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Pannoramic MIDI 1.18.1 User’s Guide

3 Operating Slides and Trays

  Note: 

The distance between slide edges and the edges of the mounted 

coverslip should be 1-2 mm, and they should be parallel with each 
other.

  Note: 

Fluorescent signals become more easily detectable for the scanner, 

therefore resulting in a brighter and better image, by treating the slide 
with a formula that prevents rapid photobleaching of fluorescent 

reagents (e.g. VECTASHIELD® Fluorescent Mounting Medium by 

Vector 

Laboratories 

and ProLong® Gold and 

SlowFade

® Gold antifade reagents

by 

Invitrogen

) during the FISH protocol.

For further information, see the homepages of the manufacturers: 

http://www.vectorlabs.com/

 and 

http://www.invitrogen.com

.

3.2  Affixing Barcode Stickers to Slides

This section describes how to affix barcode stickers to slides. Barcodes enable virtual slide 

identification.

Figure 6 – Slide with a barcode sticker

The label area is recorded by the preview camera, and can be displayed by the control and viewer 

software.

May 29, 2014 - Rev. 1

3DHISTECH Ltd.

26(127)

Summary of Contents for Pannoramic MIDI 1.18.1

Page 1: ...PM1 18 1 UG Rev1 Pannoramic MIDI 1 18 1 User s Guide May 29 2014 Rev 1 ...

Page 2: ...re 21 2 Installation 22 2 1 Control computer ports 22 2 2 Connectors and cables 23 2 3 Coupling the Lumencor Spectra 6 unit with the scanner 24 3 Operating Slides and Trays 25 3 1 Preparing Slides and Trays 25 3 2 Affixing Barcode Stickers to Slides 26 3 3 Inserting and Removing Slides 27 4 Software Description 30 4 1 Starting Exiting Pannoramic MIDI Software Application 30 4 1 1 Starting the soft...

Page 3: ...el 88 4 6 Using Fluorescent Automatic Mode 89 4 6 1 Routine work panel 89 4 6 2 Barcodes panel 94 4 6 3 Preview panel 98 4 6 4 Focus panel 99 4 6 5 Service panel 99 4 7 Scan To Server 100 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 Fl...

Page 4: ...Pannoramic MIDI 1 18 1 User s Guide Index 127 May 29 2014 Rev 1 3DHISTECH Ltd 4 127 ...

Page 5: ...P 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 a...

Page 6: ... KIND 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 A...

Page 7: ...101 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 inco...

Page 8: ...function keys such as F11 or the Ctrl M key combination Example Cross references within this document or to other documents Warning It might cause irreversible damage or harm to the user of the product or the product itself if this instruction is not followed Caution It might cause the product to not work properly if this instruction is not followed and alerts to a potential danger situation Note ...

Page 9: ...service 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 eart...

Page 10: ...e you put the cover on Caution 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 ...

Page 11: ... accepted 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 war...

Page 12: ...merical 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 May 29 2014 Rev 1 3DHISTECH Ltd 12 127 ...

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

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

Page 15: ... 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 illumination unit Figure 1 Warning and information labels May 29 2014 Rev 1 3DHISTECH Ltd 15 127 ...

Page 16: ...S VCC FC60FR19CL scan camera Flourescent option A 6 HXP 120 fiber coupled illumination unit can be used with AxioCam MRm Rev3 and Stingray cameras only 7 HXP 120 illumination adapter and cable use with AxioCam MRm Rev3 and Stingray cameras only Flourescent option B 6 Lumencor SPECTRA 6 Light Engine fiber coupled illumination unit can be used with pco edge 4 2 camera only 7 Lumencor illumination ad...

Page 17: ...nts 1 2 1 Pannoramic MIDI system The following figure shows the main parts of the Pannoramic MIDI system Figure 3 Pannoramic MIDI system overview 1 Lumencor SPECTRA 6 Light Engine illumination unit option 2 HXP 120 fiber coupled illumination unit option 3 24 V power supply 4 Pannoramic MIDI base unit 5 Monitor 6 Mouse 7 Control computer May 29 2014 Rev 1 3DHISTECH Ltd 17 127 ...

Page 18: ...1 CCD scientific cooled monochrome camera for high quality sensitive fluorescent applications CIS VCC FC60FR19CL CMOS camera for high quality brightfield applications allowing fast scanning pco edge 4 2 Equipped with a high quality sCMOS image sensor for fluorescent applications allowing fast scanning and an outstanding low read out noise High quantum efficiency cooled with Peltier element May 29 ...

Page 19: ...ages caused by an installation carried out by an unauthorized person Base Unit options Pannoramic MIDI Basic Scan Option Fast Option base unit equipped with Stingray or CIS cameras for Brightfield scanning no fluorescent accessories included Pannoramic MIDI Basic Fluorescence Option base unit completely equipped with AxioCam camera and HXP 120 illumination unit trigger cable and filters for fluore...

Page 20: ...uorescence illumination unit trigger cable and filters for fluorescence scanning NOTE If Lumencor light source is ordered the custom light source and filter modules can be variable For more information contact 3DHISTECH customer service Objectives Carl Zeiss Plan Apochromat 20 NA 0 8 Carl Zeiss Plan Apochromat 40 Corr NA 0 95 Warning Do not change correction collar settings on 40 NA objective if y...

Page 21: ...noramic Scanner control software Optional Fluorescence Extended focus Z stack Barcode reader licensed feature Pannoramic Viewer software fully functional Optional CaseCenter TMA module 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules TumorBoard module E School Encoder May 29 2014 Rev 1 3DHISTECH Ltd 21 127 ...

Page 22: ...stallation 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 ...

Page 23: ...canner 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 a pair of CameraLink cables between CIS camera and control computer pco edge 4 2 a pair of CameraLink cables between pco edge 4 2 camera and control compute...

Page 24: ...k of electrical shock 2 3 Coupling the Lumencor Spectra 6 unit with the scanner To operate the Lumencor Spectra 6 Light Engine fluorescent illumination unit it has to be connected to the Pannoramic SCAN 150 base unit the camera and the control computer 1 Turn the control computer and the pco edge 4 2 camera off 2 Connect both ends of the fiber optic cable to the coupling ports of the scanner and t...

Page 25: ...corners Edges Grounded or cut Warning Do not use a slide when it is broken or its edges are not properly cut or grounded Using such slides can lead to injury Warning Ensure that no part of the mounted coverslip protrudes from the edges of the slide Use slides with completely dried embedding medium only Otherwise the coverslip can be shifted that makes slide loading less reliable Not completely dri...

Page 26: ... reagents e g VECTASHIELD Fluorescent Mounting Medium by Vector Laboratories and ProLong Gold and SlowFade Gold antifade reagents by Invitrogen during the FISH protocol For further information see the homepages of the manufacturers http www vectorlabs com and http www invitrogen com 3 2 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides Barcodes enab...

Page 27: ...fication 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 the overall thickness must must be kept below 1 65 mm including the barcodes and the slide 3 3 Inserting and Removing Slides To insert slides into a tray Figure 7 I...

Page 28: ...be removed only by a well trained person Only original 3DHISTECH trays are allowed for use with Pannoramic MIDI Note The coverslip and the label area should be on the top To insert and remove trays Figure 8 Inserting the tray 1 Insert the tray 2 that contains at least one slide into the opening 1 on the right side of the device Push it until it cannot be pushed further 2 After digitizing slides th...

Page 29: ...kept clean from dust broken glass and other mounting media residues Slides will only operate safely and properly if trays are clean Caution Do not place objects near the device or in the movement area of the slide tray Warning Do not reach into the movement area of the tray while slides are digitized It can move partly out of the device during the digitization process both to the right or the left...

Page 30: ...review camera and the scan camera are initialized After successful initialization the Mode selection window is displayed Figure 9 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 31: ...indow 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 10 Options menu 4 2 1 Barcode Settings Figure 11 Barcode settings May 29 2014 Rev 1 3DHISTECH Ltd 31 127 ...

Page 32: ...e 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 whether the barcode reading settings are correct di...

Page 33: ... number If you select Exclude check digit then the check digit number will also be analyzed as a barcode number Foreground Color You can select the following foreground color of the barcode area Black White Barcode Image Compensation Click Use barcode compensation image to use the previously created compensation image for scanning the label area The compensation image improves the effectiveness of...

Page 34: ...deriving from the slide illumination staining or embedding medium irregularities To set compensation parameters properly follow the instructions below By moving the mouse cursor over the buttons the software displays information about the setting you are interested in Brightfield Compensation Figure 12 Brightfield Compensation May 29 2014 Rev 1 3DHISTECH Ltd 34 127 ...

Page 35: ...ll not use those areas for the creation of the compensation images Current threshold To modify the threshold settings set the desired threshold level in the box Use Selection Box Select this if you have a compensation slide that has only certain predefined areas for creating compensation images To create the compensation image s click Click the Stop button to interrupt the process The Progress bar...

Page 36: ...ype and the magnification level of the objective Camera type If Pannoramic MIDI features a manual camera changer first activate the Use manual camera changer option then set the appropriate camera types both for Brightfield and Fluorescent scanning modes in Pos 1 Camera type and Pos 1 Camera type fields The software automatically loads the camera settings upon clicking the Test and Apply Camera Se...

Page 37: ...is configured as illumination unit the corresponding Enable Lumencor hardware trigger option is displayed on the form Filter Settings Figure 15 Filter Settings panel On this panel you can define which filters occupy which turret positions May 29 2014 Rev 1 3DHISTECH Ltd 37 127 ...

Page 38: ...16 Camera rotation Caution If you have transported the product or changed the camera there is a possibility that the camera does not display the images properly If you experience such problems contact service support Do not modify these settings May 29 2014 Rev 1 3DHISTECH Ltd 38 127 ...

Page 39: ... 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 17 Z Difference panel May 29 2014 Rev 1 3DHISTECH Ltd 39 127 ...

Page 40: ...moval Position The slide 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 covers Slide Removed Manually Click this button to notify the software that you have removed the slide manually 4 2 4 Event Call Settings Figure 19 Event Call Settings May 29 2014 Rev 1 3DHISTECH Ltd 40 127 ...

Page 41: ...NAME 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 Scanning Error Occurred settings work by clicking By moving the mouse cursor over the buttons the software displays information about the s...

Page 42: ...meters can be set Message Type E mail SMTP Host Address Authentication User ID and User Password are required Secure connection SSL If activated the messages will be sent through secured connection Send Test e mail Click this button to send test e mail to the specified address There are 2 feedback messages that come up after sending the e mail An e mail has been sent to the recipient An error has ...

Page 43: ...roperly set messenger settings click OK then click Users in the Message Call section of the Event Call Settings window to address functions to the recipients that can be selected under the Send Message when field Figure 21 Users window May 29 2014 Rev 1 3DHISTECH Ltd 43 127 ...

Page 44: ...ings or single slides You can also define profiles here which can be used in the Automatic mode For more information on profiles see section 4 8 Using Profiles For more information on Automatic mode see section 4 4 Using Brightfield Automatic Mode Figure 22 Main window of control software 1 Panel with scanner functions and settings 2 Scan camera live image display area 3 Preview image recorded by ...

Page 45: ...e forthcoming 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 May 29 2014 Rev 1 3DHISTECH Ltd 45...

Page 46: ...canning 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 The Objective position field sets the o...

Page 47: ...rtual slide You can choose the following predefined image formats and a subsequent custom option from the Image Quality drop down list in the Image Encoding section of the window Excellent JPEG 90 Good JPEG 80 Medium JPEG 60 Low JPEG 30 Custom If choosing this option the Image encoding window is displayed on which you can select from different image formats May 29 2014 Rev 1 3DHISTECH Ltd 47 127 ...

Page 48: ...ailable if Stingray camera is installed on the scanner It is not accessible for configurations installed with CIS camera Image fields will be saved with native pixel resolution If this function is disabled you will work with reduced pixel resolution These resolution differences are not really visible with the human eye what is important in this feature is the resulting smaller file size Brightfiel...

Page 49: ...see section 4 7 Scan To Server If you enable the Directory function the virtual slides will be digitized in the specified folder You can browse for the folder with the Browse button If you specify a folder that does not exist the software will create it All parameter inputs are saved for the next software session 4 3 3 Preview panel The Preview panel offers options for threshold setting and select...

Page 50: ...sensitive scanning but it is possible that some of the smaller specimen areas will not be digitized Scan area inside the marker If the specimen cannot be identified as required for digitization for example weak contrast it can help to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen ...

Page 51: ...nate those areas Warning Do not use Remove coverslip function on TMA slides The layout of TMA slides may mislead the detecting algorithm Fill holes in scan area If selected the holes inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermine...

Page 52: ... preview mask or TMA grid Use selection box If selected only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned 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 enable...

Page 53: ...le 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 area inside the marker is selected in the Preview panel the preview camera detects the marker pen The inside areas appear in red color and will be digitized Areas scanned in This color is only ...

Page 54: ... on the area of interest on the preview image This will define the Live image that you can access from the Focus panel 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 100 600 To fit the preview image to the preview area click Fit Choose from the Scanned or the Not scanned option from the righ...

Page 55: ...selection settings on the following four tabs Select panel Figure 33 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 Block panel Figure 34 TMA tool Block May 29 2014 Rev 1 3DHISTECH Ltd 55 127 ...

Page 56: ...priate 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 Diameter of spots µm field or select the appropriate value with the arrows Grid panel The Grid panel displays the previously set grid settings Figu...

Page 57: ...g of the TMA selection spots that are displayed on the preview image To move the spots enter the pixel value in the Move field or use the arrows To rotate the spots enter the degree value in the Rotate field or use the rotation arrows Figure 36 TMA tool Move panel with preview May 29 2014 Rev 1 3DHISTECH Ltd 57 127 ...

Page 58: ...ser s Guide 4 Software Description Label area To rotate the label area by 180 select the Rotate image by 180 degrees checkbox Figure 37 Label area 4 3 5 Focus panel Figure 38 Focus panel May 29 2014 Rev 1 3DHISTECH Ltd 58 127 ...

Page 59: ... 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 manual focus step size by...

Page 60: ...above 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 Default settings are Number of focus levels 7 Focus step size 5 4 3 6 Service panel Figure 40 Service panel This panel contains control and maintenance functions Emergency Manual Slide Removal Position The speci...

Page 61: ...field 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 41 Display field and toolbar for live images May 29 2014 Rev 1 3DHIS...

Page 62: ...e 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 63: ...free disk space in the last line Available disk space of the Scan Progress information area 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 panel 4 4 1 Routine work panel Figure 42 Routin...

Page 64: ...the tray before the process You also find the button on this panel that you can start scanning with but it is recommended to go through all the settings before clicking it To administer profiles use the Scan Profiles field The current profile name is displayed at the bottom left corner of the screen To save the current profile click Save To select an existing profile from the selection menu click ...

Page 65: ...Pannoramic MIDI 1 18 1 User s Guide 4 Software Description 4 4 2 Barcodes panel Figure 43 Barcodes panel May 29 2014 Rev 1 3DHISTECH Ltd 65 127 ...

Page 66: ...t 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 c...

Page 67: ... 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 4 Generate name if no name was defined By choosing this option a name is generated automatically in the following format if...

Page 68: ...rofiles 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 da...

Page 69: ...nned The options 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 panel Note It is recommended to use profiles because settings cannot be modified in Automatic mode May 29 2014 Rev 1 3DHISTECH Ltd 69 127 ...

Page 70: ...n a spot on the coverslip Multilayer mode Select Single layer option if you want to scan a single layer of the slide By choosing the Extended focus option the software selects the sharpest image from each focus level for each image field and combines them into one single image Therefore those parts that were blurry in auto manual focus will also be sharp This method guarantees the maximum depth of...

Page 71: ...en 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 panel Figure 47 Service panel This panel contains control and maintenance functions Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover see section 5 3 1 Opening the protective...

Page 72: ...amp 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 48 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 digiti...

Page 73: ... User s Guide 4 Software Description 4 5 Using Fluorescent Manual Mode 4 5 1 Routine work panel Figure 49 Routine work panel The Routine work panel provides basic digitization functions May 29 2014 Rev 1 3DHISTECH Ltd 73 127 ...

Page 74: ...re 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 panel To administer profiles use the Scan Profiles field The curr...

Page 75: ...t 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 Focus channel The Objective position field sets the objective changer to the appropriate position Channel Settings Sele...

Page 76: ... 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 can set the Extended focus and Z stack values for each channel separately May 29 20...

Page 77: ...r 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 51 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 th...

Page 78: ...ption 4 5 2 Scan Options Figure 52 Scan options panel These settings determine the resulting quality and storage location of the virtual slide Image Encoding You can set the image format parameters within this group May 29 2014 Rev 1 3DHISTECH Ltd 78 127 ...

Page 79: ...mat BMP Lossless uncompressed image format but larger files due to less effective compression It is a raw data file JPEG 2000 It supports both the 8 bit and 16 bit image formats The quality can be adjusted with the JPEG 2000 quality factor slider Greater values result in better quality but larger files The default setting is 80 You can create lossless image by selecting the Lossless image compress...

Page 80: ...nning process is increased Caution If the specimen area is barely visible it is possible that the software will analyze that area as an empty one Do not use multilayer mode on empty field of views If selected the extended focus or Z stack function will not run on empty not containing specimen field of views Use stitching By selecting this function enables seamless stitching of digitized tiles Focu...

Page 81: ... filters at each field of view option if using multi band filter for multi channel digitization Digital Slide destination This field determines where to digitize the virtual slides Select the Scan to CaseCenter function to scan slides directly to a dedicated CaseCenter server For information on how to use the ScanToServer application see section 4 7 Scan To Server If you enable the Directory funct...

Page 82: ...ecimen 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 For more information see section 4 3 4 Preview area scanned by preview camera Preview Toolbar May 29 2014 Rev 1 ...

Page 83: ... Draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area If this option is selected only the 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 specim...

Page 84: ...gitized by adjusting the Speck size slider Scan area dilation Adjust the slider to the desired value to enlarge or decrease the scanned area The edge is extended discretely by 100 µm each time Use saved scan area This function is useful if the slides contain areas of interest that cannot be detected by the preview camera This function along with saving profiles helps to scan all slides with the mo...

Page 85: ...Pannoramic MIDI 1 18 1 User s Guide 4 Software Description 4 5 4 Hardware panel Figure 56 Hardware panel selected mode User controlled May 29 2014 Rev 1 3DHISTECH Ltd 85 127 ...

Page 86: ...ties window by clicking for more information see section 4 5 1 Routine work panel Note After 10 seconds an empty position is rotated into position instead of the filter However the last snapshot is still displayed In case Lumencor illumination unit is used it is triggered by the pco edge 4 2 camera so it will not emit light Exposure You can automatically detect the appropriate exposure time by cli...

Page 87: ...By selecting the Use manual focus box you can preset the coarse focus value By activating the Coarse focus function the lower limit value is set to 64 and the upper limit value is set to 64 of the current focus value Note Before entering coarse focus value turn live image on and set a suitable focus position You can accept the current z value by clicking Set Value If you select the Interpolated fo...

Page 88: ... for presetting by clicking Set Value Repeat the procedure for all other filters 4 5 5 Service panel This panel contains control and maintenance functions Figure 57 Service panel 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 covers Slide Removed Manuall...

Page 89: ...r s Guide 4 Software Description 4 6 Using Fluorescent Automatic Mode 4 6 1 Routine work panel Figure 58 Routine work panel The Routine work panel provides some basic digitization functions May 29 2014 Rev 1 3DHISTECH Ltd 89 127 ...

Page 90: ...g with 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...

Page 91: ...e 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 92: ...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 or 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...

Page 93: ... channel Figure 60 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 ...

Page 94: ... 1 User s Guide 4 Software Description 4 6 2 Barcodes panel Figure 61 Barcodes panel On this panel you can set identification features to the various slides and for assigning profiles May 29 2014 Rev 1 3DHISTECH Ltd 94 127 ...

Page 95: ... used by barcodes The positions of the characters in the barcode are defined in the mask fields It is possible to define areas using the character Characters located at different places of the barcode may be combined by using a comma Mainly 2D barcodes are used for this purpose It is possible to use 1D barcodes however it can contain less information You can create up to five sub directories by th...

Page 96: ...f_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 May 29 2014 Rev ...

Page 97: ... in 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 p...

Page 98: ...re 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 and when activating the Use selection box option the area cannot be set For more information see section 4 5 3 Preview panel Note It is recommended to use profiles because settings cannot be modified in Automatic mode May 29 2...

Page 99: ...following 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 covers Slide Removed Manually Click this button to notify the software that you have removed the slide manually Show images during scanning If you select this opti...

Page 100: ... Options on the Routine Work panel Figure 65 Scan Options button 2 Select the Scan to CaseCenter option in the Scan Option window then click Connect Figure 66 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 67 S...

Page 101: ...gure 68 Connected to server Slide settings in the Scan To Server window 1 In the Routine work panel click the button 2 The Scan To Server 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 69 and when in Automatic Mode the form contains 12 rows for all the slots on the tray Figure 70 Fi...

Page 102: ...nd Block field data cannot be modified only a profile can be selected 2 The Generate slide name if no name was defined option can be activated when you do not want to type in a unique name for each slide 3 Upon activating the Read barcode 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 a...

Page 103: ...in case 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...

Page 104: ...cess Click Done when finished or Cancel to quit the Scan To Server window If you save the form slides will be scanned to server according to the data recorded in the form after you start scanning After restarting the scanner software a dialog window appears when scanning to server is performed previously Click Yes to use the last used server or No to get back to local scan mode Figure 74 Reconnect...

Page 105: ...Options Focus frequency in Fluorescent mode Focus frequency in Brightfield mode Compression procedure Use of a fixed compensation image in Brightfield mode 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 106: ...hing channel Flat field correction ON OFF Sharpening ON OFF Use of skip empty field of views ON OFF Do not use extended focus on empty field of views ON OFF Other settings Limitation of focus range ON OFF Enable disable Multilayer options Use of extended focus or Z stack step size and focus level May 29 2014 Rev 1 3DHISTECH Ltd 106 127 ...

Page 107: ...g 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 device unless prompted a...

Page 108: ...lint free cotton cloth and gently rub the surface 5 1 2 Cleaning the trays NEVER 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 Preve...

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

Page 110: ... 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 slides ...

Page 111: ... not required Image is out of focus 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 2 2 Image Compensation 5 2 1 Fluorescent Applications optional The s...

Page 112: ...he 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 Opening the protective covers To replace the halogen lamp or to perform other maintenance work and to interrupt a running digitization procedure because of slide or tray jamming the protective covers of the Pannoramic MIDI ...

Page 113: ...e 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 pushed together again and locked A clack sound can be clearly heard Caution Make sure that no cables a...

Page 114: ... bulb with the bare fingers 1 Exit control software 2 Switch off the power supply and disconnect the power cable 3 Open the cover see section 5 3 1 Opening the protective covers 4 Hold the lamp mount 2 with your hand 5 Remove the knurled screws 1 from the heat sink body 6 completely 6 Turn the lamp mount counter clockwise for approximately 45 degrees until the two clamps 3 are aligned to the hole ...

Page 115: ...ck the lamp mount 2 with the knurled screws 1 12 Close the cover see section 5 3 1 Opening the protective covers 13 Connect power plug and turn power supply on 14 Launch control software 5 3 3 Replacing Lamp Module for Fluorescent Option NOTE This section recites some extracts from the HXP 120 operating manual For detailed information especially instructions regarding safety consult that manual Al...

Page 116: ... HXP 120 3 Press plug securing latches inward 1 then disconnect plug of the lamp module 2 see Figure 78 Figure 78 Disconnect plug 4 Loosen pressure bolt with the lever 1 and by keeping the lever pressed remove lamp module 2 see Figure 79 Figure 79 Removing the lamp module May 29 2014 Rev 1 3DHISTECH Ltd 116 127 ...

Page 117: ...c 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 7 Tighten pressure bolt again with the lever Figure 79 1 8 Re establish plug in connection 9 Screw the lateral cover plate down to the housing 10 Connect power plug 11 Set hour meter time counter to zero 5 3 4 Removing a slide If a slide got jammed or has suffered brea...

Page 118: ...slide 1 Push protective covers apart see section 5 3 1 Opening the protective covers 2 Move clamp 1 to the left so the slide could be easily removed 3 Remove the slide 2 carefully Caution If the slide is broken make sure to remove all pieces completely from the device The edge of the broken area of the slide is sharp and it can lead to injury and contagion Broken slide can be removed only by a wel...

Page 119: ...you proceed with filter module installation or removal 2 Pull the pair of the protective cover halves apart or remove the right part completely see section 5 3 1 Opening the protective covers but do not switch the main unit off 3 Select the desired filter in the corresponding software window see section 4 2 3 Microscope Settings Filter Settings The filter will be positioned in such a way that the ...

Page 120: ...Emission filter 3 7 To remove the filter module first slightly tilt it out of its bottom spring loaded fixtures 6 then pull it out of the upper spring loaded components 1 and take it off 8 Place the protective covers back again see 5 3 1 Opening the protective covers 9 If an HXP 120 illumination unit is used turn it on again consider the cooling time possibly required 5 3 6 Transporting Pannoramic...

Page 121: ...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 its protective covers Caution Readjust camera angle if necessary after transporting and reinstalling the Pannoramic MIDI May 29 2014 Rev 1 3DHISTECH Ltd 121 127 ...

Page 122: ... 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 m...

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: ... as a substitute 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 Numer...

Page 125: ...ixel 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 FC60FR19CL camera Global Shutter Type CMOS Diagonal 15 930mm Pixel size 5 5µm 5 5µm Camera resolution 2048 H 2048 V pixel Frames rates 17fps 34fps 68fps 135fps Bit depth 10 bit Pixel resolution with 20x objective ...

Page 126: ...85MHz Control computer minimum system requirements Operating System Microsoft Windows 7 Professional SP1 64 bit EN CPU 2x Intel Xeon processor 6 core 12 MB l2 cache RAM Recommended 8 GB DDR3 Hard disk Min 1 TB Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices Keyboard mouse Ports 2xDouble CameraLink port 1 FireWire 1394 A 4 USB 2 0 GB Ethernet May 29 2014 Rev 1 3...

Page 127: ...77 80 86 87 91 92 93 99 105 106 110 111 H Halogen lamp 110 112 114 124 HXP 120 15 16 17 19 20 23 24 107 108 112 115 116 119 124 L Lumencor 13 19 20 24 86 107 111 112 124 Lumencor SPECTRA 6 Light Engine 21 124 M Marker 50 53 83 105 P Pannoramic MIDI 7 9 10 11 13 14 15 17 19 20 22 28 30 36 109 112 120 121 Pannoramic SCAN 150 24 Pannoramic Viewer 21 60 71 110 Pco edge 125 Pco edge 4 2 14 79 Preview 2...

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