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3D Histech Pannoramic MIDI 1.15 User Manual Download Page 64

Pannoramic MIDI 1.15 User’s Guide

4 Software Description

  Caution!

Before starting digitization process ensure that you have enough free 
space on the destination drive. You can check the available free disk 

space in the last line (

Available disk space

) of the information area of 

Current Slide Scan Progress

.

You can interrupt a running digitization process by clicking 

. This button is only enabled 

if a digitization process is in progress.

4.4  Using Brightfield Automatic Mode

Compared to Manual mode, it has less options in some dialogs, but it has an additional Barcodes tab.

4.4.1  Routine work tab

Figure 38 – Routine work tab

The Routine work panel provides basic digitization functions.

March 13, 2012 - Rev 1

3DHISTECH Ltd.

64(131)

Summary of Contents for Pannoramic MIDI 1.15

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

Page 2: ...7 1 2 3 Control Software 19 2 Installation 21 2 1 Control computer ports 21 2 2 Connectors and cables 22 3 Operating Slides and Trays 24 3 1 Preparing Slides and Trays 24 3 2 Affixing Barcode Stickers to Slides 25 3 3 Inserting and Removing Slides 27 4 Software Description 29 4 1 Starting Exiting Pannoramic MIDI Software Application 29 4 1 1 Starting the software 29 4 1 2 Exiting the software 30 4...

Page 3: ...sing Fluorescent Automatic Mode 91 4 6 1 Routine work tab 91 4 6 2 Barcodes tab 96 4 6 3 Preview tab 100 4 6 4 Focus tab 101 4 6 5 Service tab 101 4 7 Scan To Server 102 4 8 Using Profiles 108 5 Troubleshooting and Maintenance 110 5 1 Safety Information 110 5 1 1 Cleaning the device 111 5 1 2 Cleaning the trays 111 5 1 3 Preventive maintenance 111 5 2 Troubleshooting 112 5 2 1 Fluorescent Applicat...

Page 4: ...Pannoramic MIDI 1 15 User s Guide Index 131 March 13 2012 Rev 1 3DHISTECH Ltd 4 131 ...

Page 5: ...are the sole properties of the 3DHISTECH Ltd 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including the results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitalized slide s that stems from or is ass...

Page 6: ...ND EXPRESSED IMPLIED OR OTHERWISE INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL INCIDENTAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR FOR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE AND ON ANY ...

Page 7: ... 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 8: ...nction 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 Ca...

Page 9: ...rvice 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 ...

Page 10: ...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 11: ...ccepted 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 warra...

Page 12: ...rical 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 March 13 2012 Rev 1 3DHISTECH Ltd 12 131 ...

Page 13: ... 40 0 95 NA Carl Zeiss Plan Apochromat objective Key features of the Pannoramic MIDI scanner Up to 9 freely selectable color filters for fluorescence High end fluorescent illumination device Lumencor Spectra 7 Light Engine Multiband filter support Noiseless FL scanning with the best FL camera available pco edge 12 slide automatic loading and scanning Improved permanent autofocus Small footprint Co...

Page 14: ...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 March 13 2012 Rev 1 3DHISTECH Ltd 14 131 ...

Page 15: ...parts 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 March 13 2012 Rev 1 3DHISTECH Ltd 15 131 ...

Page 16: ...wing 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 March 13 2012 Rev 1 3DHISTECH Ltd 16 131 ...

Page 17: ...nsitive 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 18: ...MIDI 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 fluorescen...

Page 19: ...scent 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 March 13 2012 Rev 1 3DHISTECH Ltd 19 131 ...

Page 20: ...amic Viewer software fully functional Optional CaseCenter Pannoramic Viewer TMA module 3D Reconstruction module HistoQuant NuclearQuant MembraneQuant FISHQuant and DensitoQuant modules ImmunoScreener module E School Encoder March 13 2012 Rev 1 3DHISTECH Ltd 20 131 ...

Page 21: ...tallation 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 f...

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

Page 23: ...ly cable between 230V 110V and CIS camera Optical cable between HXP 120 fluorescent illuminator or Lumencor Spectra 7 LE unit and scanner Trigger cable between AxioCam and HXP 120 fluorescent illuminator Trigger cable between pco edge and Lumencor fluorescent illuminator USB to RS232 serial communication cable between Lumencor fluorescent illuminator and control computer Warning Only connect exter...

Page 24: ...ded 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 fur...

Page 25: ...ding 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 stick...

Page 26: ...imen 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 27: ... 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 28: ...afely 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 29: ...review 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 b...

Page 30: ...dow 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 March 13 2012 Rev 1 3DHISTECH Ltd 30 131 ...

Page 31: ... 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 whet...

Page 32: ... 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 March 13 2012 Rev 1 3DHISTE...

Page 33: ...ank 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 mov...

Page 34: ...rightfield 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 March 13 2012 Rev 1 3DHISTECH Ltd 34 131 ...

Page 35: ...as only certain predefined areas for creating compensation images due to the type of the compensation slide or because the compensation slide has faded in some areas To create the compensation image s click Click the Stop button to interrupt the process The Progress bar at the bottom of the window displays the progress of the compensation image creation Fluorescent Compensation You have received a...

Page 36: ...Pannoramic MIDI 1 15 User s Guide 4 Software Description Figure 12 Fluorescent Compensation March 13 2012 Rev 1 3DHISTECH Ltd 36 131 ...

Page 37: ...and Focus Both the focus on the sample and the exposure time can be set either manually or automatically NOTE Different filters usually require different exposure settings Filter Selection for Compensation If you have selected a filter for a position in the Microscope Settings window the filters for each position are displayed in this field Tick the check boxes of the desired filters to be used fo...

Page 38: ...k the Stop button to interrupt the process The Progress bar at the bottom of the window displays the progress of the compensation image creation Image Browser Figure 13 Image Browser This function displays the created compensation image 4 2 3 Microscope Settings By moving the mouse cursor over the buttons the software displays information about the setting you are interested in March 13 2012 Rev 1...

Page 39: ...c MIDI 1 15 User s Guide 4 Software Description Base Settings Figure 14 Base settings Objective type You can select the type and the magnification level of the objective March 13 2012 Rev 1 3DHISTECH Ltd 39 131 ...

Page 40: ...ing modes It is also available for you to define which filters occupy which turret positions Save settings by clicking Note The function Enable HXP 120 fluorescent light source shutter is available only for AxioCam MRm Rev 3 The AxioCam and the HXP 120 must be connected by a trigger cable to enable this function Camera Rotation Caution If you have transported the product or changed the camera ther...

Page 41: ...Pannoramic MIDI 1 15 User s Guide 4 Software Description Figure 15 Camera rotation March 13 2012 Rev 1 3DHISTECH Ltd 41 131 ...

Page 42: ...Difference This function is available only for fluorescence settings it enables you to set the basic focus differences between the filters This facilitates more precise focusing during scanning Figure 16 Z Difference tab March 13 2012 Rev 1 3DHISTECH Ltd 42 131 ...

Page 43: ...pecimen 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 18 External Application Call Settings March 13 2012 Rev 1 3DHISTECH Ltd 43 131 ...

Page 44: ...rred Call ERRORTEXT transfers the error message Run defines the window mode that the external application will start in The following window modes can be set Normal window Minimized Maximized You can test whether the Error Occurred Call settings work by clicking By moving the mouse cursor over the buttons the software displays information about the setting you are interested in 4 3 Using Brightfie...

Page 45: ...ow 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 March 13 2012 Rev 1 3DHISTECH Ltd 45 131 ...

Page 46: ...thcoming 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 March 13 2012 Rev 1 3DHISTECH Ltd 46 13...

Page 47: ...button on this tab that you can start scanning with but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from the selection menu click Load To delete the current profile click Delete ...

Page 48: ...u can choose the following image formats in the Image Encoding field JPEG The quality can be adjusted with the JPEG quality factor slider Greater values result in better quality but larger files The default setting is 80 PNG lossless compressed image format BMP lossless uncompressed image format but larger files due to less effective compression It is a raw data file March 13 2012 Rev 1 3DHISTECH ...

Page 49: ...reference 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 sl...

Page 50: ...igure 22 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 March 13 2012 Rev 1 3DHISTECH Ltd 50 131 ...

Page 51: ...th 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 th...

Page 52: ...ese 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 are...

Page 53: ...only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned 4 3 4 Preview area scanned by preview camera The preview image shows the area that will be digitized with a red and or an orange mask If the Use selection box is enabled there is a black frame displayed in the image Figure 25 Preview image Colors used in preview image The following f...

Page 54: ...e 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 disp...

Page 55: ... 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 f...

Page 56: ...ts on TMA slides You can set the selection settings on the following four tabs Select tab Figure 29 TMA tool Select To create a new TMA object click New To select an existing TMA object click on the object name The selected object name will highlight To delete an existing TMA object click Delete March 13 2012 Rev 1 3DHISTECH Ltd 56 131 ...

Page 57: ...select the appropriate values with the arrows 3 Enter the distance between two spots on the X and the Y axis in µm in the Spot distance X µm and Spot distance Y µm fields or select the appropriate values with the arrows 4 Enter the average diameter of the spots in the Side length of µm field or select the appropriate value with the arrows Grid tab The Grid tab displays the previously set grid sett...

Page 58: ...f 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 32 TMA tool Move tab with preview March 13 2012 Rev 1 3DHISTECH Ltd 58 131 ...

Page 59: ...User s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degree checkbox Figure 33 Label area 4 3 5 Focus tab Figure 34 Focus tab March 13 2012 Rev 1 3DHISTECH Ltd 59 131 ...

Page 60: ...s 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 61: ...bove 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 36 Service tab This panel contains control and maintenance functions Emergency Manual Slide Removal Position The specim...

Page 62: ...eld 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 37 Display field and toolbar for live images March 13 2012 Rev 1 3DHIS...

Page 63: ...PEG 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 level This function is use...

Page 64: ...rmation 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 38 Routine work tab The Routine work panel provides basic dig...

Page 65: ...o 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 can delete the current profi...

Page 66: ...Pannoramic MIDI 1 15 User s Guide 4 Software Description 4 4 2 Barcodes tab Figure 39 Barcodes tab March 13 2012 Rev 1 3DHISTECH Ltd 66 131 ...

Page 67: ...directory the name and the profile to be used by barcodes The positions of the characters in the barcode are defined in the mask fields It is possible to define areas using the character Characters located at different places of the barcode may be combined by using a comma Mainly 2D barcodes are used for this purpose It is possible to use 1D barcodes however it can contain less information You can...

Page 68: ...arcode 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 n...

Page 69: ...files 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 70: ...s 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 March 13 2012 Rev 1 3DHISTECH Ltd 70 13...

Page 71: ...spot on the coverslip Multilayer mode Select Single layer option if you want to scan a single layer of the slide By choosing the Extended focus option the software selects the sharpest image from each focus level for each image field and combines them into one single image Therefore those parts that were blurry in auto manual focus will also be sharp This method guarantees the maximum depth of sha...

Page 72: ...ween 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 43 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 cov...

Page 73: ... 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 44 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 74: ...er s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work tab Figure 45 Routine work tab panel The Routine work panel provides basic digitization functions March 13 2012 Rev 1 3DHISTECH Ltd 74 131 ...

Page 75: ...e 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 76: ...s is done on one channel You can choose whether you want to do stitching on the focus channel or on another channel It is recommended to choose another channel if the focus channel was determined on the basis of exposition time and it would display less information It is recommended to choose a filter that is related to the staining that stained the most of the specimen The default selection is Fo...

Page 77: ...e 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 ...

Page 78: ...compensation image see section 4 2 2 Image Compensation Fluorescent compensation To move between the filters click Previous Filter or Next Filter Multilayer Settings By clicking the button the Multilayer Settings window is displayed The containing settings are the same as in Brightfield mode but you can select Extended focus or Z stack value for the specific channel Figure 47 Multilayer Settings w...

Page 79: ...Pannoramic MIDI 1 15 User s Guide 4 Software Description 4 5 2 Scan Options Figure 48 Scan options tab March 13 2012 Rev 1 3DHISTECH Ltd 79 131 ...

Page 80: ...s image compression checkbox Image Bit Depth You can choose between 8 and 12 bit depths when using AxioCam MRm Rev 3 and between 8 and 16 when using pco edge camera Scan Settings Focus frequency This value determines how many field of views will pass before the sample is refocused This value should be selected depending on the unevenness and size of the specimen Maximum exposure time A limit value...

Page 81: ...posure Time This function is used for defining time length used for determination of focus but is inactive when using AxioCam MRm Rev 3 and pco edge cameras Exposure Time Calculate exposure time for each area Calculates exposure time that is specific to each area and that varies according to the different characteristics Calculate exposure time for full slide After analyzing the slide the program ...

Page 82: ...ores the swap files necessary for scanning Scanned slide destination This field determines where to digitize the virtual slides To be able to choose the Scan to CaseCenter function you have to install the ScanToServer application For information on how to install and use the ScanToServer application see section 4 7 Scan To Server If you enable the Directory function the virtual slides will be digi...

Page 83: ...s 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 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 les...

Page 84: ...old 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 recom...

Page 85: ...he 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 TM...

Page 86: ...Pannoramic MIDI 1 15 User s Guide 4 Software Description 4 5 4 Hardware tab Figure 51 Hardware tab selected mode User controlled March 13 2012 Rev 1 3DHISTECH Ltd 86 131 ...

Page 87: ... 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 displa...

Page 88: ...this 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 89: ...ate 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 interpolate...

Page 90: ...ed 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 a...

Page 91: ...uide 4 Software Description 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work tab Figure 53 Routine work tab panel The Routine work tab panel provides some basic digitization functions March 13 2012 Rev 1 3DHISTECH Ltd 91 131 ...

Page 92: ... 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 ...

Page 93: ... 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 ...

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

Page 95: ...er 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 55 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 chann...

Page 96: ... 15 User s Guide 4 Software Description 4 6 2 Barcodes tab Figure 56 Barcodes tab On this tab you can set identification features to the various slides and for assigning profiles March 13 2012 Rev 1 3DHISTECH Ltd 96 131 ...

Page 97: ...sed 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 b...

Page 98: ...n 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 March 13 2012 Rev ...

Page 99: ...n 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 pro...

Page 100: ...described in Manual mode In Automatic mode you cannot change the threshold values it will use the threshold values that were set previously in the Manual mode and when activating the Use selection box option the area cannot be set For more information see section 4 5 3 Preview tab Note It is recommended to use profiles since the Automatic mode does not provide a preview image to check settings Mar...

Page 101: ...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 102: ...l 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_15_xx exe to launch the installation wizard 2 Accept the License Agreement then click Install to continue March 13 2012 Rev 1 3DHISTECH Ltd 102 131 ...

Page 103: ...inish to finalize the installation process of the ScanToServer application To setup a connection with a designated server follow the steps below 1 Click Scan Options on the Routine Work tab panel Figure 60 Scan Options button March 13 2012 Rev 1 3DHISTECH Ltd 103 131 ...

Page 104: ...drop down list then give the user name and password Activate the Secure connection option to enable HTTPS connection Click Connect when finished Figure 62 Server Log in window 4 Click the Connect button in the Scan Options window to connect to the server If the connection is established the server status will be modified from Not connected to Connected Click OK to close the Scan Options window Mar...

Page 105: ...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 Figure 63 CaseCenter window in Manual Mode Figure 64 CaseCenter window in Automatic Mode March 13 2012 Rev 1 3DHISTECH Ltd 105 131 ...

Page 106: ...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 The barcode 0123456789 and a mask 1 3 result that the first four characters of the barcode will be displayed and set as slide name 012 Case and Block fields can be set ...

Page 107: ...n on your keyboard is pressed down or select the entire form by clicking the gray field at the top left corner To erase reset fields to default click the Reset all button If modification is done to the folder tree of the CaseCenter server while the CaseCenter window is open click Update Tree to refresh the tree view Click Done when finished or Cancel to quit the CaseCenter window If you save the f...

Page 108: ...Focus frequency present in Fluorescent mode Interpolated Focus distance present in Brightfield mode Compression procedure Use of a fixed compensation image ON OFF Use of stitching ON OFF Determination of the area to be scanned Use of automatic threshold specimen Use of specimen threshold value Use of marker pen threshold and specimen threshold values Use of scan everything within marked area ON OF...

Page 109: ...f skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Selected image bit depth Other settings Limitation of focus range ON OFF Use of extended focus or Z stack step size and focus level Use of objective position Enable disable Multilayer options present in Fluorescent mode March 13 2012 Rev 1 3DHISTECH Ltd 109 131 ...

Page 110: ...ase 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 ...

Page 111: ...nt free 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 Preven...

Page 112: ...ective 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 a...

Page 113: ...ee section 5 3 2 Replacing the halogen lamp Virtual slide is improperly focused almost across its entire surface Focus range enabled Disable Limiting focus range 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 slide...

Page 114: ...us in 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 trigger...

Page 115: ...t source 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 ...

Page 116: ... Push 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 mus...

Page 117: ...can camera 5 3 2 Replacing the halogen lamp Figure 68 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 2012 March 13 3DHISTECH Ltd 117 131 ...

Page 118: ...g care 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 protectiv...

Page 119: ...m the mains 2 Unfix screws of lateral cover plate and remove it from the unit housing see Figure 69 Figure 69 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 70 Figure 70 Disconnect plug 4 Loosen pressure bolt with the lever 1 and by keeping the lever pressed remove lamp module 2 see Figure 71 2012 March 13 3DHIS...

Page 120: ...the contact surface of the lamp captures the corresponding pin of the lamp mount see Figure 72 7 xd Figure 72 Inserting the lamp module Caution Incorrect handling may considerably reduce the lamp module s useful life Hold it by the ceramic part in all cases Never touch the lamp s glass surface or the inside surface of the reflector Skin oil is harmful to these parts 8 Re establish plug in connecti...

Page 121: ...ide 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 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 ...

Page 122: ...en 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 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 74 Ins...

Page 123: ...elds 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 bottom spring ...

Page 124: ... find the weight data of the base unit in section 6 Technical 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 D...

Page 125: ...fter transporting and reinstalling the Pannoramic MIDI Caution If Fluorescence scanning option is available create new compensation images after transporting and reinstalling the Pannoramic MIDI For more information see section 4 2 2 Image Compensation Fluorescent Compensation 2012 March 13 3DHISTECH Ltd 125 131 ...

Page 126: ...ase 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 sit...

Page 127: ...ith 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 128: ... substitute light source Slide identification Slides are identified by preview camera TIS DFK21F04 Barcode area is saved as image and label is interpreted as a character string with capability for interpretation of the following types of 1D and 2D barcodes Interleaved 2 of 5 Code39 ASCII encoding Code93 ASCII encoding Code128 UCC EAN128 ASCII encoding EAN8 Numeric encoding EAN13 Numeric encoding U...

Page 129: ...mera 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 obj...

Page 130: ... 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 March 13 2012 3DHISTECH Ltd 130 131 ...

Page 131: ...14 118 121 122 125 126 128 Focus 3 13 19 37 42 49 52 55 59 60 61 71 72 75 76 77 78 80 81 87 88 89 93 94 95 101 108 109 113 114 H Halogen lamp 3 113 115 117 128 HXP 120 14 15 16 18 19 23 40 110 111 114 115 118 119 121 122 128 L Lumencor 13 18 19 23 87 110 115 128 M Marker 51 54 84 108 P Pannoramic MIDI 2 3 7 9 10 11 13 14 16 18 19 21 27 29 40 102 112 115 124 125 Pannoramic Viewer 20 61 72 113 Previ...

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