3D Module 1.11 User's Guide June 25, 2008
Contents
1. File Settings Window Help si ge Bf JEW OBB SY x EB Teleconsultation Server Local P pload Slides to Teleconsultation Server e Create New TMA Project e Create New IHLab Project r e ao FF FH Ls Ee Fe Ee E emo C L rs fe 3d fe agi fel Ap fe cs fe D Bic fe Fi fe Molnar fe nogyo fe scree fe Sli fe Su HH FH FH Ej Update Tree b Launch a previously saved project by simply double clicking on the name of the 3D project in MIRAX Viewer All saved 3D projects are marked by 3 icons in front of their names June 25 2008 3DHISTECH Ltd 11 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard 3 2 2 Disordered Tab With this step you can remove the slides that you do not want for the 3D image highlight them and delete them one by one using the Delete key on the keyboard or with the FANEN If you drop a slide from the slide set the 3D reconstruction will be distorted when the module reconstructs the 3D object equal slide thicknesses are used in the calculations if a slide is missing from the original slide set the module assumes the remaining neighbors of the slide as adjacent slides i button in the toolbar MIRAX Viewer 3D EJ Fie Settings Window Help SEE o D w nea Teleconsultation Server Local Disordered FO xe slides E 2x2 3D fe Adenoma fe 101 150 fe 151 200 f 2012. There are three options to choose from based on the shape of the tissue section Examples are given to aid the selection of the most appropriate algorithm Once the alignment is done you can select the area of interest using the and the CL buttons Select the Py button Holding down the left heeled oe mouse button Te a box around your area of interest than select it by clicking on the al icon This automatically zooms in the selected region a and clears the remaining area of the slide Flip through the series and check to see the alignment of all slides with this higher magnification If necessary click on the Fine Align button in place of the Align button to make the necessary corrections This procedure can be repeated any number of times until the sections in the stack match perfectly within the area of interest F Tip Perform the alignment procedure sequentially and narrow in on your area of interest gradually with increasing magnification Check the alignment of all slides every time You can see a shadow from the previous slide if the slides are not sufficiently aligned June 25 2008 3DHISTECH Ltd 13 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard b Manual Alignment you can also perform the alignment manually Manual corrections may also be necessary following an automatic alignment when adjacent sections differ significantly in size shape or texture The two adjacent slides the re
3. 250 fe 251 300 fe Normal 001 050 051 100 101 150 ra 151 200 een rr Rearrange the slides as needed click the slide that you want to move and drag it to its correct position in the series June 25 2008 3DHISTECH Ltd 12 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard 3 2 3 Adjust Tab This step aligns the slides and forms a stack so that the corresponding points of adjacent tissue sections are matched and placed directly below each other The alignment is usually a multi step procedure It can be performed automatically or manually This step is necessary since the individual tissue sections within a series are not placed on the slides in the exact same orientation So in order to match their relative position and orientation the subsequent slides need to be moved and or rotated The selected slides for the reconstruction are listed in order on the right hand column The two adjacent slides the relative position of which is currently being aligned are pictured in the middle At the same time there slides are highlighted with colored rims on the right column a Automatic Alignment the software performs an automatic alignment based on the outline and the texture of the tissue sections You can start this by simply clicking on the Align button on the top left The algorithm by which the automatic alignment is performed can be selected by clicking on the Settings button right below the Align button
4. F BE EA E En een Eee 16 Del GALLEN VAD aara E E Eee 17 A NUOPRING ges ee DD ODOC ereen ne en nee nn ee ee ee ere 18 5 3D Module REET CCCs cick cicidsndsnnmrindeiues sedwineisiadininsiketencativieaanbisiae binant dante denciaevamusannaens 19 Sil Die a E FEE EEN EET ETE E surat ede EE EO 19 Bee GUS Va E EE EE E E E 20 Di ZO NOW Tie a e E EE EE 22 EXCUS Deea a E E A E 22 Di OD VIEW Ta ei AAE A EEA E ment aeanis 24 5 5 1 Mask Definition ParameterS ssssnsssssrsnrunrnnrunrnnrnnrnnrnrnrnrnnerurunrnrnrnrnrnrnenrrrnne 24 552 Rendering Paramete S sr p diina eN ENEE E AEEA 25 5 5 3 Advanced Settings for 3D Rendering s sssssssssrssrrsrsnrenrenrenrrnrrnrerererererrrrrenne 26 June 25 2008 3DHISTECH Ltd 2 26 3D Module 1 11 User s Guide Disclaimer Disclaimer Copyright 2001 2008 3DHISTECH Ltd All rights reserved The following patents are pending for 3DHISTECH products WO 2006 030326 P0700409 and 11 826 752 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 associated with use of Product digitalized slides quality of staining quality of Stained slides quality of used method of staining 3DHISTECH Ltd assumes no
5. OR PERFORMANCE OF THIS SOFTWARE Further Information For the latest information on 3DHISTECH products and services please visit http www 3DHISTECH com June 25 2008 3DHISTECH Ltd 3 26 3D Module 1 11 User s Guide Font Types and Symbols Example Abbreviation or term that is explained in the section Terms and Abbreviations page 5 Example Words or characters that appear on the screen These in clude field names screen titles pushbuttons and menu names paths or options Keys on the keyboard For example function keys such as F11 or the Ctri O key combination Example Cross references to other documents AN Warning Indicates that you need an additional module to use the feature or that there are prerequisites for the task i Important Contains an important piece of information or a recom mendation The application will work if you choose not to follow the recommendation but its performance might be less than optimal Tip Contains a suggestion about using the application in some other way or to some interesting purpose June 25 2008 3DHISTECH Ltd Font Types and Symbols 4 26 3D Module 1 11 User s Guide Terms and Abbreviations Terms and Abbreviations 3D Project A set of digitized slides created from consecutive cuts from the specimen 3D Object A virtual reconstruction from the specimen The 3D object is not saved MIRAX 3D
6. digitalized with the MIRAX SCANNER Each digitalized slide consists of an MRXS file plus a folder with the same name as the MRXS file If you have a series of cuts from a given specimen each slide is digitalized Separately gt Digitalized slides can be inspected with MIRAX Viewer You can reconstruct the Specimen as a virtual object using the 3D module Annotations from other modules such as HistoQuant are ignored during 3D reconstruction gt If you have the Teleconsultation module you can upload the slides to a MIRAX Server gt Slides on a MIRAX Server can be shared in a teleconsultation For further information about other modules of MIRAX Viewer see MIRAX Viewer User s Guide 1 2 About MIRAX Slides to be Used in 3D Projects When working with the 3D module of MIRAX Viewer it is important to keep the followings in mind e Calculating rendering and storing 3D objects requires a significant amount of hardware resources e High quality 3D reconstructions which can be rotated and re cut require 40 100 Slides e Naming the digital slides sequentially during scanning will make it easier to keep them in order in MIRAX Viewer and in the 3D module e In order to create a 3D reconstruction that is proportionally accurate do not remove slides from the 3D project even if they do not contain a specimen cut on the relevant part of the slide When the module reconstructs the 3D object equal Slide thicknesses are used i
7. Set zoom factor Defines the size of the images the selected area on in Slide Fit to screen One picture in a Define the size and the number of images displayed on your screen at the same time row Exports the images as an image gallery in an HTML file im Saves the project 5 4 Exclusion Tab Exclusion rT ls gt amp Optons Mask Color JF amp BX Similarity fo ooo Brush Size fo ooo v Optimize 30 June 25 2008 Zoom factor 2 ny 3DHISTECH Ltd 22 26 3D Module 1 11 User s Guide 5 4 Exclusion Tab When this icon is pressed you can move the current select k on the screen Undoes the last step Saves the 3D project Eraser tool to remove the marking that you added with the brush or the filler tools ky P Brush tool to mark an area Filler tool to spread a color over the active area amp Allows filling areas that have the same color in the digi tized slide with the same color in the mask Deletes the mask ad Soom Fagrar Zooms in and out the active image according to the slider setting You can also jse the scroll button of your mouse for zoom ing MaSK COIG Click the active color to change it from the color palette PRA Ry Defines the color range that the filler tool uses aiai i Modifies the size of the brush tool Optimize 3D Makes the reconstruction faster Ju
8. calculates the ren dered object when you open the project Voxel Volumetric pixel Analogous to a pixel representing 2D image data a vox el represents 3D image data it represents a value ina grid in three dimensional space June 25 2008 3DHISTECH Ltd 5 26 3D Module 1 11 User s Guide Keyboard and Mouse Shortcuts in MIRAX Viewer and its Modules Keyboard and Mouse Shortcuts in MIRAX Viewer and its Modules Keyboard Description shortcut Up Moves the slide up Down Moves the slide down Left Moves the slide to the left Right Moves the slide to the right Increases the magnification Decreases the magnification F1 Displays the shortcuts F2 Displays the entire slide in the active window F3 1x magnification F4 2x magnification F5 5x magnification F6 10x magnification F7 20x magnification F8 40x magnification F9 Changes the magnification of the preview screen F11 Turns full screen view on off Ctrl T Turns slide tree on off ESC Returns from full screen mode to normal mode Ctrl M Shows or hides the magnifier window in the top right corner of the screen Ctrl P Shows or hides the slide preview panel Ctrl V Switches between the Fit and Full View modes in the upper preview window on the slide panel e In Fit mode the preview window shows only the digitized Specimen cut e In Full View mode the preview window shows the en
9. f 3DHISTECH 3D Module 1 11 User s Guide June 25 2008 3D Module 1 11 User s Guide Contents POS ERE EET ET EET E E 3 Font TVD 6S and VND OIG aeia Eee eee 4 TERNS aNd ADD EVAO easar n aour nN aT anea NEIEN NENN EON EEIE E a 5 Keyboard and Mouse Shortcuts in MIRAX Viewer and its ModuleS ssssssssssssnnnrnrnnrnrnnrrrrnrnne 6 1 ADOUCLTHNS SD Module ssastsdtecanssanorentontoasuxpeanseascsdieesensantiawese ROER ENER ATORRA nakan 7 LIL 3D iN the MIRAX Product Famil ror ED E E a 7 1 2 About MIRAX Slides to be Used in 3D Projects ccccecccccceceeee sees eee REE eeeeeeeesaaeeesaaaeneas 8 2 Installing the 3D Module for MIRAX VIeWwer ssessessssssrssrrnrrnrsnrrnnrnnrnnerrrrrenrnrnrnrnrnrrrenrar 9 2 1 Requirements for Installing and Using the 3D Module for MIRAX VIeWwer ss ssssssssssa 9 PR PEE USO SETE EE E E E EEA 9 2 3 Installing the Application Bundle ssssssssssssssenssssnsssensssnnssnsnssnsnsensnnenensnnnersenennnns 9 5 Creag a Virtual oD ODJECE LE aa T EE EE A ETENEE EA EE 10 LONE AE REE EET ET tion cracauestanear 10 ER RS ate a VIZ E HEER gars acess T E I 11 Be el otal WiC ao PCO CCU cimecee te E EE totes EEA 11 Ikel OI SOV GC CG FA BE ata ersversterts rae E ee nati EER EEN 12 CROC mo Cal s sere Ce ee re A rr ree rer et ree 13 3 2 4 2D View NaDaadsensccadiessqenasansnenahanssanavensaeddrensqenenensaphunnnrswianeisamsamsacantasaaraterniae 14 Re EXCISION laD aaae EET EET E E ro es SENERE 15 BZ OO VION
10. lative position of which is being corrected are highlighted in the right column and at the same time are shown in the middle with blue and red borders Click on the f icon By holding down the left mouse button you can move the top slide red border relative to the bottom slide blue border until they are perfectly aligned If necessary you can also rotate the top slide relative to the bottom by holding down the right mouse button and moving the mouse 1 MIRAX Viewer 3D EJ Fie Settings Window Help 8 x ER e amp te mesa gt me Teleconsultation Server Local Adjust Automatic Alignment aS aan Controls Transparency settings es Area of Interest z atus TR TE EEN ar HE m m C le i os Settings Segment number 0 m I Draw grid FE FE Red gt 7 fe 051 100 101 150 151 200 fe 201 250 fe 251 300 fe 3d s exe e 3d wu aginak fe Appslides f j CSB f Demo fe ECP 2007 FL fe IBD fe screenshots fe Slides_For_3D Suni fe VertMovie Ba lt prev next gt f ButtonsIcons FS align JPG Win B Module_3D_Us oe MIRAX Viewer e Use the 3 icon to zoom in on your area of interest e Use the an icon to move both slides together position them on the screen e Youcan save the project at any point by clicking on the La icon e In the Transparency Settings panel you can change the degree of the transparency the assigned b
11. lide Thickness Rotation san 17 ST e e ey aS J y S Ad d aj x a jo xpos Ypos Rot gt lin m aoe E J JE Vv Slide distance Y o HE ee Navigation 2 F ag FS ar y E Visible g lt pe I zl CO Ii Sy o fo H i Bo 4 Update Tree Disordered Adjust 2D View lt prev Pan oe MIRAX Viewer 3 2 7 Gallery Tab Allows for generating an image series of virtual cut sections in any given plane from the 3D object The number of slices to be created are to be set before this step June 25 2008 3DHISTECH Ltd 17 26 3D Module 1 11 User s Guide 4 Working with a 3D Object 4 Working with a 3D Object gt Start the project If you have not set up a project follow the instructions in section 3 2 Using 3D Wizard page 11 gt Click the 3D View Tab Make sure that the Advanced Settings checkbox is selected The 3D object is displayed You can manipulate it with setting the parameters numerically and or with the mouse Use the 3 sliders for Rotation in Advanced settings to set the basic view of the object Rotating the 3D e Enter the angle values manually next to the sliders Object e Click into the image area hold down the left mouse button and move the mouse to drag amp rotate the object Moving the 3D Click on the object hold down the right mouse button and Object move the mouse Zooming the 3D Hold down the center mouse button or the scroll wheel Object and move the mouse Ju
12. n the 3D module a wizard helps you in creating a virtual 3D image of the specimen from a series of 2D slides The reconstruction process consists of the following 5 steps e Disordered here you can delete unwanted slides from a series e Adjust aligns the tissue specimens on adjacent slides into a stack e 2D View lets you review save the complete aligned series e Exclusion lets you mask out the areas not to be reconstructed e 3D View visualize move rotate magnify and re cut the 3D object You can move forward and backward between the individual steps of reconstruction using the lt prev and next gt buttons at the bottom right corner The step you are currently on is highlighted with red on the bottom status bar June 25 2008 3DHISTECH Ltd 10 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard 3 2 Using 3D Wizard Place the digitalized series of slides into a folder from which they can be accessed by MIRAX Viewer You will not have to preselect and delete the unwanted slides before launching the 3D application you will be able to do all this within the 3D module in the Disordered step 3 2 1 Starting a 3D Project a Launch MIRAX Viewer and start a new 3D project From the menu select File New 3D In the top toolbar click on the button For using the tree view on the left panel please right click the folder that contains the slides and then select Create new 3D Project see below 7 MIRAX Viewer
13. n the calculations when a slide is missing from the original slide set the module assumes the neighbors of the missing slide as adjacent slides and the proportions of 3D reconstruction will be distorted June 25 2008 3DHISTECH Ltd 8 26 3D Module 1 11 User s Guide 2 Installing the 3D Module for MIRAX Viewer 2 Installing the 3D Module for MIRAX Viewer 2 1 Requirements for Installing and Using the 3D Module for MIRAX Viewer MIRAX 3D is not a standalone application you need MIRAX Viewer to run it Therefore it is installed together with MIRAX Viewer bundled into one executable 2 2 Prerequisites Prerequisites Description MIRAX Viewer version 1 11 Running on Microsoft Windows XP Hardware Minimum Pentium P4 3GHz 1GB RAM Recommended Pentium C2D DualCore 2 GHz 2GB RAM Disk space MIRAX Viewer bundled with the 3D module Minimum 110 MB 2 3 Installing the Application Bundle gt Click on the setup exe file that you received on a DVD or downloaded in a compressed file format zip gt Follow the instructions of the installation wizard June 25 2008 3DHISTECH Ltd 9 26 3D Module 1 11 User s Guide 3 Creating a Virtual 3D Object 3 Creating a Virtual 3D Object 3 1 Overview Scan slides as a series Copy slides into same folder Create 30 project Align slides Select area for 30 object Add annotat ons Define properties of 30 object Hiti Use recut 3D object I
14. nal plane Backgr Color Sets the background color of the display window June 25 2008 3DHISTECH Ltd 25 26 3D Module 1 11 User s Guide 5 5 3D View Tab 5 5 3 Advanced Settings for 3D Rendering pot pos Rot Advanced settings 5 m T 1 M Wisible Slide Thickness Sets the thickness of the virtual sections in um If you want a contiguous 3D object use the thickness of the specimen cuts as the value for Slide Thickness and set the Slide Distance parameter to 0 Slide Distance Sets the distance between the virtual sections in um Rotation Rotate the virtual object with the sliders Visible Allows settings per selection June 25 2008 3DHISTECH Ltd 26 26
15. ne 25 2008 3DHISTECH Ltd 18 26 3D Module 1 11 User s Guide 5 3D Module Reference 5 3D Module Reference 5 1 Disordered Tab Disordered gt A B Displays the entire virtual slide Displays only the used part of the slide where the tissue section is found Deletes the slide from the current project The slide is not deleted from the folder Saves the 3D project under a new name mx June 25 2008 3DHISTECH Ltd 19 26 3D Module 1 11 User s Guide 5 2 Adjust Tab 5 2 Adjust Tab Adjust Automatic Alignment Controls Transparency setings Sa Area of Interest e status 0 0 p ET euda colors Align aii Q f l p E ae E a mn Settings Segmentnumber Orewoid l Es Red Automatically aligns the virtual slides the slides are compared pairwise and the corresponding points of the cuts are matched Align Fine Ali ee ae Before the slides are aligned the button reads Align The button changes to Fine Align for further alignment rounds When this icon is pressed you can move the active slide the up per slide from the displayed slide pair When this icon is pressed you can move the work area that is both slides When this icon is pressed you can zoom in and out by holding down the left mouse button and moving the mouse up and down zoom out and in respectively pg When this icon is pressed you can select an area to na
16. ne 25 2008 3DHISTECH Ltd 23 26 3D Module 1 11 User s Guide 5 5 3D View Tab 5 5 1 Mask Definition Parameters 3D View Mask User mask Iw Resolutio Resolution Treshold Visible User masks Shows or hides the mask 5 5 3D View Tab Resolution Allows you to select one of the predefined resolutions for the reconstructed object Refresh Refreshes the 3D object if the threshold settings were changed Visible Cuts a white plane through the 3D object You can change the Z position for the sectioning plane June 25 2008 3DHISTECH Ltd 24 26 3D Module 1 11 User s Guide 5 5 3D View Tab 5 5 2 Rendering Parameters Rendering Options sS HB i k 4 Mavigation E Background Color Fi z i Advanced E setings I a E Clipping fa dE f 6B ef Za Slide View Sections are displayed as slices Object View Sections are displayed as blocks Transparent View Normal View No transparency used when the sections are stacked and the 3D version of the specimen is reconstructed Show or hides the panel of the mask definition parameter Export the current view as an image embedded in an HTML file i Central view After rotation or zooming returns the 3D object to its ini tial position Clip Creates virtual sections from the 3D object You can define the rotation Z and the angle Y of the sectio
17. order colors and draw a scalable grid to aid manual alignment After completion of the alignment procedure select your area of interest using the and the al buttons and click on Next gt to move to the following step i a i a 3 2 4 2D View Tab June 25 2008 3DHISTECH Ltd 14 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard This step provides an opportunity to review the aligned series The magnification can be adjusted using the sliding scale on the top left To export the selected areas asan im age library please click on M and to save the Project click on 7 MIRAX Viewer ez jo maszkolva ae File Settings Window Help cl ax SF g D amp 155 OBST ew Teleconsultation Server Local 2D View ER Se Fitto screen Export gallery f H A 22 Peers F One picture in a row Save as 3D a fg Adenoma B vu E 7 y 101 150 fe 151 200 fe 201 250 251 300 Normal 001 05 051 10 fe 101 150 fe 151 200 fe 201 250 251 300 w 3d s exe fe 3d wu fe aginak fe Appslides E CSB m e Demo fe ECP 2007 FL w Molnar_Bela fe nogyogy_anyag m e screenshots Slides_For_3D fe Suni Update Tree lt prev next gt 3 2 5 Exclusion Tab This step allows for masking selected areas of each individual slide in the series which should not be present on the virtual 3D objects This feature is most useful when the goal is
18. responsibility for the functionality and fault free condition of your application programs Workflows VBA macros Commander scripts CAUTION For research and education uses only not for use in diagnostic procedures This product has not been approved or cleared as a medical device by the U S Food and Drug Admin istration The data and images obtained or viewed using this product are not intended for clinical or diagnostic use Third Party Disclaimer LIDTIFF TIFF Library and Utilities 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 damage resulting from lost profits interruption of business loss of business information pecuniary loss or similar damage that stems from or is associated with the incorporated part of this Product that is made by Silicon Graphics Inc THE SOFTWARE IS PROVIDED AS IS AND WITHOUT WARRANTY OF ANY 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 ANY THEORY OF LIABILITY ARISING OUT OF OR IN CONNECTION WITH THE USE
19. rrow down eee the scope of the 3D reconstruction When this icon is pressed the selected area of all slide are aligned with each other consecutively First the selection on slide 2 is aligned to the selection on slide 1 then the selection on slide 3 is aligned to the selection on slide 2 and so on When this icon is not pressed the gt and icon are active you can select a primary area and separately the area for the 3D reconstruction June 25 2008 3DHISTECH Ltd 20 26 3D Module 1 11 User s Guide 5 2 Adjust Tab When this icon is pressed you can select the area for the 3D re gt BB When this icon is pressed you can select a larger area F construction besides the primary area that you selected with ane Gradually colors the slide in the front or the slide in the back so that you can check the accuracy of the alignment more easily pacueeColoks Displays the two slides with different colors pray ane Displays a grid over the workspace You can change the grid step with a slider and select the grid col or from a list of color names al Narrows the scope of the 3D reconstruction to the selected area kr area of interest Ep Undoes the last action June 25 2008 3DHISTECH Ltd 21 26 3D Module 1 11 User s Guide 5 3 2D View Tab 2D View Set zoom factor Fitte screen One picture in a row Export gallery See AS el 5 3 2D View Tab
20. tire Slide June 25 2008 3DHISTECH Ltd 6 26 3D Module 1 11 User s Guide 1 About the 3D Module 1 About the 3D Module 3D is an optional module for MIRAX Viewer It allows you to reconstruct tissue sections as virtual three dimensional objects MIRAX 3D requires a MIRAX digital slide set for the virtual reconstruction no other special tools or techniques are needed Compared to the 3D images created by confocal microscopes which are simply summations of the scanned optical slices MIRAX 3D creates virtual 3D objects which you can be moved rotated and virtually re cut This method allows for the investigation of the inner structure of the recomposed object rather than focusing on its surface only i Important The greatest care should be taken when cutting serial tissue sections in order to avoid any deformation of the slices since damaged or distorted sections might interfere with the virtual 3D reconstruction of the original specimen 1 1 3D in the MIRAX Product Family The following figure shows how the 3D module fits into the MIRAX product family as an integral part of MIRAX Viewer 1 C b CEP MIRAX SCAN SCAN file C b CEP 1 Brightfield Flurorescent slides slides TMA lid ER Teleconsultation MIRAX Viewer Measurement IH IH Lab Visualization mel Digitized slides June 25 2008 3DHISTECH Ltd 7 26 3D Module 1 11 User s Guide 1 1 3D in the MIRAX Product Family gt Slides are
21. to reconstruct smaller well circumscribed subsections within a tissue such as a gland or vessel As a result only the unmasked regions from the slides will be rendered as the 3D object Masking out the unnecessary tissue components greatly enhances the 3D out put i lg T e Tip This feature is a great help in cleaning off the artefacts that arise from histological tissue processing June 25 2008 3DHISTECH Ltd 15 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard 58 MIRAX Viewer ez jo maszkolva aS File Settings Window Help o x ER S BH te DER YES Teleconsultation Server Local Exclusion amp slides Tools Options le E Mask Color He 2x2 ko B 2 B Adenoma ASF EB X Optimize 3D fe 101 150 i Hoenn 7 page Zoom factor lt fe 251 300 2 a Normal Ried if tg ae T 001 050 E at com 051 100 101 150 151 200 fe 201 250 fe 251 300 3d s exe fe 3d wu aginak Appslides fe CSB fe Demo fe ECP 2007 fe FL fe Molnar_Bela fe nogyogy_anyag fe screenshots Slides For 3D fe Suni Update Tree The drawing and filling tools for creating the mask can be found under the Tools panel on the left The function of these tool are detailed in section 5 4 3 2 6 3D View Tab The virtual 3D object is created in this step The object can then be freely rotated using the mouse and virtually re cut These virtual cu
22. ts allow for the investigation of the inner structure of the 3D object By changing the Threshold in the left panel the transparency of the object can be modified This enhances the 3D appearance by eliminating the white cuboidal mask Surrounding the object June 25 2008 3DHISTECH Ltd 16 26 3D Module 1 11 User s Guide 3 2 Using 3D Wizard The bottom toolbar allows for the clipping creating virtual cut surfaces of the object tn all three dimensions The advanced settings allow for adjusting the slide thickness and slide distance in order to recreate the di mensions of the original object more faithfully There are also controls on this bottom toolbar for numerically adjusting the spacial position of the 3D object For information on the parameters see section 5 5 3D View Tab on page 23 5 MIRAX Viewer ez jo maszkolva File Settings Window Help T B te DSE FEM Teleconsultation Server Local 3D View k E 2x2 7 3D le Adenoma fe 101 150 Mask User mask Iv Resolution Resolution fe 151 200 fe 201 250 fe 251 300 Normal fe 001 050 fe 051 100 fe 101 150 fe 151 200 fe 201 250 fe 251 300 fe 3d s exe 3d wu aginak Appslides CSB Demo ECP 2007 fe FL f Molnar Bela nogyogy_ anyag fe screenshots fe Slides For 3D White Plane Visible B fe Suni Rendering Options Clip S
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