MIRAX DB 1.11 User's Guide July 10, 2008
Contents
1. gt offers Project and User options gives a list of the already scanned slides waiting for exporting into various DataBases by a User of CanScan Right who can assign scanned slides O makes possible to change the password of a logged in User Logging out from MIRAX DB 4 2 Creating a MIRAX DB project FF q Tip If you are using MIRAX DB to store and organize your slides that you want to use in different studies create MIRAX DB Project a separate database for each study Then you can include the same slide in several databases In the CreateDB function the user should write the name of the new Project into the textbox of label Project Name Project Description the short essence of the Project Later on both the Project Name and the Project Description can be modified See in chapter 4 2 1 July 10 2008 3DHISTECH Ltd 22 37 MIRAX DB 1 11 User s Guide 4 2 Creating a MIRAX DB project DB CreateDB od Project Project name Project Nol Project description Project Description Fields User defined fields Field name UserDefined_Field Short text Q UserDefined_Fieldd G Field type Date and time v 1 Log in to MIRAX DB The User who creates the project database will be the Project Administrator How ever you do not need to be an Administrator of the Main Database to create and manage Projects It is recommended that you create projects as a Normal User2. iz os 3DHISTECH MIRAX DB 1 11 User s Guide July 10 2008 MIRAX DB 1 11 User s Guide Contents D C oe hee ee ee ee ee ee ee 4 FORME TY Des GiGi VO S aastasaavcaseantceredsudda vas saanaveulecaccak E 5 MEPIS ANG AO ne VEO ne E E EEN EEE E E A NE T E RED se 6 LA BOE NRA D Erre T EAE EEEE 7 1 1 Overview of MIRAX DB sssssssssssssssssrrnenrrnrnenrnnrnnernrenrrnnrnrnnrenrrnrnrrenrnrnrnenenrererrnrnrnr 7 1 2 Main Database and Project DataBaseS snssssnsrsnnnrnrrnrrrrnrrrrnrrnrrnrnrrrnrnerrrnrnrrrrrnne 8 1 3 MIRAX DB in the MIRAX Product Family ssssssssssssssssssnsssnnssssnssnsnssnsnsensnnnnnsrsesenenns 9 ZIN NMG MIRA X DB arrere AEE A E NS 10 2 1 Installation Requirements sssssssssssnsnssnsnnsnsnsensnsonensensannnssnnnnsnsnssnsnsenennenensenenne 10 2 2 Installing MIRAX DB SOTWarl 6 xicicccecccdeentdondecctccsdeentdeciecstcesierstderdeeeneesieceoinesiawiseuine 10 3 Ma adino MIRAX DB Project USES ma olsen a i AEEA 12 3 1 MIRAX DB User RanKsS sssnssssssssssssssssnsssnnssnsnesnsnnsnsnnonesssnessnneasnsnsnnsesssnennnnnerneue 12 ECFE A SOM esrara E E E E E E OEN 14 3 1 2 Granting and Revoking Administrator Rig tS ss ssssssesssrsnsnsrersnnrnrnsrsrsnernrnens 14 3 1 3 Granting and Revoking Access for Scanned SIIG S cccccceeeeeeeeeeeeeeeeeeeeeeeeseeaaes 14 Ba DEA eh U OP erir are E E AEE EEEE TENA 15 4 Managing a MIRAX DB PRO TETE rreraren iee O SAAREEN 16 4 1 MIRAX DB User Interface
3. mdb Password protected file that contains a MIRAX Project DataBase Annotation A particular detail of a digitized slide Batch Import Creates DataBase rows for a set of slides that will be im ported with their barcodes as IDs Main DataBase A database in MIRAX DB that stores the schema and user information about Project DataBases Main DataBase Administrator The Supervising User of the Main DataBase MIRAX DB A database in MIRAX DB that stores slides and other infor Project mation such as diagnostic images of the slide and the an notations on it Project The Supervising User of a given Project Administrator Model DataBase Schema Slide A MIRAX Slide an interactive digital slide A dynamic interactive image that you can manage Save magnify zoom name stain evaluate complete it with your professional annotation marks and remarks send to a colleague electronically for co operation or advice etc Thumbnail A static preview image of the MIRAX Slide July 10 2008 3DHISTECH Ltd Terms and Abbreviations 6 37 MIRAX DB 1 11 User s Guide 1 About MIRAX DB 1 About MIRAX DB 1 1 Overview of MIRAX DB MIRAX DB allows you to store the slides that you digitized with MIRAX Microscope Scan ners you can save and manage the slides and other data associated with the slides in a customizable database You can also scan slides directly to a MIRAX Project Data
4. 2 Click on button Create New Project fe 3 Define the Database Model MIRAX DB Projects have predefined table structure but you can also add your own fields to them 4 Alternatively you can load predefined project structures or save the set one as a model For more details see in chapter 4 2 3 5 Press on OK 4 2 1 Project Options The Project Options can be changed only by the Administrator or by the Project Adminis trator Here you can add users for the project can change the project name or modify the project description 4 2 1 1 Change Project Name and Description 1 Login to MIRAX DB as an Administrator or as a Project Administrator 2 Open the project that you would like to modify July 10 2008 3DHISTECH Ltd 23 37 MIRAX DB 1 11 User s Guide 4 2 Creating a MIRAX DB project 3 Click on Options icon in the Toolbar gt 4 Inthe dialog box choose Project Options tab 5 Select a Project from the drop down list 6 You can change now the selected Project name and the description After changes press on Save icon 7 When you finished press Close Project name and description BB Project Options Project Options User Options first project w R new name of the project D Description This is a new Project for Mirax DB Added Users Admin Dr Who Privileges Read Read and Write Admin of Project Project users and privilegs 4 2 1 2 Add Remove Use
5. Do not forget that the slides size can be rather big up to few gigabytes Be sure that you have enough space in your hard disk Scanning method July 10 2008 3DHISTECH Ltd 35 37 MIRAX DB 1 11 User s Guide 5 2 Remote Scanning and Access to the MIRAX DB 1 Install MIRAX DB Software on your scanner computer 2 Share the MIRAX folder for Everyone user 3 Start scanning in scan options use Scan to DB option see chapter 4 3 2 4 Create users for the MIRAX DB 5 Create projects 6 Add users for the projects 7 Assign scanned slides for the projects Join to the shared database 1 Install MIRAX DB Software on client computer 2 In the login screen you see a Connect to field Press browse icon just right to this field E Open JEI C t To 7 Look in amp 2 Mirax on 3dhistech_047 Local MIRAX DB S MDB My Recent Mview Password Documents Desktop User name My Documents 59 My Computer gt File name MDB 7 My Network Files of type Ini files 3 In the dialog box choose that MDB ini file which is taking place no the scanner computer shared folder 4 Login to MIRAX DB with your valid User name and Password 5 2 2 Setting up Scheme2 The scanner computer is connecting to a slide storage which ts the MIRAX DB server Setting up the Storage 1 Install MIRAX DB on the slide storage computer 2 Share the MIRAX folder for Everyone user July 10 2008 3
6. sssssssssrsnrsnrsnrsnrrnrsnrnnrnnrnnrnnesnrsnrsrernrrnrnrnrnrnrnenerrrrune 16 4 1 1 Available Projects Descriptions and Filters cccccceceseneeeseeneeeeenneesenenenenanees 16 4 1 2 Project Database and PrevieWw cccccceeecccrsceceesenenneeeeeeeeeeseeeeessnenteesenanetenaaees 18 eE CO INC WW SING C6 iinanasancasganagaaeaake yanagskagsaaeakeuateqssagaweseieuskeqasagiaeaskaluneaaaiauessonn 20 ae Bal 0 8 8 aa nO E ee ene eee ee eee 21 Ae Creag a MIRAX DE POTE EN orden selen ETS TEE TES IEEE SES ER E E EEE 22 AZ cy OCCU ODUN jcccesbanenantcannanceeatoecnesaseranenattecetennnnesnnancens E EEEE EEA 23 4 2 2 Modifying Project Structure sssssssssssrrsrrsrrrrrsrrerrerrerrerrerrerrerrerrerrerrerrerrerrnns 25 4 2 3 Create Project Templates Save and Load MOdel S ccccccccce cece eee ee eeeeeeeeaneeees 26 4 3 Adding and Removing Slides in MIRAX DB Proje ct ccccccce eee eeee eee eee eee eeeeeeeeaneeees 27 4 3 1 Importing Slides to the DataBaSe cece eee eeeeeeeeeee eens eee ee NERE REE RENEE REE 27 4 3 2 Scanning with MIRAX SCAN Directly to DataBase cc ce cccc cee eee eee ee eee eeaneeees 2 4 3 5 Save ANNOtatiONsS If TNE PrOleCl wssisonticentionrrianniadisaansteetnies tetas keno 29 4 3 4 Adding and Deleting Attachments for a SIIdG ccccc cece cece eeeeee eee eeeeeeeeeeeeaaee 30 4 3 5 Removing Slides from DataBasSe cccccccccccccccccccccccccccceeccccecececeseeeeeteunentessaans 3
7. 0 133 08 Fagy Il 2008 02 26 16 25 47 Scanned 0 xaminec 33 08 HE 1 0 133 08 HE I 2008 02 26 16 17 55 Scanned 0 xaminec os _133 08_HE_I_2_ 0 133 08 HE I 2 2008 02 26 16 36 36 Scanned 0 xaminec i WA ad 13308 HE13 0 133 08 HE 13 2008 02 26 16 46 27 Scanned O Examinec t 13308 HE 111 0 133 08 HE II 1 2008 02 26 15 32 06 Scanned 0 xaminec 2 SA E _133 08_HE_II_2_ 0 133 08 HE II 2 2008 02 26 15 44 36 Scanned 0 xaminec i 6 _133 08_HE_II_3_ 0 133 08 HE II 3 2008 02 26 15 52 33 Scanned 0 xaminec es t _133 08_HE_III 0 133 08 HE Il 2008 02 26 17 49 18 Scanned 0 xamine aN a _133 08_HER2_II_ 0 133 08 HER2 Il 2008 02 26 2 18 36 Scanned 0 xamine i 133 08 Ki67 Il 0 133 08 Ki 67 II 2008 02 26 17 05 21 Scanned 0 xaminec _133 08_F_Il_ _133 08_Fagy_ _ _133 08_Fag_Il_ _133 08_p53_ 0 133 08 p53 2008 02 26 2 07 24 Scanned 0 xaminec _ 133 08_PR_IL 2 133 08 PR II 2008 02 26 15 20 38 Scanne 0 xamine lige 4 133 08_HE_ _ _133 08_HE_I_2_ _133 08_HE_L3_ v The following functions can be reached here 1 General tools Humber of available slides able columns Number of selected slides Delete Import slide First slide li Export side Refresh Prewous slide Last slide Show thide available projects Q First slide jump to the first slide in the Project b Previous slide jump to the previous slide in the project c Next slide jump to the next slide i
8. 0 133 08 HE 2 2008 02 26 16 36 36 Scanned 0 Examinec _133 08_HE_I_3 0 133 08 HE 3 2008 02 26 16 46 27 Scanned 0 Examinec _133 08_HE_II_1_ 0 133 08 HE II 1 2008 02 26 15 32 06 Scanned 0 Examinec _133 08_HE_II_2_ 0 133 08 HE Il 2 2008 02 26 15 44 36 Scanned 0 Examinec _133 08_HE_II_3_ 0 133 08 HE II 3 2008 02 26 15 52 33 Scanned 0 Examinec _133 08_HE_III_ 0 133 08 HE Ill 2008 02 26 17 49 18 Scanned 0 Examinec _133 08_HERZ II 0 133 08 HER2 Il 2008 02 26 2 18 36 Scanned 0 Examinec _133 08_Ki 67_II_ 0 133 08 _Ki 67 II 2008 02 26 17 05 21 Scanned 0 Examinec This is the essential part of the software Here you can see one project all data in a ma trix There are three linked with blue letters fields a Slide link If you click on it the slide opens in MIRAX Viewer b Attachment You can add any kind of attachment to a slide like documents pictures etc The number of this shows the number of attached files For more details see in chapter 4 3 4 c Annotation You also can save the snapshot of the annotated area of a slide For details see in chapter 4 3 3 July 10 2008 3DHISTECH Ltd 19 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface 4 Preview Images On the right side the slide s preview image can be seen in a matrix The number of cells in this matrix is changing if the number of rows or columns were changed by using the drop down list above them 4 1 3 List of New Slides Any t
9. 3 Description For every Project you can create a short description for a brief information about the Project You can type the description during the Project creation see in chapter 4 2 Description Field can be modified with the following procedure 1 Click on button Project Option a 2 Select a project from the drop down list 3 Edit the Description Field D 4 When you have done it click on button Save July 10 2008 3DHISTECH Ltd 17 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface 4 Attachment For every Project you can attach files which can help your work These files can include for example scanned patient data radiological images documents or spreadsheets 4 1 2 Project Database and Preview In this part the Scanned Slides and their metadata can be seen gt ped ts g rig Fee Fi Slide link Scan date Rro b BS atus back 4 _133 08_E Cadh_Il_ 0 133 08 E Cadh Il 2008 02 26 17 15 53 Scanned 0 Examined 2 We Y a _133 08_ER_Il_ 0 133 08 ER II 2008 02 26 17 27 13 Scanned 0 xaminec E a _133 08_F_I_ 0 133 08 F I 2008 02 26 16 07 31 Scanne d D xaminec _133 08_F_Il_ 0 133 08 F II 2008 02 26 17 36 15 Scanned 0 xaminec 133 08 Fayl 0 133 08 Faq 2008 02 26 16 51 57 Scanned xamined hu 13308 FRI 199 08 F 13308 Fay ll
10. 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 OR PERFORMANCE OF THIS SOFTWARE Further Information For the latest information on 3DHISTECH products and services please visit HTTP www 3DHISTECH com July 10 2008 3DHISTECH Ltd 4 37 MIRAX DB 1 11 User s Guide Font Types and Symbols Example Abbreviation or term that is explained in section Terms and Abbreviations page 6 Example i 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 Ctr 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 recommen dation The application will work if you choose not to follow the recommendation but its performance might be less than optimal i F i 4 Tip Contains a suggestion about using the application in some other way or to some interesting purpose July 10 2008 3DHISTECH Ltd Font Types and Symbols 5 37 MIRAX DB 1 11 User s Guide Terms and Abbreviations
11. DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Project i Important You are able to rename a scanned slide only if it is still in the list After exporting it is impossible to rename a scanned slide 4 3 3 Save Annotations in the Project Annotated areas snapshot can be archived in slide information storage of MIRAX DB Project It might be very useful if you do not would like to store the whole slide but just a smaller region of it In this way you can save storage space on your computer 1 Open the slide in MIRAX DB a Open the Project in MIRAX DB b Right click on the slide in the preview area and then select Open Slide using MIRAX Viewer 2 Add an annotation to the slide gt 3 Click on button Export Annotation to DB i in Slide Toolbar in MIRAX Viewer 4 Select the annotations that you want to upload with the slide to DataBase 5 Update the slide information in MIRAX DB 6 After update the number of exported annotations can be seen in the Annotation field in the Data Matrix see chapter 4 1 2 Press on the link 7 In the dialog box you will see the annotations name you also can add description for the annotation On the bottom of the dialog box you can see the previews of annotated areas 8 Right click on one of the previews you will see three possibilities in a list July 10 2008 3DHISTECH Ltd 29 37 MIRAX DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Proj
12. Database JER Available Projects EES Wee Name Date Status al TA 102 344 141 This part contains four different functionalities as follows July 10 2008 3DHISTECH Ltd 16 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface 1 Available Projects Available Projects Name Date Status A 132 08 2008 03 27 Examined im 133 08 2006 03 27 Diagnosed 135 08 2008 03 21 Examined i In this part you can see the projects that are available for you any kind of access right have been granted for you You can see the projects name the date when they were created and a special field called Status The Status Field helps you to organize your Projects It can set up four different status as New Examined Diagnosed and Reopened If you create a new project see in chapter 4 2 it s status will be New It will stay in this until all slides have not been opened in the MIRAX Viewer In this case the Project Status will turn to Examined automatically If a new slide is imported into an Examined project it s Status will turn Reopen automatically Of course the users can change the project s status manually using the drop down list on the status field 2 Filters for Available Projects You can use this function to filter your Projects by Name Creation Date or Status Filter by Hame Date from LJ v Date til 2008 j nius 256 Mm
13. Field Type Use For Integer Integer numbers up to 256 characters Date and Time Dates and time type of data in the context of day month year hour minute and second Short Text Textual alphanumerical data up to 256 characters Long Text Textual alphanumerical data up to 256 kilobyte CS Modify Structure Column Name Column Type July 10 2008 3DHISTECH Ltd 25 37 MIRAX DB 1 11 User s Guide 4 2 Creating a MIRAX DB project 1 Open a Project 2 Click on icon Modify Structure 3 Click on icon Add New Field 4 Type the Column Name 5 Define the Column Data type Integer Date and Time Short or Long Text 6 You can repeat it as many times as you need defining New Fields 7 If you would like to remove a field click on the right edge of the row select the row and press on icon Delete v 8 When you have done all you wished please press button OK P 4 2 3 Create Project Templates Save and Load Models MIRAX DB Projects Structure database fields and they properties can be saved into a Model File with mdef extension 1 Save an existing structure as a Model 1 Open a Project 2 On the Toolbar press on Save Current Project as a Model 3 3 Select the folder where you wish to save the mdef file 4 Press Save button Save a model during Create Project 1 On the Create Project form see in chapter 4 2 you can also find a Save Cur rent Project as a Mode
14. as Administrator 2 Select the slide from the list and select the appropriate option from the drop down list by clicking the arrow of a If you want to delete the entire record the DataBase row that now con tains all MIRAX DB data about the slide as well as the slide select Delete Record from Shortcut Menu of mm b If you do not need the slide MRXS file and the corresponding folder in MIRAX DB any more you can save storage space select Delete Slide from Shortcut Menu of R il This way you keep the captured image of the slide but not the original slide If you have stored the slide elsewhere for example in MRXS file and the corresponding folder you can safely select this option 4 3 6 Deleting a MIRAX DB Project 1 Log in to MIRAX DB as Administrator of the project you wish to delete 2 Click Admin Options D in the Toolbar In the dialog box select the Project Options tab 3 Select the Project from the list and then click on R to delete 4 3 7 Saving and Loading a MIRAX DB Project In MIRAX DB there is a possibility to save a whole project included it s slides annota tions attachments etc and move it to another computer Because the imported database can comprise authorized data like patient name social security ID etc all exported project is encrypted and saved by a password 4 3 7 1 Exporting DataBase 1 Open the Project as the Administrator of the Project 2 Click on Export icon in
15. example HistoQuant or IH Lab For information on the platform and the modules see MIRAX Viewer User s Manual e You can save your updates from MIRAX Viewer to the Project DataBase for example if you have just added a new annotation to any slide July 10 2008 3DHISTECH Ltd 9 37 MIRAX DB 1 11 User s Guide 2 Installing MIRAX DB 2 Installing MIRAX DB The program does not require a lot of space for installation or running but the slides do Warning Only qualified personnel may install MIRAX DB and perform the initial Start up procedure 3DHISTECH Service technicians install and configure the application and hand it over to you in operating condition 2 1 Installation Requirements For install MIRAX DB the NET 2 0 or higher framework needs to be run on your com puter You can download it from www microsoft com MIRAX DB runs under Microsoft Windows XP operation system MIRAX DB requires 13 MB free space on your hard disk to be installed 2 2 Installing MIRAX DB Software Please start either the MIRAXDB msi or the setup exe file you have downloaded from www 3dhistech com or you have got on CD 1 The installer starts the MIRAX DB Setup wizard Press Next button 2 The next screen is the Licence Agreement Please read the EULA carefully If you are Agree click on button Next on the lower right corner License Agreement Please take a moment to read the license agreement now If you accept th
16. the Toolbar July 10 2008 3DHISTECH Ltd 31 37 MIRAX DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Project 3 Select the Project from the drop down list to export and then click on Export 4 Save memorize the password generated by MIRAX DB FA Si You will need the password to import the Project to a MIRAX DB set on another machine 4 3 7 2 Importing DataBase i Important The User who imports a project into MIRAX DB will be Administrator of the imported DataBase 1 Log in to MIRAX DB 2 Click Import icon in the Toolbar Q 3 Browse for the mdb file you wish to import enter Project password see in chapter 4 3 7 1 and then click Import The importation time can be rather long depends on the slides size in the Project A progress bar showing the sta tus please be patient July 10 2008 3DHISTECH Ltd 32 37 MIRAX DB 1 11 User s Guide 5 Remote Managing MIRAX DB Projects 5 Remote Managing MIRAX DB Projects MIRAX DB allows you to access nonlocal files you can store your Digitized slides on any computer that you can access through a Microsoft Network MIRAX DB must be installed on the computer from which you want to manage MIRAX DB Projects 5 1 MIRAX DB File structure and the MDB INI file All files included the slides attachments and databases are stored in C Documents and Settings All User Application Data 3DHISTECH MIRAX folder Here you can find the MDB ini file which i
17. the right side labeled Slides Will Be Imported From this latter list the User can also take unwanted slides out by using the button 4 3 2 Scanning with MIRAX SCAN Directly to DataBase Important If the slides have barcodes it is very easy to create DataBase Entries for them using consecutive barcode numbers 1 Install a MIRAX DB Software on the scanner computer For network usage please see chapter 5 2 In the MIRAX Scan Software press on button T Scan Options of MIRAX Scan ner program a window called Scan Options appears in the lower four fifth part of which the user can define the destination of slide scanning If you choose MI RAX DB as slide destination see the label Scanned Slide Destination then you click on button Select the slide digitalizing process gets a start July 10 2008 3DHISTECH Ltd 27 37 MIRAX DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Project D Slides 080619 3 After the end of digitalization login to MIRAX DB 4 Click on Scanned Slides button in the Toolbar for displaying the list of scanned slides The slides can renamed 5 Assign the scanned slides to various projects either one by one or by groups You can also leave some slides in the list or to erase them Assign the selected slides to Selecta Project ow Slide name Barcode Scandate Status Assign to EST 3 mn DELETE LEAVE July 10 2008 3DHISTECH Ltd 28 37 MIRAX
18. 1 4 5 0 Deleting a MIRAX DB POS Cl EA n a a a 31 4 3 7 Saving and Loading a MIRAX DB Project ccc eee eeeeeeeeeeeeee seen ee eeeeeeeeaneeees 31 5 Remote Managing MIRAX DB PlOlCClSwiegectuwietotsewiudestevindeiesuiednstediedusreriegestesiatabteviadewnees 33 5 1 MIRAX DB File structure and the MDB INI fil ccccccccccccc cece eee ee eee eeeeeeeeeeeseeeeeneeeaaes 33 5 1 1 The MDB INI Til Cia casaccnaernncesacanntansprenceuacaustans piuaiaashenntans pieaiansarseiets prensa estas 33 5 2 Remote Scanning and Access to the MIRAX DB ccccceeee cece eee eeeeeeeeeeeeeeeeeenaneeees 35 5 2 1 Setting up Scheme1 MIRAX Scanner computer is the slide storage and the MIRAX July 10 2008 3DHISTECH Ltd 2 37 MIRAX DB 1 11 User s Guide BERGER SEE A S E E A A A E E A E E Eee 35 5 2 2 Setting up Scheme2 The scanner computer is connecting to a slide storage which Ane MIRAX DB SOVET errire A A EA 36 July 10 2008 3DHISTECH Ltd 3 37 MIRAX DB 1 11 User s Guide Disclaimer Disclaimer Copyright O 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 erroneo
19. Base from MIRAX SCAN and you can define your own Database Model Projects Available Projects Filter by Name i Description IHLab project Date from 2008 m jus 23 ml 2008 m jus 23 ESTP f i Row s 1 Row Columnis 1 Column alfa_2UG_001 LE Em O eee a alfa_2UG_008 Search in Em alfa 2ZUG 021 a g a alfa 2UG 026 Filter from Ed2008 05 23 2 39 42 ga au ix to 2008 05 23 8 39 42 Slide name Scan Process J AEE Ir Annotation Scan date EE Attachments ctatus alfa 2UG_001 0 2006 07 21 17 36 21 Scanned 0 alfa 2UG_008 0 2006 08 25 14 20 34 Scanned 0 alfa_2UG_021 0 2006 07 21 17 14 14 Scanned 0 E alfa 2UG_026 0 2006 08 25 13 51 39 Scanned 0 By ate 3 ht feet Feed iy Foe is Sf ae reen Ea k Th mis Shs cc ar MES d 32 sg BE Bo 2 aris alfa_2UG_001 le You can grant access to the Project DataBase for other Users working on the Machine or in your Intranet You can also export the Project DataBase and move it to another machine which is able to run MIRAX DB July 10 2008 3DHISTECH Ltd 7 37 MIRAX DB 1 11 User s Guide 1 2 Main Database and Project DataBases 1 2 Main Database and Project DataBases MIRAX DB consists of several databases all information about slides and annotations are stored in so called Project D
20. DHISTECH Ltd 36 37 MIRAX DB 1 11 User s Guide 5 2 Remote Scanning and Access to the MIRAX DB 3 Create users for the MIRAX DB 4 Create projects 5 Add users for the projects Setting up the Scanner computer 1 Install MIRAX DB on the slide storage computer 2 Start MIRAX DB Software 3 In the login screen you see a Connect to field Press browse icon just right to this field 4 In the dialog box choose that MDB ini file which is taking place no the scanner computer shared folder 5 Logout from MIRAX DB 6 Start scanning in scan options use Scan to DB option see in chapter 4 3 2 Join to the shared database 5 Install MIRAX DB Software on client computer 6 In the login screen you see a Connect to field Press browse icon just right to this field preci fe VD Look in 52 Mirax on 3dhistech_047 P ga i gt a Local v User name N Emrax DB 19 gt MDB My Recent Mview Password Documents g B Desktop My Computer File name MDB ed 7 My Network Files of type Ini files 7 Inthe dialog box choose that MDB ini file which is taking place no the server computer shared folder 8 Login to MIRAX DB with your valid User name and Password July 10 2008 3DHISTECH Ltd 37 37
21. as Administrator User 2 Click Admin Options amp and then select the User Options tab 3 Select the user from the list and move between the list of Regular and Administra P and 9 buttons 3 1 3 Granting and Revoking Access for Scanned Slides tor Users as needed with the 1 Log in to MIRAX DB as the Administrator User July 10 2008 3DHISTECH Ltd 14 37 MIRAX DB 1 11 User s Guide 3 1 MIRAX DB User Ranks 2 Click Admin Options and then select the User Options tab 3 Select a user from the list of users and use the Can scan check box for grant or revoke the access that the user can assign scanned slides for any project 3 2 Deleting a User AN Warning To prevent situations in which data cannot be used from a database each MIRAX DB Project must have at least one User Therefore you cannot delete the last User associated with a database 1 Log in to MIRAX DB as the Administrator User 2 Click Admin Options amp and then select the User Options tab 3 Select the User from the list and then click on button RI to delete July 10 2008 3DHISTECH Ltd 15 37 MIRAX DB 1 11 User s Guide 4 Managing a MIRAX DB Project 4 Managing a MIRAX DB Project 4 1 MIRAX DB User Interface After logging in the software you will see the following graphical user interface It con tains four different fields EJ MIRAX Database JER About 4 1 1 Available Projects Descriptions and Filters EJ MIRAX
22. ataBases The Model and the User Data of the Project DataBases are stored in the Main Database y Tip If you are using MIRAX DB to store and organize your slides that you want to use in different studies create a MIRAX DB Project a separate database for each study In this case you will be able to use the same slide in several projects MIRAS DB Man DEB Project A Project D Project B July 10 2008 3DHISTECH Ltd 8 37 MIRAX DB 1 11 User s Guide 1 2 Main Database and Project DataBases 1 3 MIRAX DB in the MIRAX Product Family MIRAX products wonderfully support various tasks in a research pathologist s workflow The following figure shows the MIRAX Product Family and how the MIRAX DB cooperates with other MIRAX products 1 MIRA MIRA SCAN 1 Brightfield LAA slides slides 4 Flurorescent slides MIRAR Viewer Measurement Visualization I SI Digitized slides Teleconsultation e You digitize slides which can be also tissue microarrays or slides stained with fluorescent probes with a MIRAX microscope for example with MIRAX SCAN For information on the microscope see MIRAX SCAN User s Manual e You scan slides directly to a MIRAX DB Project DataBase e You view the virtual slides in MIRAX Viewer In the basic application you can inspect the slides and you can record annotations on them marking their most interesting areas MIRAX Viewer is a platform for several applications for
23. e terms below click Agree then Next Otherwise click Cancel General Terms and Conditions of End User License Agreement of the License for MIRAX DB By downloading or installing the software MIRAX DB the Softvrare the Licensee accepts you accept the following terms and conditions You agree to be bound by the terms and conditions of this End User License Agreement EULA by installing copying or otherwise using the Software If you do not agree with this agreement do not install copy or use the software click on Do not accept and you may return it to your place of purchase for a full zj C Do Not Agree Agree Cancel lt Back July 10 2008 3DHISTECH Ltd 10 37 MIRAX DB 1 11 User s Guide 2 2 Installing MIRAX DB Software 3 You can define an alternative path by using the button Browse or accept the default installation path for MIRAX DB After you set it up please press Next ig MIRAX DB Select Installation Folder 5 Please wait while for the installation process is done When it is finished press Close fe MIRAX DB July 10 2008 3DHISTECH Ltd 11 37 MIRAX DB 1 11 User s Guide 3 Managing MIRAX DB Project Users 3 Managing MIRAX DB Project Users MIRAX DB is a multi user software It means that e on the one hand several users with different rights are allowed to work in a given MIRAX DB project e on the other hand each user s right can be diffe
24. ect MIRAX DB Bookmarks of MiraxStide1 OR QOJ of 2 Filter from Caption Description Captionasd3e Caira i Rowls 3 Rows gt Column s 3 Columns z Captionasd3e Open bookmark in Mirax Viewer Show bookmark thumbnail Copy bookmark thumbnail to clipboard a Open bookmark in MIRAX Viewer The slide will open in the MIRAX Viewer centered with the annotated area b Show bookmark thumbnail The annotation s snapshot will open in your de fault image viewer like Microsoft Image Viewer IrfanView ACDSee etc c Copy bookmark thumbnail to clipboard Will copy the annotation s snapshot to clipboard 4 3 4 Adding and Deleting Attachments for a slide 1 2 3 Open a Project In the Data Matrix select a slide Press on Attachment field In the dialog box press on Add Attachment button Choose a file you would like to attach for the slide Press Open button The attached file name will be seen in the table If you click on it will opened by it s default application You also can add a description for the attachment if you press on the description field If you would like to delete the attachment s select it or them on the left side of the table and press Delete Attachments button July 10 2008 3DHISTECH Ltd 30 37 MIRAX DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Project 4 3 5 Removing Slides from DataBase 1 Open the Project
25. ime when a user adds a slide to a Project the slide gets the state New and will be part of the Root Structure Field s List of the above MIRAX DB User Interface Window When the User wants to open a slide firstly always the Project which contains the searched slide will be opened up then the chosen slide opens up automatically in MIRAX Viewer application july 10 2008 3DHISTECH Ltd 20 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface In this List of the MIRAX DB User Interface Window Users can find all slides grouped Project by Project already added to any Project If the State of an opened slide changes either to Examined or to Closed it will be auto matically taken out of the Root Structure Field s List till anybody changes its Status to ei ther New or Reopened 4 1 4 Toolbar In the Toolbar of the MIRAX DB User Interface window are placed the operational but tons and icons of e the Project in use e the logged in User and e the already scanned in slides Functions of the Toolbar s buttons are as follows B opens the Project that the User has chosen from the list Available Project A closes the Project in use E creates a new Project F exports a Project July 10 2008 3DHISTECH Ltd 21 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface Q imports an exported Project saves the model of the opened Project s Structure Model gt modifies the opened Project s Structure
26. l icon Use it after you finished the new project definition 2 Load a Model Press on Create New Project icon Press on Load Model icon Select the mdef file which you wish to use KR W N e Press Open button July 10 2008 3DHISTECH Ltd 26 37 MIRAX DB 1 11 User s Guide 4 3 Adding and Removing Slides in MIRAX DB Project 4 3 Adding and Removing Slides in MIRAX DB Project 4 3 1 Importing Slides to the DataBase 1 After opening the Project the user can start the slide import by clicking on button Im port Slide r DB Import Slides HJE Browse Slides Scanner FT MiraxSlide1 3 53 Slides MiraxSlide12 gt 080606 MiraxSlide2 2D MiraxSlide3 CQ 080611 MiraxSlided 080612 2008041 Slides will be imported Status SlideN ame New E Slides O80606 MiraxSlidel 2 E Slides 080606 MiraxSlide2 New New E Slides O80606 MiraxSlide3 r 4 tmp 1g Bz DVD RW Drive son tsclient S 83 My Network Places 4 My Documen ts Caillebere Number of slides will be imported into new records 3 Number of slides will be imported into existing records 0 gt Number of slides wont be imported because of conflicts 0 Q 2 On the dialog box select a folder where your slides are taking place The slides list will be seen right to the file tree view 3 Choose the slides to be imported adding them by using the button to the list of slides seen on
27. n the project Q Last slide jump to the last slide in the project e Delete Delete the whole record or the slide See in chapter 4 3 5 July 10 2008 3DHISTECH Ltd 18 37 MIRAX DB 1 11 User s Guide 4 1 MIRAX DB User Interface f Export slide Exporting the selected slide g Import slide Importing the selected slide See in chapter 4 3 1 h Refresh Refreshing the screen some changes are visible after refresh only i Visible columns Show hide fields columns in the project data matrix j Show hide available project Hiding or makes visible the Available Projects part of the screen see chapter 4 1 1 2 Search and Filter Search Q A D Q Search in Filter from D x Al to E x You can search or filtering the data by this function You can search for any character in the marked fields search in check boxes 3 Data matrix e Annotation Slide link Scan date ara Attachments Erocess gt _133 08_E Cadh_Il_ 0 133 08 E Cadh Il 2008 02 26 17 15 53 Scanned 0 Examined _133 08_ER_Il_ 0 133 08 ER II 2008 02 26 17 27 13 Scanned 0 Examinec _133 08_F_I_ 0 133 08 F 2008 02 26 16 07 31 Scanned 0 Examinec _133 08_F_Il_ 0 133 08 F Il 2008 02 26 17 36 15 Scanned 0 Examinec _133 08_Fagy_ _ 0 133 08 Fagy 2008 02 26 16 51 57 Scanned 0 Examined 1133 08 Faw I O 133 08 Fagy Il 2008 02 26 16 25 47 Scanned 0 Examinec _133 08_HE_I_ 0 133 08 HE 2008 02 26 16 17 55 Scanned 0 Examinec _133 08_HE_I_2
28. path of that MIRAX folder which is containing the MiraxDB folder and it s all sub folder SCANFOLDER The path where the MIRAX SCAN software puts the slides e SCANDB The path of that MainDB mdb which is registering the scanned slides 2 CONNECTION HISTORY This part is contains the used connection paths e LASTUSED the last successfully used MIRAX DB e FOLDERCOUNT how many successful connection you had FOLDERO FOLDER The paths of successful connections oF id Tip You can copy the whole MIRAX folder in another place in your computer as well So if you do not have enough space in the drive C just copy the whole folder to another hard disk drive and log in there July 10 2008 3DHISTECH Ltd 34 37 MIRAX DB 1 11 User s Guide 5 2 Remote Scanning and Access to the MIRAX DB 5 2 Remote Scanning and Access to the MIRAX DB If you would like to use MIRAX DB as a network database you can follow two different scheme Scheme 1 The scanner computer is the slide Scheme 2 The scanner computer is connecting to a slide storage which is the MIRAX DB server storage and the MIRAX DB server Warning If you would like to use MIRAX DB as network database you have to share the MIRAX folder C Documents and Settings All User Application Data 3DHISTECH MIRAX for Everyone user in Windows 5 2 1 Setting up Schemel MIRAX Scanner computer is the slide storage and the MIRAX DB Server Warning
29. r in various MIRAX DB projects 3 1 MIRAX DB User Ranks There are two levels of user rank that can be defined in MIRAX DB The first level be longs to the MIRAX Main DB while the second level belongs to the actual Projects i Important The Administrator User has a default user name and password Admin and Admin You are supposed to change the password after you first logged into the MIRAX DB as Administrator User The following rights are accepted as global settings in a MIRAX DB environment User Ranks in MIRAX MAIN DB Environment Kind of User Access Rights Operating Rights Tasks Main DB Ad Has full active ac e Restores MIRAX DB in case of a major ministrator cess database crash e Adds and removes Ordinary Users e Creates and controls projects e Has full access for all projects e Assigns scanned slides for projects e Modifies the Ordinary User s access rights Can scan e Can create projects and scans e Can assign scanned slides for projects Normal User if Administrator User grants this right Cannot scan e Can create projects but cannot scan July 10 2008 3DHISTECH Ltd 12 37 MIRAX DB 1 11 User s Guide 3 1 MIRAX DB User Ranks For more details see in chapter 3 1 1 The following so called project specified access rights can differ for each User in ev ery single project of the MIRAX DB environment User Ranks in MIRAX DB Project Environment Kind of User Acce
30. r to a Project Changing Privileges 1 Login to MIRAX DB as an Administrator or as a Project Administrator 2 Open the project that you would like to modify 3 Click on Options icon in the Toolbar gt 4 Inthe dialog box choose Project Options tab 5 Select a Project from the drop down list 6 Select a user you would like to add the project from the left column 7 Press on Add icon 7 Now the user moved to the Added User column 8 Set the privilege of the user Admin of Project Read and Write or Read see in chapter 3 1 July 10 2008 3DHISTECH Ltd 24 37 MIRAX DB 1 11 User s Guide 4 2 Creating a MIRAX DB project 9 If you would like you can remove a user from the project select an added user and press on Remove icon 10 You can modify the already added users privileges as well 11 When you finished press close 4 2 2 Modifying Project Structure MIRAX DB Projects structure DataBase fields and their properties can be modified Users can add or remove fields columns from the DataBase structure In MIRAX DB there are obligate fields which are defined by the Software These fields cannot be deleted but you can make them invisible using View menu Obligate fields are as follows slide ID slide Name Barcode Annotation Slide link Scan date Scan status Thumb nail path Attachments Process status Users can define additional database fields columns according to their needs Data
31. s initializing where are the MIRAX DB working files databas es Slides etc In this folder s sub folders containing the slides snapshots database files and all attached documents As it was mentioned in chapter 1 2 MIRAX DB Software has a hierarchical database structure All databases has mdb extension The ultimate level is the MainDB This database storing the users project names and user rights and the scanned slides The ProjectDBs can be numerous are connecting to MainDB These databases contain ing the slides the attachments and all metadata of the slides 5 1 1 The MDB INI file The MDB ini file storing the MIRAX DB Software work folders path When you start work ing the software reads the working folders path from here The default working MIRAX DB is always the last time used That is while if you would like to scan to remote computer you need to install the MIRAX DB on your scanner com puter and even on the remote computer and you have to log in to the remote computer see in chapter 5 2 After the log in was success your will scan to the remote computer The MDB ini can be changed manually as well AN Warning Be carefully about the right syntax during the edit The MDB ini file contains two main part July 10 2008 3DHISTECH Ltd 33 37 MIRAX DB 1 11 User s Guide 5 1 MIRAX DB File structure and the MDB INI file 1 GENERAL this part contains the MIRAX folder path as MIRAXFOLDER The
32. ss Rights Operating Rights Tasks Project Administrator Admin Can modify Project DB also the MIRAX Main DB structure Administrator Can read and write stored slides Can add attachments to both a project and a slide Can add users for the project User Read and Write Can read write and add attachments to projects and slides but cannot add users to the project Read Only Can read data including slides of the given projects in Read Only Mode i Important This DataBase Model allows to create a User who can scan but does not belong to any project This user can be typically a laboratory assis tant who scans slides but needs no access for example to patients data July 10 2008 3DHISTECH Ltd 13 37 MIRAX DB 1 11 User s Guide 3 1 MIRAX DB User Ranks 3 1 1 Creating a User ad Project Options Project Options User Options Add New User Password Username Confirm Password C Can assigne scanned slides Manage Users Users Admins Username i Usemame Nagy P ter Admin Zalatnai Attila Schonl ber Julia Diczhazi Csaba Sapi Zoltan P pay Judit Turanyi Eszter 1 Log in to MIRAX DB as Administrator User 2 Click Admin Options gt in Toolbar see in chapter 4 1 4 and then select the User Options tab 3 Enter the user name and assign a password to the User and then click Add 3 1 2 Granting and Revoking Administrator Rights 1 Log in to MIRAX DB
33. us 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 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 Administration 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
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