website at the following URL http www 3dhistech com Company Address 3 Öv street 1141 Budapest HUNGARY December 7 2018 Rev 1 3DHISTECH Ltd 6 144 ...

Page 7: ...uirements IEC 61010 2 101 2002 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 2 101 Particular requirements for in vitro diagnostic IVD medical equipment UL 61010 1 2004 R10 08 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Conformity with Directive IEC 61010 2 101 is marked by on the...

Page 8: ...ch 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 to not work properly if this instruction is not followed and alerts to a potential danger situation Note Calls attention ...

Page 9: ...ngle parts no liability will be assumed by the Manufacturer This shall also apply to service or repair work of any kind which is performed by other than authorized service personnel All claims for warranty and warranty services will be null and void in any such case Note The safety level of the equipment after servicing will be identical with level of the original equipment Warning Insert the powe...

Page 10: ...ch influences to a maximum possible degree During periods of non use the Pannoramic MIDI II must be protected with a dust cover Check that power is turned off before you put the cover on Caution Do not position the equipment so that it is difficult to operate and to disconnect the device if necessary Crush hazard There is crush hazard in the movement area of the slide insert during operation Pleas...

Page 11: ...es of natural wear notably wear and tear 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 warranty Except for...

Page 12: ... 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 to a colleague electronically for co operation or advice and so on December 7 2018 Rev 1 3DHISTECH Ltd 12 144 ...

Page 13: ... of information loss Warning Any modification to a hardware or software component of the PC will highly affect the functionality of the scanner program 1 1 2 Features and Benefits The Pannoramic MIDI II offers world class brightfield and fluorescent whole slide scanning on up to 9 channels An outstanding 0 12 µm pixel in Brightfield and 0 16 µm pixel in Fluorescent resolution is achieved with the ...

Page 14: ... stable manufacturing 3MP camera for barcode reading and preview image Image sharpening for both Fluorescence and Brightfield feature to improve the visual appearance of digital slides Focus algorithm finds the focus which is most appealing to the human eye Pannoramic MIDI II is an optimal choice for customers who want to scan in brightfield and in fluorescent mode where the quantity of scanned sl...

Page 15: ...3 Warning and Information Labels The following figure contains the labels used on the Pannoramic MIDI II main unit the external mains power supply unit and the Lumencor SOLA SM II illumination unit Figure 1 Warning and information labels December 7 2018 Rev 1 3DHISTECH Ltd 15 144 ...

Page 16: ...otective covers 2 Point Grey Grasshopper 3or pco edge 4 2 camera Fluorescent option A 3 Lumencor SOLA SM II fiber coupled illumination unit can be used with Point Grey Grasshopper 3 camera only with Lumencor illumination adapter and cable Fluorescent option B 4 Lumencor SPECTRA 6 Light Engine fiber coupled illumination unit December 7 2018 Rev 1 3DHISTECH Ltd 16 144 ...

Page 17: ... the main parts of the Pannoramic MIDI II system Figure 3 Pannoramic MIDI II system overview 1 Pannoramic MIDI II base unit 2 24 V external power supply unit for Pannoramic MIDI II 3 Lumencor SPECTRA 6 Light Engine illumination unit option 4 SOLA SM II fiber coupled illumination unit option 5 External power supply unit for SOLA SM II 6 Slide tray 7 Control computer 8 Keyboard 9 Mouse 10 Monitor De...

Page 18: ...asshopper 3 1 CCD monochrome camera for high quality sensitive fluorescent applications pco edge 4 2 Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast scanning and an outstanding low read out noise High quantum efficiency cooled with Peltier element Camera adapters 0 63 adapter for Point Grey Grasshopper 3 only 1 adapter December 7 2018 Rev 1 3DHISTECH Ltd ...

Page 19: ...nit completely equipped with Point Grey Grasshopper 3 camera and Lumencor SOLA SM II non triggered or Lumencor SPECTRA 6 fluorescent illumination unit with filters for fluorescence scanning Pannoramic MIDI II Advanced Brightfield and Fluorescence Option base unit completely equipped with pco edge 4 2 camera and Lumencor SPECTRA 6 fluorescence illumination unit trigger cable and filters for fluores...

Page 20: ...iption Lumencor SOLA SM II Fluorescent illumination unit can be used with Point Grey Grasshopper 3 camera only Lumencor SPECTRA 6 Light Engine illumination unit 1 2 3 Control Software Pannoramic Scanner control software Optional Fluorescence Extended focus Z stack Barcode reader licensed feature December 7 2018 Rev 1 3DHISTECH Ltd 20 144 ...

Page 21: ...ramic Viewer software fully functional Optional CaseCenter TMA module 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules TumorBoard module E School Encoder December 7 2018 Rev 1 3DHISTECH Ltd 21 144 ...

Page 22: ... 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 for safe and efficient operator maintenance Caution If the temperature of the location where the scanner is operated is much lower than the temperature of the equipment for example the device is brought in from an outer sto...

Page 23: ...detaching hardware components from each other Figure 4 Ports on control computer 1 Status display 2 DVD drive RW 3 Power on off button 4 Earphone and microphone 3 5mm Jack ports 5 2x USB port 6 Power supply connector 7 PS 2 mouse port 8 PS 2 keyboard port 9 4x USB port 10 2x USB port 11 Network port 12 Matrox Radient eCL CameraLink ports for pco edge 4 2 camera 13 4x USB 3 0 ports for Point Grey G...

Page 24: ...le between 230V 110V and pco edge 4 2 camera Optical cable between Lumencor SOLA SM II fluorescent illumination unit and scanner Trigger cable between pco edge 4 2 or Point Grey Grasshopper 3 camera and Lumencor SPECTRA 6 fluorescent illumination unit USB to RS232 serial communication cable between Lumencor SPECTRA 6 fluorescent illumination unit and control computer Warning Only connect external ...

Page 25: ...2 option B 3 Connect power supply cables both of the scanner and the illumination unit 4 Connect TTL trigger cable between pco edge 4 2 camera out 4 or Point Grey Grasshopper 3 camera and the Lumencor SPECTRA 6 unit TTL port and USB to RS232 communication cable between the Lumencor SPECTRA 6 unit and the computer Figure 5 Lumencor SPECTRA 6 Light Engine connecting ports 2 5 External power supply u...

Page 26: ...ure 6 24V external power supply unit 2 6 Power the scanner on off To turn the scanner on press down the I side of the rocker switch at the front panel of the 24V external power supply unit Figure 6 1 and press O to power the scanner off December 7 2018 3DHISTECH Ltd 26 144 ...

Page 27: ...ished or cut Warning Always wear personal protective equipment safety goggles gloves and coat when working with biohazardous material or slides Warning Do not use a slide when it is broken or its edges are not properly cut or grounded Using such slides can lead to injury Warning Ensure that no part of the mounted coverslip protrudes from the edges of the slide Use slides with completely dried embe...

Page 28: ...er Note 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 informat...

Page 29: ...ff the barcode sticker 2 from the roll 2 Stick it on the colored label area 1 of the slide on the specimen side Caution 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 Do not let barcode sticker protrude from slide edges or stick on the coverslip surface 3 The thickness of the barcode sticker on ...

Page 30: ...ides into a tray Figure 8 Inserting slides into a tray A tray can contain a maximum of 12 slides Push a slide 1 into the desired slot 4 of the tray 3 with its barcode end 2 first Make sure that the slides are inserted correctly in the tray Figure 9 Incorrectly inserted slides December 7 2018 Rev 1 3DHISTECH Ltd 30 144 ...

Page 31: ...ntagion Broken slide can be removed only by a well trained person Only original 3DHISTECH trays are allowed for use with Pannoramic MIDI II Note The coverslip and the label area should be on the top To insert and remove trays Figure 10 Inserting the tray 1 Insert the tray 2 that contains at least one slide into the opening 1 on the right side of the device Push it until it cannot be pushed further...

Page 32: ... mounting media residues Slides will only operate safely and properly if trays are clean 2 Attach the FL tray covers on the insert sled Figure 11 FL tray cover Warning After the tray is inserted into the device the FL tray covers must be attached thus securing the tray movement area from external impacts and the effectiveness of Fluorescent scanning while slides are digitized Caution Do not place ...

Page 33: ...ee buttons represent Microscope and Planner scanner modes and the Service mode Microscope mode for digitization of individual slide or individual rack set scanning profile of the slide run Live teleconsultation use Live microscope Planner mode plan the entire scanning procedure assign one or more profiles to each slide define Brightfield and Fluorescence or mixed scanning mode within a run define ...

Page 34: ...anner 2 0 5 main window The following 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 Brightfield mode the camera set for brightfield scanning is initialized Fluorescence mode the camera set for fluorescence scanning is initialized Remote server hosting Start ...

Page 35: ...ition where the tray should be moved can be defined Slide removed Click this button to inform the control software that the slide has been removed manually Objective changer Live view is on Live view is on with the shutter closed Toolbar for live images Click to display the toolbar for Live view These functions are only available for the displayed live image i e Live view is ON but not available f...

Page 36: ... is reset to 100 ms Therefore the resulting images will have a higher noise level This function is useful for fluorescent live view where in spite of the higher noise level the resulting image will be refreshed as in normal mode Image intensity Screenshot Displays the magnifier window Displays or hides the vertical and horizontal scale bars Calculate white balance accessible in Brightfield mode on...

Page 37: ... space Free space capacity of selected local drive Use Barcode Select the type of barcode profile for slide naming By using Default barcode profile the barcode of the slide is being matched with all the barcode types selected in the Barcode settings window Slide name Can be defined by manual or generate automatically with Generate name setting Scan separately The FOV areas of the preview image wil...

Page 38: ...reate another server connection Define the following details of the Server in the Server editor window Display Name Host Name Protocol 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 With the Filters function you can narrow down the results by searching for a specific server data By double clicking a list item server dat...

Page 39: ...d if CaseCenter is connected with the supported HIS LIS This way the barcode read by the software is being identified and the predefined location of that specific case 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 modified only a profile can be s...

Page 40: ... barcode types Code 39 Code 128 Code 16K Interleaved 2 of 5 Standard 2 of 5 IATA 2 of 5 Matrix 2 of 5 Telepen Code 93 Code 11 MSI Codabar Patch Code Pharmacode EAN 13 EAN 8 UPC A UPC E 2D barcode types Aztec Data Matrix PDF417 Compact Micro PDF417 QR Micro QR MaxiCode December 7 2018 Rev 1 3DHISTECH Ltd 40 144 ...

Page 41: ...w selector Each preview of slides in the tray is taken automatically Preview types are the following from top to bottom Brightfield Darkfield Pre Scan Pre Scan High Resolution Pre Scan High Resolution Activate Retake Preview for all the slides in the magazine if necessary This operation can be initiated from the slide preview window as well Auto attach Actual profile is assigned to the loaded slid...

Page 42: ...reated here as well and you can also search for a specific profile by filtering based on the following data Profile name Objective type None 20x 40x Multilayer mode Extended focus Z stack Illumination None Brightfield Fluorescent Filters Modify date Last use date Click Search to run search based on the set criteria Click to make parameters of the selected profile available for editing After modifi...

Page 43: ...to the text field and clicking Save as Reset Zoom This function is active only in Live view at 1 1 magnification Live image magnification Settings and Service function descriptions are detailed in section 5 6 Settings and Service Help In the About window the version of the software and licensing details are included December 7 2018 Rev 1 3DHISTECH Ltd 43 144 ...

Page 44: ...Services and Settings for more information Settings see section 5 6 Services and Settings for more 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 different sections Main functions Located at below the window header these functions are identical in both mod...

Page 45: ...the desired value in the selection boxes This is useful if focusing was not targeted on the specimen but on a spot on the coverslip Focus distance the distance of focal points can be set to create a focus map based on which the software calculates interpolated focus values one step in distance means one FOV Sample detection This panel offers options for threshold setting and selection of the area ...

Page 46: ...t some of the smaller specimen areas will not be digitized Auto Threshold By clicking the specimen will automatically be detected in the preview image Caution Make sure that the detection result is acceptable for you Otherwise set the threshold value manually or append missing areas with the help of appropriate functions in the Preview window Use marker with threshold If the specimen cannot be ide...

Page 47: ...ctivate this function Figure 21 Scan everything within the marked area selected not selected Threshold enhancement 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 22 Preview image with and without coverslip edge December 7 2...

Page 48: ...r Dilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by 100 µm each time Scanmap A previously saved scanmap can be loaded and applied Use Threshold Preview settings defined in the Microscope Controller Panel Preview window are applied as the basis of scanmap Load scanmap This function is useful if the slides contain areas of interest that cannot b...

Page 49: ...d Figure 23 Focus level and step size Z stack Both for Extended focus and Z Stack scanning methods you can determine the desired number of focus levels with the Levels selection box The current focus value is the starting point If you set 5 for example one current two focus levels above and below FOVs are captured Therefore it is advised to choose an odd number for the focus levels Separate layers...

Page 50: ...efined by calibration Gamma value is not included sRGB standard Color scheme is defined by calibration standard Gamma value 2 2 is applied sRGB standard Microscope Like Color scheme is defined by calibration standard Gamma value White Point D50 Legacy a Color scheme calibrated for the previous software version is applied Custom Color profile set in Service is applicable if needed Image settings Yo...

Page 51: ...impossible For such slides use an empty slide with coverslip to grab a compensation image If you select this the software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading Save focus quality The measurement of focus quality correctness of average focus on layers is saved This option is inactive when Extended focus o...

Page 52: ... and selection of the area to be scanned Figure 25 Preview panel 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 fi...

Page 53: ...en 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 26 Preview image with and without coverslip edge Caution It requires lots of time since it cannot find focus neither on the edges nor on specks ...

Page 54: ...n Make sure that the detection result is acceptable for you Otherwise set the threshold value manually Make sure that the detection result is acceptable for you Otherwise set the threshold value manually Manual threshold Set threshold value manually or calculate value on the actual preview with Calculate Threshold function which is active only if setting the value manually This sets the sensitivit...

Page 55: ...shold selection box in the range of 0 255 This sets the sensitivity of the specimen detection inside the marker area To set the desired threshold value manually change the setting in the Threshold selection box in the range of 0 255 The default value is 212 Everything within marker This function is available only to select if the Use marker with threshold function is activated To scan everything w...

Page 56: ...ine the Live image that you can access from the Live view Union Add the selected areas to the preview Mark area for scanning based on the shape selected in the Preview Toolbar This area will not be scanned Erase Delete selected areas from the preview image Deselection is made based on the selected shape from the Preview Toolbar This area will not be scanned Figure 28 Not scanned selection Edit The...

Page 57: ...abled only if a TMA grid has already been placed on the preview image Set grid parameters row and column numbers and spot shape round or rectangle Figure 30 TMA 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 Columns fields or select the appropriate valu...

Page 58: ...d 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 specks will not be scanned Figure 31 Use selection box The following colors are used in the preview image to demonstrate digitization and selection settings Figure 32 Colors in preview image and Label area sw...

Page 59: ...d on the basis of their position for example they are outside the selection box They are detected by the selected threshold value Marker If Scan area inside the marker is selected in the Preview panel the preview camera detects the marker pen The inside areas appear in red color and will be digitized Areas scanned in This color is only displayed during scanning Hide all layers All the layers will ...

Page 60: ...imits 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 32 of the current focus value This is useful if Auto Focus does not find the focus on the specimen but on the coverslip Also this makes the focusing sequence faster For manual focusing define the manual focus step size by a...

Page 61: ...ty or gray level of the image at that point The pixel intensity at the coordinate pointing at with the cursor is displayed in the Image Intensity window Figure 36 Window of Image Intensity 5 1 2 4 Stage positioning Click to activate Stage Positioning Tool to navigate on the slide so to perform microscope movements on the Live image with this control function The number at the center of the control...

Page 62: ...o main preview related functions Drag Draw Erase Retake preview Settings Toggle deletion always on top Reset zoom Window auto size Clean scanmap Figure 38 Quick toolbar 5 1 3 Quick microscope functions A quick microscope functions 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 MIDI II ...

Page 63: ... MIDI II 2 0 5 User s Guide 5 1 3 Quick microscope functions Autofocus Live tools Fast mode Screenshot Magnifier Ruler Image processor plugins Add scanmap Auto exposure December 7 2018 Rev 1 3DHISTECH Ltd 63 144 ...

Page 64: ...g Exp Time If Auto Exp is inactive exposure time of each filter can be defined manually Values such as Calc Exposure time in Microscope Control panel and those that are specified manually are loaded in these fields Value units can be the following microsec millisec sec Exc The given value specifies the excitation intensity in percentage of the illumination unit DG Digital Gain This is camera depen...

Page 65: ... value turn live image on and set a suitable focus position You can accept the current Z value by clicking Assign Current Interpolated focus If you select the Interpolated focus option the coarse focus level is calculated from three different focus points of the specimen Carry out a manual focusing sequence in the preview image on those three points Set the correct focus value of the desired previ...

Page 66: ...f the specimen Focus Exposure The exposure time during focusing it can have three states Short Normal Long Sample detection The Sample detection panel offers options for setting threshold and the selection of scannable areas Source Brightfield preview a normal type of illumination in the microscope for scanning the slide This option is recommended when scanning in Brightfield mode Darkfield sample...

Page 67: ...is 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 specimen areas will not be digitized Auto Threshold By clicking the specimen will automatically be detected in the preview image Caution Make sure that the detection result is acceptable for you Otherwise set the threshold value manually or a...

Page 68: ...ctivate this function Figure 41 Scan everything within the marked area selected not selected Threshold enhancement 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 42 Preview image with and without coverslip edge December 7 2...

Page 69: ...er Dilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by 100 µm each time Scanmap option The previously saved scanmap can be loaded for use Select one of the following as Scanmap source Use Threshold Preview settings set in Microscope Controller Panel Preview window are applied to create a scanmap Loaded scanmap This function is useful if the slid...

Page 70: ...ess however it reduces digitization speed Z stack Both for Extended focus and Z Stack scanning methods you can determine the desired number of focus levels with the Focus levels selection box The current focus value is the starting point If you set 5 for example one current two focus levels above and below FOVs are captured Therefore it is advised to choose an odd number for the focus levels Separ...

Page 71: ...onsuming Note Make sure to select the Change filters at each field of view option if using multi band filter for multi channel digitization Caution If the specimen area is barely visible it is possible that the software will analyze that area as an empty one Multiple shots Maximum exposure time A limit value can be set to determine that the exposure time cannot be longer than the time of focusing ...

Page 72: ...ied Extended focus Select the type of the extended focus algorithm used during scanning Legacy uses original extended focus algorithm it is recommended for wide field fluorescence scanning Maxima the final image is made up from all of the layers created areas pixel groups with the highest intensity are combined together AVG an average of the layers is used for the final image Max AVG the final ima...

Page 73: ...NG Lossless compressed image format JPG The quality can be set in the value box Greater values result in better quality but larger files The default setting is 80 Bit depth 8 bit Stitching Use Stitching function enables the seamless stitching of digital tiles Sharpening Select this option to improve the visual appearance of digital slides Save focus quality Saves the focus quality December 7 2018 ...

Page 74: ...nned Figure 45 Pre scan preview image 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 scan map December...

Page 75: ...within the selected area in single layer DAPI with an illumination time of 20ms that is displayed in the Profile Wizard window Scanning process takes a couple of minutes only and cannot be interrupted Pre scan high resolution creates a High Resolution fast FL preview image of every FOV within the selected area in single layer DAPI with an illumination time of 20ms that is displayed in the Profile ...

Page 76: ...oles inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filtering specks and other uninteresting objects out Set the maximum volume of specks manually in the setting window Threshold Auto threshold Select this option...

Page 77: ...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 Manual setting of Use marker with threshold If this option is selected only the area encircled with a marker pen will be scanned You can define the ...

Page 78: ...f the preview image Save scanmap Click this icon to save the currently selected areas to scanmap Position To position the specimen holder that holds the current slide 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 Mark area for scanning based on the ...

Page 79: ...lection is made based on the selected shape from the Preview Toolbar This area will not be scanned Figure 48 Not scanned selection Edit The size of selected area positive or negative can be modified at the borderlines or corners Figure 49 Edited negative and positive selection masks December 7 2018 Rev 1 3DHISTECH Ltd 79 144 ...

Page 80: ...election by defining a polygon shape Finish area selection by double clicking with the mouse at or near the starting point TMA tool TMA tool is used for selecting TMA spots on TMA slides You can set the selection settings on the following four tabs TMA Grid Setting This function is enabled only if a TMA grid has already been placed on the preview image Set grid parameters row and column numbers an...

Page 81: ...r the average diameter of the spots in the Core size field or select the appropriate value with the arrows Clear scanmap The entire scanmap area will be cleared and reset to default Use selection box restriction 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 and the crop function is selected a black frame displayed in th...

Page 82: ...n the basis of user settings for example Fill holes in scan area and not detected by the selected threshold value Detected sample areas that will be scanned These areas are digitized They are detected on the basis of the selected threshold value Detected 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...

Page 83: ...pear in red color and will be digitized Areas scanned in This color is only displayed during scanning Hide all layers Separate scanning Discrete sample areas will be scanned separately as individual slides If there are two samples on a slide two separate virtual slides will be created Show pre scans pseudo colorized Figure 53 Pseudo colorized pre scan image December 7 2018 Rev 1 3DHISTECH Ltd 83 1...

Page 84: ...s a coarse focus level from the three values determined this way as a basis for the fine focusing routine You can only define the start parameter here This will however speed up the focusing process If you deselect the Use fine focus checkbox the software immediately starts scanning on the basis of the interpolated values without pre fine focusing To define focus limits select Limits of the range ...

Page 85: ... in the EXC column define the excitation of the Lumencor illumination in TW define exposure time weight and in the DG the amount of digital gain is displayed It is also available for you to enable Extended Focus EF and or Z stack ZS functions in this field Exposure Settings You can set the Exposure time weight here displayed under TW in the Channel Settings frame Set Lumencor excitation intensity ...

Page 86: ...nt The pixel intensity at the coordinate pointing at with the cursor is displayed in the Image Intensity window Figure 57 Window of Image Intensity 5 2 2 4 Stage positioning After clicking you can perform microscope movements on the Live image with this control function The number at the center of the controller defines the step size by which the stage is moved Value can be entered by hand or with...

Page 87: ...1 Quick toolbar of preview window Figure 59 Settings of preview quick toolbar A Quick Toolbar pops up by right clicking any of the control menu items It allows a quick access to main functions and for FL these are the following Drag Draw Erase Retake preview Settings Toggle delation always on top Reset Zoom Window auto size Clear Scanmap December 7 2018 Rev 1 3DHISTECH Ltd 87 144 ...

Page 88: ...e displayed upon right clicking on the background of the main window outside the preview window It includes quick access buttons to main functions for MIDI II Figure 60 Quick toolset for microscope Autofocus Figure 61 Autofocus Objective type Figure 62 Objective type 20x 40x Filters Figure 63 Filters December 7 2018 Rev 1 3DHISTECH Ltd 88 144 ...

Page 89: ...Microscope mode Brightfield Fluorescence Figure 64 Microscope mode Live tools Fast mode Screenshot Magnifier Ruler Image processor plugins Use pseudo color Add scanmap Figure 65 Live tools Auto exposure Figure 66 Auto exposure December 7 2018 Rev 1 3DHISTECH Ltd 89 144 ...

Page 90: ...t the bottom left corner of the main window Figure 67 Progress of the profile modification history Once you are moving the mouse cursor over a unit all of the parameters will become visible in a pop up window Figure 68 Details of parameter modification For the easier perspicuity modifications can be observed in a pop up window by clicking the button in which both the original and the modified valu...

Page 91: ...Pannoramic MIDI II 2 0 5 User s Guide 5 2 4 Bottom menu bar of the main window Figure 69 Profile history tree December 7 2018 Rev 1 3DHISTECH Ltd 91 144 ...

Page 92: ...loaded tray can be planned but also profile assignment to slides of prepared virtual trays is available to be performed It is also possible to scan to different locations with each profile and virtual slides can be created and stored in different folder or server Planner module includes three appearance types for planning scans located under the Preferences Planner Layout Selector menu Slide view ...

Page 93: ...be initiated Stop scan Stop actual process Take all previews Preview images of all the slides on the tray are taken automatically Select the required preview type from the following from top to bottom Brightfield Pre scan Pre scan high resolution Pre scan high resolution Figure 70 Take all preview selector Load Save Plan menu Opens a drop down menu including the following Load plan The previously ...

Page 94: ... can be performed Add current profile to all racks Open profile for all racks Detach current profile from all racks Detach profiles from racks Clear planner Clear all slide result from every rack Figure 71 Profile management for all the magazines menu Jump to scanned Loads the planner view of the actual slide during scanning Settings Help December 7 2018 Rev 1 3DHISTECH Ltd 94 144 ...

Page 95: ...slides Clear all slide results 5 3 3 General functions at the slide menu Mark empty slide positions Define range in the Empty slide range boxes to set multiple slide positions as empty For single slides enter set slide position with the arrows in the Empty single slide box or right click on a slide and select Mark as empty Figure 72 General functions at the slide menu Click Reset empty definitions...

Page 96: ...s Planner layout selector to activate this view Depending on the actual view preference selected at slide positions can have a horizontal or vertical layout Slide preview and the list of the assigned profiles are displayed Figure 73 Vertical and horizontal Slide view with card By clicking or profiles can be added or removed for from the slide respectively The parameters of the assigned profile is ...

Page 97: ...rogress No of scanned FOVs Scan duration Slide actual status of the slide is presented here If the slide is under scanning the Scanning if scanning has been interrupted by some error the Failed text is visible NOTE If slide status is marked as Failed delete status before scanning by clicking If the virtual slide is created the scanning is finished the location path of the destination folder is dis...

Page 98: ...her be BF or FL if the scanner is capable to operate in these two scanning modes Figure 75 Table view mode In Table view the following information are displayed in the profile strip based on the loaded profile Profile name Illumination Priority Objective type Filters Progress Scan properties The location of the virtual slide with the selected profile can be defined Scan result Scan duration Scanne...

Page 99: ...collection view mode If you click the button each of the slide previews are displayed in the window Add profiles by clicking and detach profiles by clicking Functions are the same as with the other modes Figure 76 Card collection view mode December 7 2018 Rev 1 3DHISTECH Ltd 99 144 ...

Page 100: ...with the view type of the Profile Setting panel Slide preview is displayed in the Preview window in which the scanmap can be modified until beginning the scanning process Every aforementioned profile setting can be modified depending on the scan profile type being either Brightfield or Fluorescence Click to load the planner view of the actual slide during scanning Figure 77 Profile editor for Sche...

Page 101: ...whenever there is a running hardware operation or scanning procedure Progress content can be therefore different depending on the type of the running procedure The following information is included in the progress log list during scanning Filter Elapsed time Location Slide name Free space FOV number December 7 2018 Rev 1 3DHISTECH Ltd 101 144 ...

Page 102: ...y clicking and Services by clicking at the right side of the main menu bar 5 6 1 Settings Activate Settings by clicking at the right side of the main menu bar Preferences This panel contains user settings that have global effect on the GUI and some of its functions December 7 2018 Rev 1 3DHISTECH Ltd 102 144 ...

Page 103: ... Jelly light Flat style light Planner style editor Slides with card Table Card Collection Default scanner mode selector Microscope or Planner mode Default illumination mode selector Brightfield or Fluorescence mode Simplified Scan Progress for Brightfield scanning only Preview window start position Initial position Last position Center screen December 7 2018 Rev 1 3DHISTECH Ltd 103 144 ...

Page 104: ...be visible in CaseViewer Calculate exposure time for barcode grabbing Three images are recorded for barcode image creation Exposure times will be recalculated each time thus creating prefect light conditions for barcode reading so to make sure that barcode identification is successful Rotate barcode image by 180 degrees Unload slide after planner scan Scanning History Hardware log Scanner hardware...

Page 105: ...ation mode Scan type Scan Start Scan Finished URL Error Filtering for the following parameters is available Scanning date Profile name Illumination mode URL Slide name Slide index Rack index General naming settings Naming pattern The set string defines the slide naming pattern shown by the example below the text box Click Reset to set pattern to default The abbreviations and their meaning are list...

Page 106: ...ations Profile behavior settings Use profile history save With this function each profile modification is saved in Profile History from which the different stages can be reloaded Save interval Profile content is automatically saved at the specified time frames Enable setting of focus time Parameters Short Normal Long related to focus time will be enabled on the profile settings panel Normal is set...

Page 107: ...e 5 6 1 Settings Prescan settings Unlike scan settings in Microscope or Planner mode Prescan toolbar includes the same settings for pre scanning but these depend on the hardware filter settings December 7 2018 Rev 1 3DHISTECH Ltd 107 144 ...

Page 108: ... software can be opened after scanning is finished You can define external application call settings for the following cases Slide Scanning Finished Scanning Error Occurred For Slide scanning has finished and Scanning error has occurred you can define the external software by entering the file path in the Application box or by browsing for it by clicking December 7 2018 Rev 1 3DHISTECH Ltd 108 144...

Page 109: ...all section of the window complex messaging functions can be defined Here you can setup parameters of the mail server add or remove users and also 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 sending an e mail to the address defined in the E mail T...

Page 110: ...e top of the section Click Delete user if you want to remove a user from the list after selection Report sender settings Add new recipients to the list by clicking or remove selected from the list by clicking To send an example mail to the selected recipient click Open E mail settings window to modify recipient data by clicking Emergency slide functions This panel contains control and maintenance ...

Page 111: ...6 2 Services 5 6 2 Services Activate Service menu by clicking at the right side of the main menu bar Service password Enter password first to enable service settings for modification Camera settings December 7 2018 Rev 1 3DHISTECH Ltd 111 144 ...

Page 112: ...efined by calibration standard Gamma value 2 2 is applied sRGB standard Microscope Like Color scheme is defined by calibration standard Gamma value White Point D50 Legacy a Color scheme calibrated for the previous software version is applied Custom parameters are freely customizable as follows Color Scheme Calibrated Scheme is defined by the color calibration slide Legacy a Color scheme calibrated...

Page 113: ... Stitching overlap Set the amount how much the FOVs should extend over Measure camera rotation Camera rotation angle is measured Alpha blending The two images are blended Lower image position Moves the upper image sideways in distinctive steps Reset all camera rotation Click this button to set camera rotation values to default Save settings by clicking Filter settings December 7 2018 Rev 1 3DHISTE...

Page 114: ...lter type Filter channel and Filter name Check Available for scanning Set Lumencor LED light source set Excitation and Emission wavelength bandwidth values for the selected filter Set Pseudo color Select channels used for grayscale conversion Select Enable Lumencor hardware trigger Click Save to save settings Z difference This function is available only for fluorescence settings it enables you to ...

Page 115: ... value in the box To create the compensation image s click Take Comp image 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 Export image Save compensation image Barcode settings By predefining barcode type foreground color black or white the color of the barcode and other settings you enable the Rea...

Page 116: ...ote 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 message Barcode detection unsuccessful There might be no barcode present December 7 2018 Rev 1 3DHISTECH Ltd 116 144 ...

Page 117: ...ond barcode priority The software is capable to read two barcodes at the same time If activated the second barcode will be the barcode used for slide identification Note When having two barcodes on the slide barcode layout must be consequential Resize image Label imaged is downsized to 1 4 before barcode reading Apply erode algorithm The Erode algorithm is run before barcode reading It is a useful...

Page 118: ...tfield illumination Barcode area light Backlight illumination intensity Objective guide Step size X Y values or navigation arrows Goto Goto Preview Origin RGB LED Set illumination intensity per channel Sync with microscope Calculate white balance Save RGB intensity December 7 2018 Rev 1 3DHISTECH Ltd 118 144 ...

Page 119: ...age during a real time counseling even if being in laboratories far away from each other This means multiple users can connect to the device at the same time The user of the scanner will be the host with direct access to the scanner Note Both the client s and the host s scanner software version must be identical Once client users have connected they will be able to reach the following functions of...

Page 120: ...tation as a client 1 Start the Lite version of the scanner software 2 Type in your nickname used during the session 3 Enter Host address and Port number 4 Click Connect On Client side the following functions are unavailable inactive Selection box Scan properties Separate scanning Note During a fluorescence Live consultation the shutter of light path will be closed automatically during the host tim...

Page 121: ...y in Fluorescent mode Focus frequency in Brightfield mode Compression procedure Use of a fixed compensation image in Brightfield mode ON OFF Use of Save focus 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 values Use of scan everything within marked...

Page 122: ...ensity reducing Intensity equalization Sharpening ON OFF Use of skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Custom extended focus Other settings Limitation of focus range ON OFF Focus quality ON OFF Enable disable Multilayer options Use of extended focus or Z stack step size and focus level Output resolution December 7 2018 Rev 1 3DHISTECH Ltd 122 144 ...

Page 123: ...after use Slides that are not used any longer do not classify as domestic waste and must be treated as hazardous materials and disposed in compliance with the currently valid legal requirements 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 There is crush hazard during operation...

Page 124: ...oisten the cloth with water To clean greasy surfaces it is recommended to apply soapy water on a piece of lint free cotton cloth and gently rub the surface 7 1 2 Cleaning the trays NEVER clean the trays with Xylene because it might harm the plastic We recommend to apply Isopropanol on a piece of lint free cotton cloth and gently rub the surface instead In case the tray is damaged use either order ...

Page 125: ...ble 3 Remove protective covers Follow the steps in section 7 3 1 Opening the protective covers 4 Remove slide manually see section 7 3 2 Removing a slide 5 Reattach protective covers 6 Reconnect 24V power supply and control computer to line power supply 7 Switch on the 24 V power supply 8 Switch on the control computer 1 Launch control software Tray jammed 1 Exit control software 2 Switch off cont...

Page 126: ...ify the camera driver settings as the default factory settings give the most accurate images Virtual slides show poor stitching in Pannoramic Viewer Scan camera is not properly adjusted for example due to loose fixture Contact 3DHISTECH Service for support Slide is often positioned incorrectly Guiding fault in transport system Contact 3DHISTECH Service for support Digitization process is extremely...

Page 127: ...ges show a shading effect Algorithm failed to find empty image fields Capture a reference image with a blank slide 7 2 1 Fluorescent Applications optional The switching of the Lumencor SPECTRA 6 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 Lumencor SOLA SM II is switched off Swi...

Page 128: ...ers of the Pannoramic MIDI II need to be opened in order to eliminate the problem Before removing the cover exit the control software switch off the 24 V power supply and disconnect the power cables exception filter change Note To improve access to special points you can remove the covers completely Figure 79 Removal of covers The protective cover is composed of two halves locked to each other Loc...

Page 129: ...learly heard Caution Make sure that no cables are squeezed as you replace the cover s This refers in particular to the cable s of the scan camera 7 3 2 Removing a slide If a slide got jammed or has suffered breakage during the process of digitization stop the process and if possible move the slide holder to a position where the slide can be easily removed by clicking the Emerg position button Warn...

Page 130: ...ing the clamp pushed to the left remove the slide 2 carefully Caution 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 and contagion Broken slide can be removed only by a well trained person 4 Push protective covers together again see section 7 3 1 Opening the protective covers 5 Launch cont...

Page 131: ...cover halves apart or remove the right part completely see section 7 3 1 Opening the protective covers but do not switch the main unit off 3 Select the desired filter and click Set filter wheel to insert position on the Filter settings panel see section 5 6 1 and the filter will be positioned in such a way that you will have free access to the filter without having to turn the filter wheel manuall...

Page 132: ...otective covers 10 If a Lumencor SOLA SM II illumination unit is used turn it on again consider the cooling time possibly required 7 3 4 Transporting Pannoramic MIDI II The following procedure shows how to transport Pannoramic MIDI II in house For transporting the whole system to other location see Appendix Note The base unit does not have carrying handles for transporting Two people can carry the...

Page 133: ...oting and Maintenance Caution Do not lift or transport Pannoramic MIDI II by holding its protective covers Caution Readjust camera angle if necessary after transporting and reinstalling the Pannoramic MIDI II December 7 2018 Rev 1 3DHISTECH Ltd 133 144 ...

Page 134: ...unit with fluorescent option approx 26 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 25 75 Operation Permissible ambient temperature 10 C to 35 C Permissible relative air humidity 25 75 Altitude at installation s...

Page 135: ...26 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 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 wi...

Page 136: ...ional SPECTRA 6 individually addressable solid state light sources Average service life 20 000 hours Preview camera Preview camera VRmagic VRmC 8 PRO Sensor CMOS rolling shutter Sensor size Resolution 2056x1544 Pixel size 3 2 um x 3 2 um Max frame rate 13 Hz Bit depth 8 10 bit Objectives Plan Apochromat 20 NA 0 8 or 40 Corr NA 0 95 Scan cameras Point Grey Grasshopper 3 GS3 U3 51S5M C Global Shutte...

Page 137: ...mount adapter 0 33µm Pixel resolution with 20x objective and 1 6x C mount adapter 0 20µm Pixel resolution with 40x objective and 1x C mount adapter 0 16µm Pixel resolution with 40x objective and 1 6x C mount adapter 0 10µm Cooling Peltier with forced air fan Connection type Dual Camera Link Full 10 taps 85MHz Control computer minimum system requirements Operating System Microsoft Windows 7 Profess...

Page 138: ... the scanner with the main switch located on the backside of the device Disconnect all the cables of the scanner 4 Remove the main camera and camera adapter 5 Turn off and disconnect all the cables of the workstation and display Main parts and their accessories 1 BOX 1 Big carton box a fixing foams for the angles of the scanner box 2 BOX 2 MIDI II scanner large carton box a Scanner unit b objectiv...

Page 139: ...mouse has a separated small carton box f 3DH mouse pad 4 BOX 4 Accessories 3 pcs a main camera b main camera trigger cable c power supply connector d power supply cable e dongles software and driver CDs in 3DH SW box f trays g slide checker 5 BOX 5 Cables a 3 m USB cable b USB cable of the scanner 6 BOX 6 FL lamp if any a FL lamp b lamp power supply c power supply cable d adapter e light guide Dec...

Page 140: ...ackaging Packaging The whole system is packed in a big carton box This is divided into two areas with a vertical carton slab Space 1 for accessories PC cables etc Space 2 for BOX 2 scanner Figure 2 December 7 2018 Rev 1 3DHISTECH Ltd 140 144 ...

Page 141: ... 5 User s Guide Packaging 1 BOX 2 scanner box 2 Fixing foams for underneath BOX 2 3 Fixing foams for above BOX 2 4 Bottom part of BOX 1 5 Top of BOX 1 6 BOX 3 7 BOX 4 5 6 Figure 3 December 7 2018 Rev 1 3DHISTECH Ltd 141 144 ...

Page 142: ...The scanner should be lifted up by holding the scanner at its motherboard between its feet and taken inside the BOX 2 s lower part onto the foams inside it The shape of the rubber foam defines the orientation how they should put on After the scanner and foams are taken in you can place the upper part of the box of the scanner Now place the BOX 2 into BOX 1 and place the fixing foams around Figure ...

Page 143: ...s symbol must be protected from excessive humidity and must accordingly be stored under cover If particularly large or bulky packages cannot be stored in warehouses or sheds they must be carefully covered with tarpaulins Recycling This indicates that an object is capable of being recycled CE The symbol shows that the device complies with the essential requirements of the relevant European health s...

Page 144: ...32 F Fluorescent 13 14 18 19 20 24 28 123 124 129 133 136 Focus 14 20 84 116 123 124 128 129 L Lumencor 13 19 24 25 125 129 Lumencor SPECTRA 6 20 M Marker 123 P Pannoramic 7 25 Pannoramic MIDI II 7 9 10 11 13 14 15 17 19 20 22 24 31 33 127 130 134 135 Pannoramic Viewer 21 128 Pco edge 4 2 14 139 Preview 24 29 84 S Scan 84 115 117 123 Scanner 7 117 December 7 2018 Rev 1 3DHISTECH Ltd 144 144 ...

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