Report Generator. Installation & Quick User. Guide

Transcription

1 Report Generator Installation & Quick User Guide Introduction This is a short installation & operation manual for the Report Generator. It describes how to install and setup the application. A quick guide will explain the main components of the Report Generator. Installation: First, install the assay software and the SDK s used for the assay software. Instructions for the installation of assay software and the SDK s are described in a separate installation manual. It is also necessary to have the latest version of the Iconoclust software installed. Without the software installed the report generator will not function properly! Please visit After the installation of the assay software and the SDKs, install the Report Generator by double clicking the Report Generator_Setup.exe. A Setup Wizard will appear

2 Now press only Next > Install > Finish. And the Software installation is successfully finished. Operation Manual After the installation the Report Generator starts. After The top window is the console window. It displays log and error information during the process of the software. The lower window is the software s main window. On the splash screen, the software version is displayed. Click on the splash screen to close it

3 Process Single File To process a single image or result TXT (raw signal data) file, choose the corresponding Assay ID from the list below. You can find the Assay ID on your ArrayTube label. The name of the chosen assay will be displayed in the field below the list. Enter an operator name without any special characters. (optional) click on the Single File tab. On the Single File tab it is possible to choose between processing an existing image or text file by clicking the Process Single File Button, or you can take an image from (the array placed in the) reader device

4 Setting up the image acquisition device This steps to configure the image acquisition device in Iconoclust. You only have to do once! Start Iconoclust. In Iconoclust s main window click on the camera button. In the appearing IconoScan window click on the options button In the options click on source and choose the ICCAM File for your reader system (e.g. ATR03.iccam) Press OK and close all windows of the iconoclust application. Taking a picture first, it is important to choose the assay ID according to the array chip s assay. (e.g for Stau PM7 Plus) (See the Arraytubes label assay id) Click the button. In the appearing window enter a valid name for the image file and press Save. Important: Don t use special characters for your image or result text file names! This will result in errors! allowed are : A-Z ; a-z ; 0-9 ; _ ; - ; () - 4 -

5 The image acquisition is now taking place. If the process has successfully finished, you can preview the image. If the image is ok click on Yes in the Image OK? dialog. Else, it will restart the image acquisition. After the successful image acquisition the experiment reports can be generated. It is important to choose the right assay ID before starting the image acquisition. If the AssayID is not correct, you can change it by clicking Change Assay. If you want to generate the experiment reports click on Yes. Process the Image To process the Image taken select the image file that was created by the image acquisition. In case you already have an image you want to process, press the button. The File Dialog will open where you can choose an image (.bmp) or a text file (.txt). Important: Don t use special characters for your image or result text file names! This will result in errors! allowed are : A-Z ; a-z ; 0-9 ; _ ; - ; () - 5 -

6 A Dialog window for the selection of the calibration file will open. Choose the calibration file of your reader system and the used disposable type and press OK. (e.g. ATR03_2.0 for AT1 or AT2_ATR03_2.0 for AT2) Now the Image processing and evaluation of the data is taking place. The process log data is shown in the console window. (This process takes a while, so please be patient) After the process has successfully finished the console windows looks like this. Now press the Tab on the Report Generators main window and press the button to open the folder that contains the result data. Note: For each file a separate folder will be created to prevent overwriting existing files. Enter the Subfolder with the name of the Image / text file. Depending on the Assayplugin used this folder will contain a different number and kind of files

7 Process Multiple Files To process multiple Files press the button. Tab. On the multiple Files tab press the A Directory Dialog will open where you can choose a directory. Navigate to the place where the images and/or Result txt Files are located. If there are images on the folder a dialog for the selection of the calibration file will open. Choose the Calibration file of your Reader System and the used disposable type and press OK. (e.g. ATR03_2.0 for AT1 or AT2_ATR03_2.0 for AT2) For each valid file located in the chosen folder a separate folder is created. (e.g. Filename_bmp / Filename_txt) If you wish to have all files gathered in just one folder click the folder. A Directory Dialog will open to choose the destination Directory. button to collect all data into one Important: The image files on the folder must be taken with the same reader system, because it s only possible to choose one calibration file for Iconoclust! (i.e. ATR03_2.0.iccal) The will open a Directory Dialog where you can choose a directory that contains one or multiple.bmp images. Navigate to the place where the images are located. Then a second Dialog will open asking for the ICPCK file Navigate to the folder that contains the Iconoclust Assay Package for the Images you want to process, and select it. This option is designed to let you process a number of images at once using Iconoclust. The result will be a folder containing the image, the segmentation image and the raw signal data file (.txt) for each image in the chosen folder. Tools The Tools tab contains icons for different options: view console window show Info show installed Iconoclust version show settings window overwrite existing files create PDF for each report Partisan Result (CSV) Converter (s.b.) Search local Database create a log file create a database entry (local DB) show log directory delete log directory - 7 -

8 Partisan Result Converter It is possible to generate Result.TXT files (containing the experiment Raw Signal Data) from a partisan Database export. How To export the experiment data from Partisan (Lims): Open the Project in Partisan where the experiments are placed and click on functions -> export exp results In the following window you only have to change the field DATA COLUMN to Signal or in some cases VALUE2 Press the export button

9 When the process has finished, download the file to your desktop or to a place where you can find it. In the Report Generators main window click on the Tools Menu item and choose Partisan Result Converter (small red icon) A File Dialog will open. In the file dialog, choose the File you have exported from the Partisan DB and click open. If the process has successfully finished an information dialog will appear. After this you can reprocess the results using the Report Generator. See Process Multiple Files. Configure the Application The application offers a configuration window to configure the path s to the plugin-, sdk-, iconoclust- installations and to the calibration files for the devices. The application is configured to the default paths of the installations. This means the application will search for installed assays and SDKs where they re usually installed. However if it is necessary to change a path it can be done by opening the Configuration Window by clicking the Tools menu tab and select The configuration window appears. Here the path to the plugin-, sdk-, iconoclust- installations and to the calibration files for the devices can be configured. Also the Look and Feel (Theme) of the application can be changed there

10 Trouble Shooting Filename conventions : Useable characters : A-Z ; a-z ; 0-9 ; _, -, +, (), {} No or incorrect / implausible results 1 st - check the segmentation image (*.bmp.png) : Good Bad correct assayid was entered - layout as expected - segmentation correct wrong assayid was entered - different layout as expected - segmentation not possible Solution: Please select the assay ID according to your AT / AT2 or Strip Image See AT Label / Strip Bag Good Bad Correct calibration file was selected - in this case arraymate_strip - segmentation correct Wrong calibration file was selected - in this case ArrayMate_AT - segmentation failed Solution: Please select the calibration file according to the device and chip format used in your experiment (see page 6)

11 Default Configuration values of the Application Windows 32bit Plugin Path : C:\Program Files\clondiag\ArrayMate_R_D\Parameter\assays SDK Path : C:\Program Files\clondiag\ArrayMate_R_D\ Calibration File Path : C:\Program Files\Icono\Parameter\Calibration\ Icono Clust Path : C:\Program Files\Icono\ Theme : Windows Windows 64bit Plugin Path : C:\Program Files (x86)\clondiag\arraymate_r_d\parameter\assays SDK Path : C:\Program Files (x86)\clondiag\arraymate_r_d\ Calibration File Path : C:\Program Files (x86)\icono\parameter\calibration\ Icono Clust Path : C:\Program Files (x86)\icono\ Theme : Windows Information Thomas Meyer em@il: Thomas.Meyer@clondiag.com Tel.: