Data migration from Operetta High Content Imaging System to Columbus Image Data Storage and Analysis System

Transcription

1 CELLULAR IMAGING AND ANALYSIS Data migration from Operetta High Content Imaging System to Columbus Image Data Storage and Analysis System Introduction Images acquired on the Operetta High Content Imaging System are stored as TIF files in the Operetta Database (ODA). The ODA also contains all image-related metadata as well as image analysis sequences and results that have been generated with the Harmony High Content Imaging and Analysis Software. There are two ways to migrate images and the associated metadata from the Harmony software to the Columbus Image Data Storage and Analysis System, either by using the Columbus Transfer function or via the export of images and metadata. Here, we provide detailed step-by-step instructions for both methods. Data migration using the Columbus Transfer function We recommend using the Columbus Transfer function for data migration because it reduces the time needed for image export from the ODA. Please note that you can only use this function if your Columbus system can establish a network connection to the PC running the ODA, which is usually the instrument PC. 1. Start the Harmony software and open the Settings window. In the Harmony Settings window, open the Data Management window.

2 2. In the Data Management window you will find the Columbus Settings and the Columbus Transfer dialogs. Open the Columbus Settings dialog and enter the URL of your Columbus start page. You can copy and paste the URL directly from your browser. By clicking the Test button you can check whether the URL entered is correct. This step only has to be performed the first time, after that the system will remember the URL. 3. Open the Columbus Transfer dialog. Click on Select Data and select the measurements that are to be transferred. All related assay layouts, analysis sequences and image analysis results will be transferred with the measurement. Next, specify an export path and start the export process. After the export is finished click on the Go to Columbus button to be redirected to the start page of your Columbus system. 4. Log into your Columbus System and click on the Import button (orange frame). The Columbus Helper Required dialog will appear if this is the first data management process of your Columbus system session. If you have not yet installed the Columbus Helper follow the instructions to install the Columbus Helper (blue arrow). Otherwise, follow the instructions to download the connection file and connect your already installed Columbus Helper (red arrow). 2/5

3 5. In the following dialog specify the Import Type and the import Source Folder. Choose Operetta REF/TIF as the Import Type. Enter the Source Folder by browsing to the folder that you have specified as the export path in the Harmony software. 6. Next, select the import options such as Import Mode and Screen Name. You do not have to change the default values, but you do have to provide a screen name, which is used to organize your data in the Columbus database. Please refer to the Columbus system Help page for a detailed description of the import options. 7. To start the import click on the green arrow. You can monitor the import process on the Job Status page, which can be reached via a link at the top of the Columbus system page. After the import has finished you may need to click the Refresh tree button on the left to refresh your Screen List. Data migration via image export The method described here can be used in situations where the PC running the ODA and the Columbus system do not share a network connection. Please note that this method is much more time consuming. 1. Start the Harmony software and open the Settings window. In the Harmony Settings window open the Data Management window. 3/5

4 2. In the Data Management window open the Export Data dialog. Specify Columbus Export (Index and Images) as the method for image export. Click on Select Data and select the measurements that are to be transferred. All related assay layouts, analysis sequences and image analysis results will be transferred together with the measurement. Next, specify an export path (e.g. a USB drive) and start the export process. Note that this process can take a long time for large volumes of data. 3. Log into your Columbus System and click on the Import button (orange frame). The Columbus Helper Required dialog will appear if this is the first data management process of your Columbus System session. If you have not yet installed the Columbus Helper follow the instructions to install the Columbus Helper (blue arrow). Otherwise, follow the instructions to download the connection file and connect your already installed Columbus Helper (red arrow). 4. In the following dialog specify the Import Type and the import Source Folder. Choose Operetta IDX/TIF as the Import Type. Specify a Source Folder for the import to the Columbus system (e.g. a USB drive) 5. Next, select the import options such as Import Mode and Screen Name. You do not have to change the default values, but you do have to provide a screen name, which is used to organize your data in the Columbus database. Please refer to the Columbus system Help page for a detailed description of the import options. 4/5

5 6. To start the import click on the green arrow. You can monitor the import process on the Job Status page, which can be reached via a link at the top of the Columbus system page. After the import has finished you may need to click the Refresh tree button on the left to refresh your Screen List. PerkinElmer, Inc. 940 Winter Street Waltham, MA USA P: (800) or (+1) For a complete listing of our global offices, visit Copyright 2012, PerkinElmer, Inc. All rights reserved. PerkinElmer is a registered trademark of PerkinElmer, Inc. All other trademarks are the property of their respective owners. 5/5