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3D Histech Pannoramic MIDI 1.16 User Manual Download Page 79

Pannoramic MIDI 1.16 User’s Guide

4 Software Description

4.5.3  Preview tab

The Preview tab offers options for threshold setting and selection of the area to be scanned. 

Figure 48 – Preview tab

Use threshold

•

Scan specimen with auto threshold – 

This automatically detects the specimen in the 

preview image.

•

Scan specimen with user set threshold – 

This sets the sensitivity of the specimen detection. 

To set the desired threshold value manually, change the setting in the 

Specimen threshold 

level 

selection box in the range of 0-255. The default value is 35.

Setting smaller values result in a more sensitive scanning, meaning that more 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 
specimen areas will not be digitized.

January 16, 2013 - Rev 1

3DHISTECH Ltd.

79(127)

Summary of Contents for Pannoramic MIDI 1.16

Page 1: ...PM1 16 UG Rev1 Pannoramic MIDI 1 16 User s Guide January 16 2013 Rev 1 ...

Page 2: ...Software 18 2 Installation 20 2 1 Control computer ports 20 2 2 Connectors and cables 21 3 Operating Slides and Trays 23 3 1 Preparing Slides and Trays 23 3 2 Affixing Barcode Stickers to Slides 24 3 3 Inserting and Removing Slides 26 4 Software Description 28 4 1 Starting Exiting Pannoramic MIDI Software Application 28 4 1 1 Starting the software 28 4 1 2 Exiting the software 29 4 2 Options 29 4 ...

Page 3: ...tomatic Mode 87 4 6 1 Routine work tab 87 4 6 2 Barcodes tab 92 4 6 3 Preview tab 96 4 6 4 Focus tab 97 4 6 5 Service tab 97 4 7 Scan To Server 98 4 8 Using Profiles 105 5 Troubleshooting and Maintenance 107 5 1 Safety Information 107 5 1 1 Cleaning the device 108 5 1 2 Cleaning the trays 108 5 1 3 Preventive maintenance 108 5 2 Troubleshooting 109 5 2 1 Fluorescent Applications optional 111 5 3 M...

Page 4: ...re the sole properties of the 3DHISTECH Ltd 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including the results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitalized slide s that stems from or is asso...

Page 5: ...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 6: ... Particular requirements for in vitro diagnostic IVD medical equipment EN 55011 1998 Group 1 Class A Limits and methods of measurement of radio disturbance characteristics of industrial scientific and medical ISM radio frequency equipment This product has been tested to the requirements of CAN CSA C22 2 No 61010 1 second edition including Amendment 1 or a later version of the same standard incorpo...

Page 7: ...ction 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 to not work properly if this instruction is not followed and alerts to a potential danger situation Note Cal...

Page 8: ...vice personnel All claims for warranty and warranty services will be null and void in any such case Warning Insert the power cord plugs only into a grounding outlet The protective action must not be rendered ineffective by extension cables without protective conductor The Pannoramic MIDI has a built in protection which must not be rendered ineffective by extension cables without protective earth g...

Page 9: ...tion Avoid touching the lamp bulb Disconnect power and allow the bulb to cool down by waiting for about 15 minutes before replacing it Crush hazard There is crush hazard in the movement area of the slide insert during operation Please note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the insert Warning Clogged or covered...

Page 10: ...cepted in cases 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 warran...

Page 11: ...ical Aperture Virtual Slide Slide A digital image of a thin glass plate on which specimens are mounted for microscopic study a dynamic interactive image that you can manage save magnify zoom name evaluate annotate mark comment send to a colleague electronically for co operation or advice and so on January 16 2013 Rev 1 3DHISTECH Ltd 11 127 ...

Page 12: ... 1 1 2 Features and Benefits The Pannoramic MIDI offers world class brightfield and fluorescent whole slide scanning on up to 9 channels An outstanding 0 12 µm pixel resolution is achieved with the 40 0 95 NA equivalent to 62 magnification Carl Zeiss Plan Apochromat objective Key features of the Pannoramic MIDI scanner Up to 9 freely selectable color filters for fluorescence High end fluorescent i...

Page 13: ...slides will be regularly over 10 slides per day It has the best price performance ratio with a reliable loading scanning mechanism 1 1 3 Warning and Information Labels The following figure contains the labels used on the Pannoramic MIDI main unit the external mains power supply unit and the HXP 120 illuminator Figure 1 Warning and information labels January 16 2013 Rev 1 3DHISTECH Ltd 13 127 ...

Page 14: ...arts of base unit 1 Protective covers 2 Slide tray 3 CIS VCC F52U25CL scan camera 4 HXP 120 fiber coupled illuminator option 5 HXP 120 illumination adapter option 6 Fiber optic cable 1 2 System Overview The standard scope of delivery of the product includes the following hardware and software components January 16 2013 Rev 1 3DHISTECH Ltd 14 127 ...

Page 15: ...ing figure shows the main parts of the Pannoramic MIDI system Figure 3 Pannoramic MIDI system overview 1 HXP 120 fiber coupled illuminator option 2 24 V power supply 3 Pannoramic MIDI base unit 4 Monitor 5 Mouse 6 Control computer 7 Keyboard 8 Slide tray January 16 2013 Rev 1 3DHISTECH Ltd 15 127 ...

Page 16: ...sitive fluorescent applications CIS VCC F52U25CL 3 CCD camera for high quality brightfield applications allowing fast scanning pco edge Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast scanning and an outstanding low read out noise Cooled with Peltier element Stingray F146C IRF Medical camera 1 CCD camera for normal brightfield application and entry level ...

Page 17: ...IDI Basic Fluorescence Option base unit completely equipped with Stingray or CIS VCC F52U25CL camera for Brightfield scanning with AxioCam camera and HXP 120 illuminator trigger cable and filters for fluorescence scanning Pannoramic MIDI Advanced Fluorescence Option base unit completely equipped with CIS VCC F52U25CL camera for Brightfield scanning and with pco edge camera and Lumencor fluorescenc...

Page 18: ...cent 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 Scan To Server January 16 2013 Rev 1 3DHISTECH Ltd 18 127 ...

Page 19: ...c Viewer software fully functional Optional CaseCenter Pannoramic Viewer TMA module 3D Reconstruction module HistoQuant NuclearQuant MembraneQuant CytoFISHQuant and DensitoQuant modules ImmunoScreener module E School Encoder January 16 2013 Rev 1 3DHISTECH Ltd 19 127 ...

Page 20: ...allation carried out by an unauthorized person Only qualified service assistants are allowed to install the hardware and software The product is ready for use after installation 2 1 Control computer ports The following figure shows the location of the connectors in order to enable easier transportation of the product for a short distance by disconnecting cables and detaching hardware components fr...

Page 21: ...AxioCam MRm Rev3 cameras 2 2 Connectors and cables Caution It is not recommended to use USB and FireWire cables longer than 2 5 meters Control USB between scanner and control computer Preview camera USB cable between scanner and control computer Stingray FireWire 1394 B cable between Stingray camera and control computer AxioCam FireWire 1394 A cable between AxioCam camera and control computer CIS ...

Page 22: ...V and CIS camera Optical cable between HXP 120 fluorescent illuminator or Lumencor Spectra 7 LE unit and scanner Trigger cable between AxioCam and HXP 120 fluorescent illuminator Trigger cable between pco edge and Lumencor fluorescent illuminator USB to RS232 serial communication cable between Lumencor fluorescent illuminator and control computer Warning Only connect external devices that are safe...

Page 23: ...ed or cut Note FISH fluorescent signals become more easily detectable for the scanner therefore resulting in a brighter and better image by treating the slide with a formula that prevents rapid photobleaching of fluorescent reagents e g VECTASHIELD Fluorescent Mounting Medium by Vector Laboratories and ProLong Gold and SlowFade Gold antifade reagents by Invitrogen during the FISH protocol For furt...

Page 24: ...ing medium If not so the coverslip can be shifted that makes slide loading less reliable Not completely dried embedding might also influence the operation of objectives and other device parts Warning Do not change correction collar settings on 40 NA objective if you need it to be set contact customer service 3 2 Affixing Barcode Stickers to Slides This section describes how to affix barcode sticke...

Page 25: ...men side Note Ensure that a marginal space of 1 2 mm remains on all sides between the sticker and the label area outer limits It is vital for barcode identification Caution Do not let barcode sticker protrude from slide edges or stick on the coverslip surface 3 The thickness of the barcode sticker on the slide must not exceed 0 4 mm Do not stick more than four barcode stickers over each other and ...

Page 26: ...area of the slide is sharp and its removal can lead to injury and contagion Broken slide can be removed only by a well trained person Only original 3DHISTECH trays are allowed for use with Pannoramic MIDI Figure 6 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 Note The coverslip and the label ...

Page 27: ...fely and properly if trays are clean 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 2 After digitizing slides the tray is moved to the output position where it can be removed Caution Do not place objects near the device or in the movement area of the slide tray Warning Do not reach into the movement ...

Page 28: ...eview camera and the scan camera are initialized After successful initialization the Mode selection window is displayed Figure 8 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 specimen staining and where ideal parameters need to be...

Page 29: ...ow the Mode selection window turns active again To exit the software click X in the title bar of the Mode selection window 4 2 Options The Options menu can be activated from the main menu of the Mode selection window Figure 9 Options menu 4 2 1 Barcode Settings Figure 10 Barcode settings January 16 2013 Rev 1 3DHISTECH Ltd 29 127 ...

Page 30: ...the slide that you want to load To load a slide from the tray to the specimen holder click A preview image is automatically generated To unload the slide click To remove the tray click It will then be moved to the position where you can remove it manually 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 wheth...

Page 31: ...types Data Matrix PDF417 MicroPDF417 Maxicode QR code 1D barcodes with check digit CDV You can select the following 1D barcodes with check digit CDV Code 39 Interleaved 2 of 5 The check digit is always the last digit of the barcode It is an additional checking number If you select Exclude check digit then the check digit number will also be analyzed as a barcode number January 16 2013 Rev 1 3DHIST...

Page 32: ...nk barcode sticker by clicking Prepare a slide with a label area covered fully by a white sticker The compensation image improves the effectiveness of barcode reading 4 2 2 Image Compensation You can create a new compensation image when there are compensation errors deriving from the slide illumination staining or embedding medium irregularities from an empty slide by setting these options By movi...

Page 33: ...ightfield Compensation Figure 11 Brightfield Compensation Camera Selection This field displays the active camera Currently there is only one active camera for Brightfield mode and one active camera for Fluorescent mode January 16 2013 Rev 1 3DHISTECH Ltd 33 127 ...

Page 34: ...tings 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 click Click the Stop button to interrupt the process The Progress bar at the bott...

Page 35: ...ware Description 4 2 3 Microscope Settings By moving the mouse cursor over the buttons the software displays information about the setting you are interested in Base Settings Figure 13 Base settings January 16 2013 Rev 1 3DHISTECH Ltd 35 127 ...

Page 36: ...ilable for you to define which filters occupy which turret positions Save settings by clicking Note If Lumencor is configured as illumination unit the corresponding Enable Lumencor hardware trigger option is displayed on the form The function Enable HXP 120 fluorescent light source shutter is available only for AxioCam MRm Rev 3 The AxioCam and the HXP 120 must be connected by a trigger cable to e...

Page 37: ...Pannoramic MIDI 1 16 User s Guide 4 Software Description Figure 14 Camera rotation January 16 2013 Rev 1 3DHISTECH Ltd 37 127 ...

Page 38: ...ifference 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 15 Z Difference tab January 16 2013 Rev 1 3DHISTECH Ltd 38 127 ...

Page 39: ...ecimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective cover Slide Removed Manually Click this button to notify the software that you have removed the slide manually 4 2 4 External Application Call Settings Figure 17 External Application Call Settings January 16 2013 Rev 1 3DHISTECH Ltd 39 127 ...

Page 40: ...AME transfers the slide name For Error Occurred Call ERRORTEXT transfers the error message Run defines the window mode that the external application will start in The following window modes can be set Normal window Minimized Maximized You can test whether the Error Occurred Call settings work by clicking By moving the mouse cursor over the buttons the software displays information about the settin...

Page 41: ...ghtfield Automatic Mode Figure 18 Main window of control software 1 Tab panel with scanner functions and settings 2 Scan camera live image display area 3 Preview image recorded by the preview camera 4 Preview image editor toolbar 5 Information area about the digitization progress January 16 2013 Rev 1 3DHISTECH Ltd 41 127 ...

Page 42: ...hcoming section To insert and remove slides To move a slide to the loading position click the number of the slide that you want to load To load a slide from the tray to the specimen holder click A preview image is automatically generated To unload the slide click To remove the tray click It will then be moved to the position where you can remove it manually January 16 2013 Rev 1 3DHISTECH Ltd 42 1...

Page 43: ...utton on this tab that you can start scanning with but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from the selection menu click Load To delete the current profile click Delete T...

Page 44: ... 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 January 16 2013 Rev 1 3DHISTECH...

Page 45: ...eference images for all slides Use this function when the slide is completely covered by the specimen for example blood smear thereby making compensation image capture impossible For such slides use an empty slide with coverslip to grab a compensation image for more information see section 4 2 2 Image Compensation If you select this the software will not create new compensation images for each sli...

Page 46: ...gure 21 Preview tab Use threshold Scan specimen with auto threshold This automatically detects the specimen in the preview image Important Make sure that the detection result is acceptable for you Otherwise set the threshold value manually or append missing areas with the help of Scanned function located at the preview toolbar January 16 2013 Rev 1 3DHISTECH Ltd 46 127 ...

Page 47: ...h the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area If this option is selected only the area encircled with a marker pen will be scanned You can define the threshold level by changing the threshold value in the Marker threshold level selection box in the range of 0 255 This sets the sensitivity of the specimen detection inside the...

Page 48: ...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 49: ...nly 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 24 Preview image Colors used in preview image The following fo...

Page 50: ... areas that will not be scanned These areas are not digitized on the basis of their position for example they are outside the selection box They are detected by the selected threshold value Marker If Scan marker specified area is selected in the Preview tab the preview camera detects the marker pen The inside areas appear in red color and will be digitized Areas scanned in This color is only displ...

Page 51: ...and then click on the area of interest on the preview image This will define the Live image that you can access from the Focus tab To display the original image created by the preview camera click To shrink or enlarge the preview image set the zoom level at the left Size selection box 25 400 To fit the preview image to the preview area click Fit Choose from the Scanned or the Not scanned option fr...

Page 52: ...s on TMA slides You can set the selection settings on the following four tabs Select tab Figure 28 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 January 16 2013 Rev 1 3DHISTECH Ltd 52 127 ...

Page 53: ...elect 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 The Grid tab displays the previously set grid setti...

Page 54: ... 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 31 TMA tool Move tab with preview January 16 2013 Rev 1 3DHISTECH Ltd 54 127 ...

Page 55: ...ser s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degree checkbox Figure 32 Label area 4 3 5 Focus tab Figure 33 Focus tab January 16 2013 Rev 1 3DHISTECH Ltd 55 127 ...

Page 56: ... set to 32 of the current focus value Use the two arrow buttons to focus manually This is useful when you are interested in an area that remained blurry with Auto Focus for example the specimen is thicker in that area This does not influence the way slides are digitized in Automatic mode The manual focus is mainly for setup purposes not for using the product as a traditional microscope Define the ...

Page 57: ...ove and below FOVs are captured Therefore it is advised to choose an odd number for the focus levels 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 3 6 Service tab Figure 35 Service tab This panel contains control and maintenance functions Emergency Manual Slide Removal Position The specime...

Page 58: ...ld This slows down digitization process and should be activated only with purpose 4 3 7 Display field and toolbar for live images The display field for live images displays images of the scan camera The live image is displayed if no current digitization process is running or Show images during scanning option is enabled Figure 36 Display field and toolbar for live images January 16 2013 Rev 1 3DHI...

Page 59: ... current image as BMP or JPEG file Fast live mode live images are displayed with a frequency of at least 10 images per second If an exposure time is set to more than 100 ms the pixel values are multiplied accordingly for example if an exposure time of 200 ms is set the pixel values are multiplied by 2 and the exposure time is reset to 100 ms Therefore the resulting images will have a higher noise ...

Page 60: ... space in the last line Available disk space of the information area of Current Slide Scan Progress You can interrupt a running digitization process by clicking This button is only enabled if a digitization process is in progress 4 4 Using Brightfield Automatic Mode Compared to Manual mode it has less options in some dialogs but it has an additional Barcodes tab 4 4 1 Routine work tab Figure 37 Ro...

Page 61: ...ay before the process You also find the button on this tab that you can start scanning with but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at 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 You...

Page 62: ...Pannoramic MIDI 1 16 User s Guide 4 Software Description 4 4 2 Barcodes tab Figure 38 Barcodes tab January 16 2013 Rev 1 3DHISTECH Ltd 62 127 ...

Page 63: ...irectory 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 You can ...

Page 64: ...rcode 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...

Page 65: ...iles for slides Only those positions are active that have slides in it Current Profile is the profile loaded in Routine Work Scan Profiles You can save the entered names and assigned profiles by clicking You can define a name before saving The information will be saved in a CSV format 1 slide position slide name profile name You can export this information into Excel where you can change the data ...

Page 66: ... in Automatic mode are the same as described in Manual mode In Automatic mode you cannot change the threshold values It will use the threshold values that were set previously in the Manual mode For more information see section 4 3 3 Preview tab Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings January 16 2013 Rev 1 3DHISTECH Ltd 66 1...

Page 67: ...pot on the coverslip Multilayer mode Select Single layer option if you want to scan a single layer of the slide By choosing the Extended focus option the software selects the sharpest image from each focus level for each image field and combines them into one single image Therefore those parts that were blurry in auto manual focus will also be sharp This method guarantees the maximum depth of shar...

Page 68: ...een focus levels One step is around 0 2 µm The default settings are Number of focus levels 7 Focus step size 5 4 4 5 Service tab Figure 42 Service tab This tab contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective cove...

Page 69: ...is added to each step 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 43 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 ...

Page 70: ...r s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work tab Figure 44 Routine work tab panel The Routine work panel provides basic digitization functions January 16 2013 Rev 1 3DHISTECH Ltd 70 127 ...

Page 71: ... only applicable if you do not use profiles If you use profiles the profile settings are used Scanning Mode Full automatic focus and exposure time are automatically determined by the software User controlled you can define focus and exposure time manually The selection of scanning mode influences the number of options on the Focus tab To administer profiles use the Scan Profiles field The current ...

Page 72: ...nnel This is done on one channel You can choose whether you want to do stitching on the focus channel or on another channel It is recommended to choose another channel if the focus channel was determined on the basis of exposition time and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of the specimen The default selecti...

Page 73: ... Exposure Settings You can set the Exposure time weight here displayed under TW in the Channel Settings frame In full automatic mode the system automatically calculates the exposition time to the given channel You can increase or decrease this amount here in a range of 50 200 Multilayer Settings Enable Multilayer function and the concerning settings can be activated in this field accordingly you c...

Page 74: ...ter 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 46 Multilayer Settings window Set the focus level value under the Number of focus levels box and the Focus step size one step 0 2 µm Once you have set ...

Page 75: ...1 16 User s Guide 4 Software Description 4 5 2 Scan Options Figure 47 Scan options tab These settings determine the resulting quality and storage location of the virtual slide January 16 2013 Rev 1 3DHISTECH Ltd 75 127 ...

Page 76: ...m MRm Rev 3 and between 8 and 16 when using pco edge camera Scan Settings Focus frequency This value determines how many field of views will pass before the sample is refocused This value should be selected depending on the unevenness and size of the specimen Maximum exposure time A limit value can be set to determine that the exposure time cannot be longer than the time of focusing and calculatio...

Page 77: ...ight intensity statistical data not to modify the average intensity of the slide Quantitative measurements can be made on the slide Sharpening image contrast is increased the image may become noisier Note Do not use this option if you want to take quantitative measurements since it may minimally affect the results Exposure Time Calculate exposure time for each area Calculates exposure time that is...

Page 78: ...er for multi channel digitization Digital Slide destination This field determines where to digitize the virtual slides To be able to choose the Scan to CaseCenter function you have to install the ScanToServer application For information on how to install and use the ScanToServer application see section 4 7 Scan To Server If you enable the Directory function the virtual slides will be digitized in ...

Page 79: ...s the sensitivity of the specimen detection To set the desired threshold value manually change the setting in the Specimen threshold level selection box in the range of 0 255 The default value is 35 Setting smaller values result in a more sensitive scanning meaning that more areas will be digitized however this may also include specks or other imperfections of the slide Greater values result in a ...

Page 80: ...ld level 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 Specimen threshold level selection box in the range of 0 255 The default value is 35 To scan everything within the marked area check the Scan everything within marked area selection box Note This step is recomm...

Page 81: ...e scanned area The edge is extended discretely by 100 µm each time Use saved scan area This function is useful if the slides contain areas of interest that cannot be detected by the preview camera This function along with saving profiles helps to scan all slides with the most adequate settings To save a new mask click Save It will display a drop down menu Select whether to save preview mask or TMA...

Page 82: ...Pannoramic MIDI 1 16 User s Guide 4 Software Description 4 5 4 Hardware tab Figure 50 Hardware tab selected mode User controlled January 16 2013 Rev 1 3DHISTECH Ltd 82 127 ...

Page 83: ...display the live image with from the Filters selection box The selected filter will be rotated into position only after displaying the Live image by clicking You can display the Filter properties window by clicking for more information see section 4 5 1 Routine work tab Note After 10 seconds an empty position is rotated into position instead of the filter However the last snapshot is still display...

Page 84: ...his makes the focusing sequence faster By using Set Current 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 Use the two arrow buttons to focus manually This is useful when you are interested in an area that remained blurry with Auto Focus for example the specimen is thicker in that area This does not influence the way ...

Page 85: ...te Goto button To delete the stored values click Clear Values The software calculates 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...

Page 86: ...d 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 option you will be able to see the currently scanned image field during scanning in the live image display field This slows down digitization process and should be ac...

Page 87: ...ide 4 Software Description 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work tab Figure 52 Routine work tab panel The Routine work tab panel provides some basic digitization functions January 16 2013 Rev 1 3DHISTECH Ltd 87 127 ...

Page 88: ...but it is recommended to go through all the settings before clicking it Scan Range You can select a range of slides to be scanned here by entering the first and last slides in the selection boxes To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from t...

Page 89: ...and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of the specimen The default selection is Focus Channel Channel Settings Select what types of filters you want to use during scanning You can select the filter types and the number of channels to be used Those filters are displayed automatically that you have previously d...

Page 90: ...n channel You can increase decrease this amount here in a range of 50 200 Multilayer Settings Enable Multilayer function and the concerning settings can be activated in this field accordingly you can set the Extended focus and Z stack values for each channel separately Digital Gain Note This function is camera dependent works only with AxioCam MRm Rev 3 camera Index value ranges from 0 to 4 and pc...

Page 91: ...nel Figure 54 Filter properties window Set the focus level value under the Number of focus levels box and the Focus step size one step 0 2 μm Once you have set the correct values tick the multilayer checkbox EF or ZS column of the channel for which you want to apply these settings or activate Enable Multilayer function in the Filter Properties window For more information about Extended Focus see s...

Page 92: ...16 User s Guide 4 Software Description 4 6 2 Barcodes tab Figure 55 Barcodes tab On this tab you can set identification features to the various slides and for assigning profiles January 16 2013 Rev 1 3DHISTECH Ltd 92 127 ...

Page 93: ...ed 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 ba...

Page 94: ... Folder is the folder for saving Vir is the name of the virtual slide 123_prof_n is the profile name The barcode control will then look like the following Folder mask 1 1 6 Folder mask 2 empty Folder mask 3 empty Folder mask 4 empty Folder mask 5 empty Name mask 8 10 Profile mask 12 21 Note The Profile mask row is inactive if the option Apply one profile to all slides is active January 16 2013 Rev...

Page 95: ... column Profiles if you intend to use different profiles for slides Only those positions are active that have slides in it Current Profile is the profile loaded in Routine Work Scan Profiles Load Names and Profiles from File You can import previously saved names and assigned profiles by clicking Save Names and Profiles to File By clicking the button you can save the entered names and assigned prof...

Page 96: ...escribed 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 Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings Janu...

Page 97: ...ng 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 option you w...

Page 98: ... the ScanToServer which is an embedded application that can be run under the Pannoramic MIDI scanner software Follow these steps to install the ScanToServer application 1 Run the ScanToServer_1_16_RTM exe to launch the installation wizard 2 Accept the License Agreement then click Install to continue January 16 2013 Rev 1 3DHISTECH Ltd 98 127 ...

Page 99: ...re Description 3 After checking the prerequisites click Install to start the installation of ScanToServer application 4 Click Finish to finalize the installation process of the ScanToServer application January 16 2013 Rev 1 3DHISTECH Ltd 99 127 ...

Page 100: ...utton 2 Select the Scan to CaseCenter option in the Scan Option window then click Connect Figure 60 Scan to CaseCenter option 3 Type in or select the server address from the Connect to drop down list then give the user name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 61 Server Log in window January 16 2013 Rev 1 3DHISTECH Ltd 100...

Page 101: ...igure 62 Connected to server Slide settings in the CaseCenter window 1 In the Routine work tab panel click the button 2 The CaseCenter window opens Slide data is displayed in a form for the slides loaded in the tray If in Manual Mode only the data of the actually loaded slide can be set see Figure 63 and when in Automatic Mode the form contains 12 rows for all the slots on the tray Figure 64 Figur...

Page 102: ...ode if no name is defined on the list option the slide barcode will be read and set in the Barcode field Use masks for automatic fills Activate the Use mask option and the mask fields turn fillable To save masks click the Save Mask button To modify masks click Set Mask For example by creating a string for the slide name fields based on the characters of the barcode a unique name will be generated ...

Page 103: ...se you do not use masks or select an item from the drop down list With the Multi fill option the selected slides will be given the same input data to their specific fields Profile Folder Case and Block fields can be auto filled this way by clicking the drop down lists at the Multi fill section at the bottom of the window Rows can be selected one by one clicking the row headings while the Ctrl butt...

Page 104: ... the CaseID containing slide and patient data stored on HIS LIS Therefore Slide name Folder Case and Block field data cannot be modified only a profile can be selected Figure 67 CaseCenter window during the barcode parsing process Click Done when finished or Cancel to quit the CaseCenter window If you save the form slides will be scanned to server according to the data recorded in the form after y...

Page 105: ...ocus 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 marker pen threshold and specimen threshold values Use of scan everything within marked area ON OFF...

Page 106: ...harpening ON OFF Use of skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Selected image bit depth Other settings Limitation of focus range ON OFF Use of extended focus or Z stack step size and focus level Use of objective position Enable disable Multilayer options present in Fluorescent mode January 16 2013 Rev 1 3DHISTECH Ltd 106 127 ...

Page 107: ...or harm the operating capability of the device Protect it with dust cover when not in use Switch the power off before covering it Avoid touching the lamp bulb Wait for about 15 minutes to allow the bulb to cool down and disconnect the power plug before changing the bulbs There is crush hazard during operation in the area of input or output Trays should be moved through software Never open the devi...

Page 108: ...ree cotton cloth and gently rub the surface 5 1 2 Cleaning the trays Do not clean the trays 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 tray is damaged use either order a new one as inserting a deteriorated tray could lead into unsafe loading of slides 5 1 3 Preventive...

Page 109: ...ve covers Follow the steps in section 5 3 1 Removing the protective covers 4 Remove slide manually see section 5 3 5 Removing the slide 5 Reattach protective covers 6 Reconnect 24V power supply and control computer to line power supply 7 Switch on the 24 V power supply 8 Switch on the control computer 9 Launch control software Tray jammed 1 Exit control software 2 Switch off control computer and 2...

Page 110: ...ection 5 3 2 Replacing the halogen lamp Virtual slide is improperly focused almost across its entire surface Focus range enabled Disable Limiting focus range function Poor image quality Imaging error for example chromatic aberrations Contact 3DHISTECH Service for support Warning Do not modify the camera driver settings as the default factory settings give the most accurate images Virtual slides sh...

Page 111: ...n Manual mode Focus range limit is activated Deactivate the Limiting focus range option Focus range setting is incorrect Change focus range setting All individual images show a shading effect Algorithm failed to find empty image fields Capture a reference image with a blank slide see section 4 3 2 Scan Options 5 2 1 Fluorescent Applications optional The shutter of the HXP 120 cannot be triggered i...

Page 112: ...urce on When using Lumencor Contact 3DHISTECH Service for support 5 3 Maintenance This section describes the most common maintenance solutions that can be performed by the user of the product For maintenance solutions not described in this manual contact the service personnel 5 3 1 Removing the protective covers To replace the halogen lamp or to perform other maintenance work and to interrupt a ru...

Page 113: ...h with a blunt or long object for example with a 3 mm Allan key against the opener lever behind the hole to open the lock You will hear a clack 2 The two halves can be pushed apart Note If necessary one or both halves can be removed completely For this purpose push them to the right or to the left until they can be detached 3 On completion of the maintenance or repair work the cover halves must be...

Page 114: ...camera 5 3 2 Replacing the halogen lamp Figure 70 Replacing the halogen lamp Warning Hot surface Wait for the lamp surface to cool down Keep a cool down time of approximately 15 minutes When changing the lamp avoid touching the replacement bulb with the bare fingers 1 Exit control software 2 Switch off the power supply and disconnect the power cable January 16 2013 Rev 1 3DHISTECH Ltd 114 127 ...

Page 115: ...re that the two clamps 3 on the lamp mount are correctly aligned to the hole 5 on the heat sink body carefully push the lamp mount into the heat sink as far as you can 11 Turn the lamp mount 2 clockwise for approximately 45 degrees aligning its bores with the ones on the heat sink body 12 Lock the lamp mount 2 with the knurled screws 1 13 Close the cover see section 5 3 1 Opening the protective co...

Page 116: ...tly 1 Disconnect power plug separate all poles from the mains 2 Unfix screws of lateral cover plate and remove it from the unit housing see Figure 71 Figure 71 Removing the lateral cover of the HXP 120 3 Press plug securing latches inward 1 then disconnect plug of the lamp module 2 see Figure 72 Figure 72 Disconnect plug January 16 2013 Rev 1 3DHISTECH Ltd 116 127 ...

Page 117: ...t the new lamp module Make sure that the groove 1 in the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 74 Figure 74 Inserting the lamp module Caution Incorrect handling may considerably reduce the lamp module s useful life Hold it by the ceramic part in all cases Never touch the lamp s glass surface or the inside surface of the reflector Skin oil is harmfu...

Page 118: ...y removed by clicking the Emergency Manual Slide Removal Position button see section 4 3 6 Service tab Warning Crush hazard Before you remove a jammed slide cancel the running digitization process terminate the software session and turn the power off Any manipulation performed on a mechanical component must be followed by a complete device initialization routine software restart Figure 75 Removing...

Page 119: ...ury and contagion Broken slide can be removed only by a well trained person 4 The clamp 1 can be pushed slightly to the left to facilitate slide removal 5 Push protective covers together again see section 5 3 1 Removing the protective covers 6 Launch control software 5 3 5 Installing and Removing the Filter Module Fluorescent Option Figure 76 Installing and removing the filter module January 16 20...

Page 120: ...n the input fields Warning Crush hazard Rotating the filter turret motorically during installation or removal may lead to injury 5 Hold the filter module by its handling pads 5 one on the right one on the left side of the module and insert its upper part in forward tilted position under the upper spring loaded clamps 1 6 Press the filter module by its handling pads until it safely connects to the ...

Page 121: ...echnical Data Caution Be sure that the scan camera is not moved during transportation To transport Pannoramic MIDI do the following 1 Turn power supply off and detach all cables 2 Remove the slide tray if necessary 3 Transport Pannoramic MIDI with the help of another person 4 After finishing transportation reestablish cable connections Caution Do not lift or transport Pannoramic MIDI by holding it...

Page 122: ...se 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 75 Operation Permissible ambient temperature 10 C to 35 C Permissible relative air humidity 75 Altitude at installation site...

Page 123: ...th EN 61326 2 6 2005 Base unit input voltage 24V DC 1V Power consumption of the complete device 75 VA 24V external mains power supply unit Intended site closed room facilities Electrical protection class I Internal protection degree IP 20 Electrical safety in compliance with UL 2601 1 TÜV EN 60601 CE EN60601 1 2 2001 Over voltage category II Radio interference suppression in accordance with CISPR ...

Page 124: ...titute light source Slide identification Slides are identified by a VRmagic VRmC 8 PRO preview camera Label area is saved as image and barcode is interpreted as a character string with capability for interpretation of the following types of 1D and 2D barcodes Interleaved 2 of 5 Code39 ASCII encoding Code93 ASCII encoding Code128 UCC EAN128 ASCII encoding EAN8 Numeric encoding EAN13 Numeric encodin...

Page 125: ...era resolution 1388 x 1040 pixel Camera max speed 5 frames per second Bit depth 12 bit Pixel resolution with 20 objective and 1 C mount adapter 0 32µm Cooling Peltier element Connection type FireWire 1394 A CIS VCC F52U25CL camera 1 1 8 PS IT CCD Pixel size 4 40 4 40 µm Camera resolution 1624 H 1224 V pixel Camera max speed up to 30 frames per second Bit depth 10 bit Pixel resolution with 20x obje...

Page 126: ...type dual Camera Link full 10 taps Control computer minimum system requirements Operating System Microsoft Windows 7 SP1 64 bit EN HU CPU Intel Xeon E5630 2 53 GHz RAM 4 GB Hard disk 1 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices keyboard mouse Ports 2 x Fire Wire 1394 A 1394 B 4 x USB 2 0 GB Ethernet January 16 2013 3DHISTECH Ltd 126 127 ...

Page 127: ...106 111 115 119 122 124 Focus 12 18 38 45 48 51 55 56 57 67 68 71 72 73 74 76 77 83 84 85 89 90 91 97 105 106 110 111 H Halogen lamp 110 112 114 124 HXP 120 13 14 15 17 18 22 36 107 108 111 112 115 116 120 124 L Lumencor 12 17 18 22 83 107 112 124 M Marker 47 50 80 105 P Pannoramic MIDI 6 8 9 10 12 13 15 17 18 20 26 28 36 98 109 112 121 Pannoramic Viewer 19 57 68 110 Preview 21 25 28 30 34 40 41 4...

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