Suite User's Guide Version 1.3 built with precisionware

Transcription

1 Suite User's Guide Version 1.3 built with precisionware

2 Legal Notices Revision 1.3 of the User s Guide for softworx Suite. Part number Rev C Applied Precision, Inc. All rights reserved. No part of this manual may be reproduced, transmitted, stored in a retrieval system, or translated into any language in any form by any means without the written permission of Applied Precision, Inc. Information in this document is subject to change without notice. Applied Precision and softworx are registered trademarks of Applied Precision, Inc. Apple Mac, QuickTime, MATLAB, Microsoft Windows, CentOS, and all other registered names and trademarks referred to in this manual are the property of their respective companies. If you have questions about softworx Suite, first refer to this manual or consult the online Help system. If you don t find the information you need, contact us by using the Customer Service Hotline. Customer Service Hotline Phone: Applied Precision, Inc th Ave. NW Issaquah, WA (425) FAX: (425) Other Manuals Bitplane 5.0 Operating Instructions Manual. (To display this manual, open the Imaris_1_9.pdf file in the./docs directory on the CD.) softworx Explorer 1.2 User's Guide (Access this manual from the Start menu)

3 i Contents Customer Service Hotline...2 Other Manuals...2 Preface 1 About This Manual...1 Conventions...1 Lists...1 Notes, Warnings, and Cautions...2 Typographical Conventions...2 Contacting Applied Precision, Inc....3 Customer Service Hotline...3 Corporate Offices...3 Introduction 5 What is softworx Suite?...5 The Browser...6 Batch Processing...6 Deconvolution Tools...6 The Viewer...7 3D Visualization and Analysis...8 Advanced Option...9 Requirements...9 Other Requirements...9 Installing and Licensing...10 Installing...10 Licensing Imaris...10 Licensing softworx Suite...12 Setting Memory Allocation...15 Using the softworx Browser 17 About the Browser Window...18 Open softworx Suite...19 Open a File...19 Preview Files...23 Display Images in Thumbnail View...23 Display Image Previews...24 Adjust Brightness of Preview Images...25 Show or Hide Channels in Preview Images...25 Scroll Through Time Points...26 Scroll Through Z Sections or Time Points...27 Play Animations...27 Define Defaults for Thumbnail Images...29 Image Display Scaling...30 Deconvolve Image Data...32 Add Lens Information Rev C /1008

4 ii Contents Use FTP...39 About FTP and Secure FTP...39 Connect To Previously Configured FTP Sites...39 Connect To a New FTP Site...40 View Files on FTP Sites...41 Browse To a File on an FTP Site...42 Manage Files and Folders on an FTP Site...42 Transfer Files or Folders From an FTP site...42 Transfer Files or Folders to a Network Drive...45 Edit an FTP Site...45 Disconnect From a Site...46 Manage File Systems...47 Sort Files...47 Add an FTP Folder to the Favorites List...47 Copy, Delete, or Rename Files or Folders...48 View File Properties...50 Send Files to Other Applications...51 Send a File to an Application...52 Create and Use a Favorites Folder...53 Connect to a softworx DMS Database...54 Connecting to a New Database Site...54 Change Database View...55 Create New Project Folder...55 Create New Dataset Folder...55 Upload Data log files...57 Set up for Log Files Log Files to Applied Precision...59 Run Batch Jobs...59 Create Tasks and Task Chains...60 Edit Tasks and Task Chains...62 Customize Actions...64 Customize the Task Menu...66 Run a Job...67 Set Preferences...73 Index Applied Precision, Inc.

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7 1 Preface About This Manual This manual describes softworx Suite and shows how to use the softworx Browser. For instructions that show how to use softworx viewer, see the softworx Explorer 1.2 User's Guide. Conventions Lists Before you start using this guide, it is important to understand the terms and typographical conventions used in the documentation. 1 Numbered items are sequential steps Indented bullets indicate options in procedures. Bullets indicate items in a list or single step procedures Rev C /1008

8 2 softworx Suite User's Guide Notes, Warnings, and Cautions Note indicates information about the previous paragraph or step in a procedure. CAUTION Indicates important information regarding potential damage to equipment or software or loss of data. Tip indicates helpful advice. Typographical Conventions The following types of formatting within the text identify special information: Formatting convention Triangular Bullet( ) Boldface Italics CAPITALS Uniform width font Initial Capitals KEY+KEY Type of Information Step-by-step procedures. You can follow these instructions to complete a specific task. Items you must select, such as menu options, command buttons, or items in a list. Used to emphasize the importance of a point or for variable expressions such as parameters. Names of keys on the keyboard. For example, SHIFT, CTRL, or ALT. Indicates text to enter on a command line or in the GUI. Indicate the names of windows, dialog boxes and tabs. Key combinations for which the user must press and hold down one key and then press another, for example, CTRL+P, or ALT+F Applied Precision, Inc.

9 Preface 3 Contacting Applied Precision, Inc. Customer Service Hotline Corporate Office If you have questions about softworx Suite, first refer to this manual, the softworx Explorer User's Guide, or the online Help system. If you do not find the information you need, use the following information to contact us. Phone: servicehotline@api.com Hours: 8:00AM - 5:00PM, Pacific Time, Monday - Friday Applied Precision, Inc th Avenue NW Issaquah, WA USA Phone: (425) Fax: (425) Internet Address: Rev C /1008

10 4 softworx Suite User's Guide 2008 Applied Precision, Inc.

11 5 C HAPTER 1 Introduction This chapter introduces softworx Suite for Windows. What is softworx Suite? softworx Suite provides sophisticated multi-dimensional data for visualization, analysis, image restoration, image correction and image viewing management, all within an easy-to-use streamlined browser interface that's Window's based. The suite of tools includes a browser, a viewer, and 3D visualization and analysis tools Rev C /1008

12 6 softworx Suite User s Guide The Browser From the browser window, you can access files on your own computer or across networks through FTP or secure FTP connections, as well as database connections. The browser displays interactive image previews and file metadata. Files in the browser window can be sent to off-the-shelf tools such as Adobe Photoshop. Files can also be batch processed or sent to the other softworx Suite components. Batch Processing From the browser window, you can set up jobs for batch processing of image data. Tasks are defined and applied to files to create jobs. Each job can include any of the tasks supported by the browser and different types of tasks can be combined into a single job. Deconvolution Tools You can process images on a Windows desktop with the industry acclaimed Constrained Iterative 3D Image Restoration and Image Correction tool, a quantitatively validated deconvolution solution generating the most accurate measure of sample fluorescence available. Comparison of an unprocessed image (left) and a deconvolved image (right) 2008 Applied Precision, Inc.

13 Chapter 1 Introduction 7 The Viewer The softworx viewer allows you to view individual channels in a variety of colors, adjust image brightness and contrast, perform 5D measurements, and play animations. The softworx Suite Viewer You can display scale bars on the images, copy them into other applications, print them, and save the image pixel data as Photoshop, JPEG, MPEG, or QuickTime files. For complete instructions on using the softworx Viewer, see the softworx Explorer User s Guide Rev C /1008

14 8 softworx Suite User s Guide 3D Visualization and Analysis softworx Suite provides the most advanced visualization and analysis package available on a Windows-based platform. Surface rendering techniques enhance 3D visualization 3D Image Visualization and Analysis tools powered by BitPlane include: Real-time display with slice, multi-pane sectioning, and multi-processing standard shadow projection. Image processing with baseline correction, noise removal, 3D image rotation, emission attenuation, and cross-talk correction. 3D Visualization with real-time 3D and high-resolution visualization, maximum intensity projection, arbitrary lighting and shadowing, and an animation editor producing QuickTime and AVI output. Measurement tools with Free points, Ortho Slice Points and iso-surface points, intensity measurements, intensity thresholding segmentation, and manual object segmentation. Image output and management using standard.tif file format, QuickTime and AVI, and data exchange with image data basing. For instructions on how to use the 3D Image Visualization and Analysis tools, see the Bitplane 5.0 Operating Instructions Manual. (To display this manual, open the Imaris_1_9.pdf file in the./docs directory on the CD.) 2008 Applied Precision, Inc.

15 Chapter 1 Introduction 9 Advanced Option The Advanced Option for the 3D visualization and analysis package includes a complete colocalization analysis application and 5D particle tracking functionality, all seamlessly integrated into the package. For instructions that show how to use the Advanced tools, open the Imaris_1_9.pdf file in the./docs directory. Requirements Before you attempt to install softworx Suite, make sure that your system meets or exceeds the following requirements. SoftWoRx Suite System Requirements Operating System CPU Graphics Card RAM Free Hard Disk space Network Microsoft Windows XP(SP2) 2.8+ Ghz Processor 32 MB Minimum NVidia chipset combatable 1 GB Minimum (2 GB for best performance. Win64 systems support > 2GB) 300 MB required for installation Ethernet Card Other Requirements To play QuickTime animations, you must first install the QuickTime viewer (available online at Rev C /1008

16 10 softworx Suite User s Guide Installing and Licensing Installing You will need to install and license softworx Suite on your computer before you can use it. First, follow the instructions in the Installing section to install the software on your computer. Then follow the instructions in the Licensing section to obtain and install a license. To adjust the size of the memory buffer, follow the instructions in Setting Memory Allocation (on Page 15). To install softworx Suite: 1 Place the CD in the CDROM drive of the computer. (If AutoRun is not enabled, double click the instal_sws.exe file in the Windows directory of the CD.) 2 Follow the instructions provided in the installation wizard. 3 To install Imaris, go to the windows folder on the CD and find the Imaris 5_0_3 file. CAUTION If you are upgrading softworx Suite, be sure you have a licence for Imaris 5_0_3 before you install it. Note If you accidentally install the new version of Imaris or install a trial version and do not have a license, you can uninstall it and install the previous version (available on the CD, or downloadable from the web). Licensing Imaris You can license Imaris online or offline. If you choose to license it offline, you will need to use another computer with access to the Internet. To license Imaris (online or offline), you will need the Imaris Order I.D. number printed on the inside of the softworx Suite CD cover. To license Imaris: 1 Start the Imaris software on the computer on which you want to install the license. When the following dialog box appears, click Yes Applied Precision, Inc.

17 Chapter 1 Introduction 11 2 Follow the online instructions to license the software. For additional instructions, see the License Installation Guide section in the Bitplane 5.0 Operating Instructions Manual. (To display this manual, open the Imaris_1_9.pdf file in the./docs directory on the CD.) Rev C /1008

18 12 softworx Suite User s Guide Licensing softworx Suite Before you can use softworx Suite, you will need to obtain and install a license on your computer. A license is a personalized file that must reside on the computer for the software to run. There are two methods of registering: over the Internet or over the phone. The easiest and fastest way to register is over the Internet. To license your product, you will need the Certificate number that was affixed to the CD case. It is labeled softworx Suite Certificate: XXXXXXXXXXXXX. You will use this number later in the registration process. Important You must use the computer on which you are installing softworx Suite to register with Applied Precision. If you use another computer to register, the license will not work. (The license key only works for the computer that is used to register.) If the computer uses a wireless LAN card, the card must be installed before you run the Register Product wizard. Failing to do so will prevent the application from working when only the LAN card is installed. To register for your softworx Suite license: 1 From the Start menu, choose All Programs Applied Precision softworx Suite softworx Suite to start softworx Suite. The Manage Applied Precision Licenses window opens. 2 Click Run Purchase and Registration Wizard to open the wizard that guides you through the registration process. Then choose to register by Internet or by phone. If you choose to register by Internet, click Next and continue to Step 3. If you choose to register by phone, call from 8:30 to 5:00 PST. Be ready to provide the System ID displayed on the Register Product dialog. After you have received your license, copy it to the directory in which you installed softworx Suite. This completes the registration process using the phone Applied Precision, Inc.

19 Chapter 1 Introduction 13 3 In the Register Product dialog box, enter your contact information. Required information includes: Licensee Name, , and the Certificate Number included on your CD Rev C /1008

20 14 softworx Suite User s Guide 4 Click Next to install the license. 5 Review the displayed feedback information. One or more s will be sent to you with the same information. If you feel that the feedback contains erroneous information, please contact Applied Precision either by phone or Applied Precision, Inc.

21 Chapter 1 Introduction 15 Setting Memory Allocation The performance of softworx Suite is directly related to the amount of memory it has at its disposal. You can adjust this memory buffer. To configure softworx Suite 1 From the main menu, choose Edit Preferences. The Preferences dialog box is displayed. 2 Slide the Buffer Size slider under Memory Settings to the right to increase the size of the memory buffer or to the left to decrease it. The best performance can be gained by setting the value to 256 Mb less than your total available physical memory. For example: if your computer has 1Gb of memory, setting the memory buffer size to a value around 768 Mb will provide the best performance. (The new memory buffer size will be used the next time that you start softworx Suite.) 3 Click Save to save the settings and close the dialog box Rev C /1008

22 16 softworx Suite User s Guide 2008 Applied Precision, Inc.

23 17 C HAPTER 2 Using the softworx Browser The softworx Browser provides a streamlined interface for asset management. From the browser window, you can view and manage files, access FTP sites, access databases, and perform batch processing. You can preview images and text files on your workstation to view interactive image previews and file metadata. You can also access files locally or across networks through FTP or secure FTP connections. Local files can be sent to other softworx tools such as the Deconvolution processing tool, the Viewer, softworx 3D Visualization tools, or to off-the-shelf tools such as Adobe Photoshop Rev C /1008

24 18 softworx Suite User s Guide About the Browser Window The browser window is the main softworx Suite window. From this window, you can download files from FTP sites, browse to files, connect to external databases, view previews, open image files or send them to modeling and visualization software applications Applied Precision, Inc.

25 Chapter 2 Using the softworx Browser 19 Open softworx Suite Open a File The Folder View is used to navigate to file directories and to connect to FTP sites. The File View displays the files in the folder (directory) or FTP site that is selected in the Folder View. The Preview Area displays a preview of the file currently selected in the File View. The Information View contains three tabs: Image Properties displays information for the file selected in the File View; File Transfers displays the status of files that are copied or transferred to or from FTP sites; Batch Jobs displays the status of batch processing. The Status Bar contains three status sections that show: the status of actions (e.g., selecting a file), file transfers, and batch processing jobs. To open softworx Suite From the Windows Start menu, choose All Programs Applied Precision softworx Suite softworx Suite. To open a file in the softworx browser 1 In the Browser Window folder view, click the File System tab and navigate to the folder that contains your image files. 2 In the File View, select a file. After you select the file: The Preview Area displays the image Rev C /1008

26 20 softworx Suite User s Guide The Information View displays metadata about the image. The Status bar displays the action (loading a slide). 3 In the File View, right-click on a file to open a context sensitive menu Applied Precision, Inc.

27 Chapter 2 Using the softworx Browser 21 Important Many of the features in the Browser are available only through context sensitive menus. These menus are opened by right-clicking with the mouse on a view in the Browser window. The context sensitive menu for each view is sensitive to other window settings. For example, rightclicking on the File View when the File System is selected opens a different menu than right-clicking on the same view when the FTP tab is selected. 4 On the context sensitive menu, click Open File. The file opens in the viewer. Tip You can use the CTRL+O keyboard shortcut to open files Rev C /1008

28 22 softworx Suite User s Guide 5 Click the icon on the left side of the status bar to display an action log that shows all of the actions you have performed in this session Applied Precision, Inc.

29 23 Preview Files Display Images in Thumbnail View To display images in thumbnail view 1 On the Browser menu, choose View Thumbnails. 2 To adjust thumbnail size, select a size in the Thumbnail size list. 3 To adjust thumbnail brightness, select the files you want to adjust and right-click on the browser View area. On the context sensitive menu, choose the Thumbnail Brightness adjustment Rev C /1008

30 24 softworx Suite User's Guide Display Image Previews You can view previews of files in the browser window. Previews are available for both images and text. To display an image preview: On the File View (in the right pane of the Browser), select a file. If you select a file with a recognized image format, (e.g., a DeltaVision or TIFF file), the image is displayed in the preview window. If you select a text file, the text is displayed in the Preview window. Image files or text files can be displayed in the Preview window 2008 Applied Precision, Inc.

31 Using the softworx Browser 25 Adjust Brightness of Preview Images You can adjust the brightness of each channel in a preview image. To Adjust brightness of preview images: With an image selected in the File View and displayed in the Preview area, right-click on the preview image. On the context menu, choose Brightness. Then choose Make Brighter or Make Darker. Show or Hide Channels in Preview Images To show or hide channels in preview images: 1 With an image displayed in the Preview area, right-click on the preview image Rev C /1008

32 26 softworx Suite User's Guide 2 On the context sensitive menu, select a channel to display it or unselect it to hide it (selected channels have a check mark). Scroll Through Time Points For images that contain both Z sections and multiple time points, the mouse controls the Z sections by default. To use the mouse to control time points for these images, you will need to change the mouse settings. To set up the mouse to control time-lapse images: With an image selected in the file list and an image displayed in the Preview area, right-click on the Preview area to open a context menu. Then choose Mouse Changes Time Points Applied Precision, Inc.

33 Using the softworx Browser 27 Scroll Through Z Sections or Time Points Use the mouse to scroll though image data with more than one Z section or time point. If the image has time-lapse data with more than one Z section, dragging the mouse scrolls the Z sections by default. To scroll through time lapse or Z data: With an image displayed in the Preview area, hold the left mouse down on the image and then drag it up or down across the image to scroll through image sections. Notes If the image has more than one Z section and only one time point, dragging the mouse down displays deeper Z sections and dragging it up displays shallower sections. If the image is a time-lapse image with only one Z section, dragging the mouse up displays shorter time points and dragging it down displays longer time points. Play Animations You can play animations in the Preview area. If the images have been volume rendered, rotating 3D volumes are displayed. If not, the images are scrolled through Z sections or time points. You can play animations for single images or you can set up the Browser to automatically play animations for all images after you select them Rev C /1008

34 28 softworx Suite User's Guide To play animation previews: TIP Use the CTRL+M keyboard shortcut to toggle animation previews. With an image selected in the File View and an image displayed in the Preview area, right-click on the Preview area to open a context menu. Then choose Play Animation. TIP Use the ALT+M keyboard shortcut to toggle the autoplay option. To automatically play animations in the Preview Area: On the Browser menu, choose View Auto Play Images. The check mark next to the Auto Play Images menu item indicates that this option is selected. As you select images, animations are played in the Preview Area. Note The Auto Play Images menu is a toggle switch. If this option is selected, choosing this item on the menu unselects it. If it is not selected, choosing this item selects it Applied Precision, Inc.

35 Using the softworx Browser 29 Define Defaults for Thumbnail Images To define default thumbnail image size and quality. 1 On the Browser menu, choose Edit Preferences to open the Preferences dialog box. 2 Under User Preferences, select Thumbnail View. 3 In the Size list, select the desired default thumbnail image size. 4 In the Quality list, select the desired default thumbnail image quality Rev C /1008

36 30 softworx Suite User's Guide Image Display Scaling You can improve the contrast of selected data in a channel by changing the channel's intensity scale. softworx Suite uses shades of the color that is selected for a channel to display an intensity scale. The darkest shade is mapped to the lowest (dimmest) intensity value in the wavelength and the lightest shade is mapped to the highest (brightest) intensity value. The remaining shades are mapped to values between the lowest and highest values. Color shades can be mapped to create linear or nonlinear intensity scales. In linear scales, the color shades are mapped to values that are distributed evenly from the minimum to the maximum intensity values. In nonlinear scales, the shades are mapped to values that are distributed unevenly throughout the range. Note Changing intensity scale values only adjusts the display of the data. It does not alter the image data. To change the intensity scale: 1 On the Image window, select Tools Image Scaling to open the Image Display Scaling dialog box. This dialog box shows the image intensity scale Applied Precision, Inc.

37 Using the softworx Browser 31 The Image Display Scaling dialog box is used to adjust the intensity scale. The histogram on this dialog box is a frequency plot that shows the distribution of pixel intensities in the image file. The Y-axis shows the number of pixels for a given intensity. 2 In the Channel field, select which channel to scale. 3 To change the minimum or maximum scale value, click and drag on the Left or Right handles. 4 To slide the range to the left or right, click and drag on the Center handle. 5 To change the intensity scale distribution, click anywhere in the histogram (except on the handles) and drag the mouse up or down. TIPS #1 You can improve contrast at the low end of the intensity range by reducing the gamma value. To improve contrast at the high end of the range, increase the gamma value. #2 Another way to scale the image is to enter values into the Min and Max fields. #3 You can restore all of the default values by clicking the Restore Default Scale button Rev C /1008

38 32 softworx Suite User's Guide Deconvolve Image Data You can use softworx Suite to deconvolve image data from a variety of locations. Using the context sensitive menus in the softworx Browser, you can right-click in the Folder View, the Preview Area, or the File View to perform deconvolution tasks on individual files or groups of files. If you are using nonstandard lenses to acquire data, you can add the information required for deconvolution (lens data and Optical transfer files) to the softworx Suite lens database. To deconvolve images from the softworx Browser 1 In the Browser File View area, select a file and right-click on the file name to open the context sensitive menu. Note Unprocessed files have an.r3d extension. Deconvolved files have a.dv extension. 2 Select Tasks Deconvolve. Note If a message box indicates the file is not associated with a lens or OTF (Optical Transfer File) in the softworx Suite lens database, add this information as shown in Add lens information (on Page 37). The Job List Review dialog box is displayed Applied Precision, Inc.

39 Using the softworx Browser 33 3 Double-click on. The Deconvolution Action dialog box is displayed. 4 From the General Options tab, you can: Verify the OTF is correct and make any necessary modifications using the Change button. Set the desired deconvolution method to Ratio (conservative) or Enhanced Ratio (aggressive). Adjust the desired number of deconvolution cycles. Determine whether or not correction should be applied. Set noise filtering to High, Medium, Low, or Manual Settings. Select an output file name. 5 If you only want to deconvolve part of the data, click the ROI tab to: Determine which channels to use in the deconvolution process Rev C /1008

40 34 softworx Suite User's Guide Adjust the Z Section or Timepoints sliders. Select a region of interest using the X and Y Offset sliders and the Width and Height sliders. Note For a more exact ROI, enter the appropriate numbers directly into the ROI Position fields. 6 Click Save Settings to return to the Job List Review dialog box 7 Click Start Jobs to begin the deconvolution process. The deconvolution status is displayed on the softworx Browser Status bar. Deconvolution Succeeded is displayed when the process is complete. 8 To view the deconvolved file, double-click on the output file name you selected. The deconvolved image is displayed in the softworx Suite Viewer Applied Precision, Inc.

41 Using the softworx Browser 35 To deconvolve images from the softworx Suite Viewer 1 In the Browser File View area, double-click on a file name to open the file in the Viewer. Note unprocessed files have an.r3d extension. Deconvolved files have a.dv extension Rev C /1008

42 36 softworx Suite User's Guide 2 On the Viewer menu, select Process Deconvolution. Note If a message box indicates the file is not associated with a lens or OTF (Optical Transfer File) in the softworx lens database, add this information as shown in Add lens information (on Page 37). 3 To deconvolve part of the data, click the ROI tab and adjust the Z Section or Timepoints sliders. 4 Click Deconvolve to process the data Applied Precision, Inc.

43 Using the softworx Browser 37 The deconvolution status is displayed on the Viewer Status bar. When processing is complete, the following message box is displayed. 5 To view the deconvolved file, click View Deconvolved Image. The deconvolved image is displayed in the Viewer. Add Lens Information softworx Suite includes a database that contains information about lenses typically used to acquire data on DeltaVision systems. This database includes general information about the lens as well as the optical transfer file associated with each lens. (The Optical Transfer File (OTF) is required by the deconvolution algorithms. It provides information about the blurring and scattering patterns of light associated with a specific objective lens.) To add lens information 1 On the Browser menu, choose Edit Preferences Rev C /1008

44 38 softworx Suite User's Guide 2 To add a lens to the database, click Add New Lens and enter the Name, ID, and other information about the lens. 3 Click Change and select an OTF (optical transfer function) for the lens. Note If you need to create an OTF, see the DeltaVision Help for details Applied Precision, Inc.

45 Using the softworx Browser 39 Use FTP You can connect to standard FTP or secure FTP sites. After you configure a site, you can add a folder on the site to your Favorites list, just as you can add file directories to this list. About FTP and Secure FTP SoftWoRx Suite supports both Standard FTP and Secure FTP protocols. (Secure FTP includes strong authentication and encryption features that are designed to resolve security problems with Standard FTP.) Connect To Previously Configured FTP Sites To connect to a site that is already configured: 1 On the Browser window Folder View, click the FTP / Secure FTP tab. 2 Right-click on an FTP icon to display the context menu and then select the Connect To menu item. TIP You can also connect to a site by double-clicking on its icon under the FTP Sites folder Rev C /1008

46 40 softworx Suite User's Guide After the connection is established, the folders on the FTP site appear in the Folder View. Connect To a New FTP Site To set up a new FTP site: 1 On the Browser window menu, choose FTP Connect to new FTP site. 2 In the Address field, enter the FTP address of the site (e.g., quiet.api.com or ) Applied Precision, Inc.

47 Using the softworx Browser 41 3 In the Shortcut Name field, enter an alias for this connection (an alias is a name that is easier to remember than the actual connection name). 4 In the Initial Login Folder, enter the remote directory (you can leave this field blank). 5 If you are logging on to a password protected site, select Personal. Then enter your Login and Password. 6 Click Connect to connect to the site. Note After you have configured a site, the the FTP/Secure FTP tab. icon is displayed under View Files on FTP Sites When you are connected to an FTP site, you can view files on the Viewer. To View a file on an FTP site: 1 In the File View, double click a.dv file to open the File Download dialog box. 2 Click Open to view the file in the Viewer Rev C /1008

48 42 softworx Suite User's Guide Browse To a File on an FTP Site To browse to a file on an FTP site: 1 Connect to the FTP site. The browser displays the folders on the site under the FTP/Secure FTP tab. 2 Click on the folders to open them (just as you would with any typical file management system) and browse to the file. Manage Files and Folders on an FTP Site When you connect to an FTP site, a set of folders is displayed under the FTP/Secure FTP tab. When you open a folder, the files are displayed in the File View on the right side of the Browser window. You can rename or delete files on the FTP site. You can also transfer files to or from the site. Transfer Files or Folders From an FTP site You can transfer files or folders from an FTP site to a file directory on a network or local drive. You can also transfer files or folders from a file directory to an FTP site. To transfer a file from an FTP site to a network drive: 1 On the FileSystem tab, select the folder to which you want to copy file(s). 2 Connect to the FTP site and navigate to the folder on the site. 3 In the Browser File View, select a file or group of files. 4 Right-click on the File View to open a context sensitive menu Applied Precision, Inc.

49 Using the softworx Browser 43 5 On the context sensitive menu, choose Copy To and then choose the current File directory, browse to a location, or select a favorites folder. TIP Use CTRL+A to select all files and CTRL + SHIFT + A to unselect all files. To transfer files from a folder to an FTP site: 1 On the FTP/SecureFTP tab, navigate to the folder to which you want to copy files. 2 Click the File System tab and browse to the directory that contains the files to upload. 3 In the Browser File View, select a file or group of files. 4 Right-click on the Browser File View to open a context sensitive menu. 5 Choose Copy To and choose the folder on the FTP site that you want to copy the folder to Rev C /1008

50 44 softworx Suite User's Guide As the files are copied, the status bar displays the status of the file transfers. TIP Hold down the CTRL key while selecting files to select multiple files from different portions of the file list. Hold down the SHIFT key to select multiple consecutive files. 6 To view a log of all file transfers, click the icon on the status bar Applied Precision, Inc.

51 Using the softworx Browser 45 To transfer a folder from a network drive to an FTP site: 1 Click the File System tab and browse to the directory that contains the files to upload. 2 In the Browser Folder View, select a folder and right-click on it to open a context sensitive menu. 3 Choose Copy To Favorites and select the FTP site where you want to copy the folder. Transfer Files or Folders to a Network Drive To transfer files or folders from an FTP site to a network drive: 1 Connect to the FTP site and navigate to the folder on the site. 2 In the Browser, select a file or folder and right-click on it to open a context sensitive menu. 3 Choose Copy To and then choose the current File directory, browse to a location, or select a favorites folder. Edit an FTP Site You can edit settings of an FTP site to change the username, password, or other information. To edit an FTP site: 1 On the Browser window, choose FTP Edit FTP sites to open the Edit FTP Sites dialog box Rev C /1008

52 46 softworx Suite User's Guide 2 Select the site to edit and click the Edit button to open the Edit FTP/Secure FTP Site dialog box. 3 Edit the fields that you want to change and click the Save button. Disconnect From a Site To disconnect from a site: Under FTP/FTP Secure FTP, right-click the name of the FTP site and choose Disconnect Applied Precision, Inc.

53 Using the softworx Browser 47 Manage File Systems Sort Files To sort files To sort files in Details View, click on the Name, Type, Size, or Date Modified buttons. To reverse the sort order, click the button for which the list is sorted. The gray triangle is displayed in the header of the current sorting header. This triangle indicates whether the sort order is ascending or descending. To sort files in Thumbnail View, choose the sort criteria in the Sort By list and select or unselect Sort Ascending. Note: When Sort Ascending is unselected, the files are sorted in descending order. Add an FTP Folder to the Favorites List To create a favorite FTP site: 1 Under the FTP/Secure FTP tab, browse to the folder that you want to add to the Favorites list. On the Browser Favorites menu, choose Add Current Location to add the folder to the Favorites list Rev C /1008

54 48 softworx Suite User's Guide 2 Select Save on the Add Favorite window. Copy, Delete, or Rename Files or Folders You can copy, delete, or rename files or folders that are in your local directories. To copy, delete, or rename a file: 1 In the Browser window File View, select a file and right-click to open a context sensitive menu. 2 Copy, delete, or rename a file as follows: 3 To copy the file, choose Copy To and browse to the directory to which you want to copy the file. 4 To delete a file, choose Delete Applied Precision, Inc.

55 Using the softworx Browser 49 5 To rename a file, choose Rename to open the Rename File dialog. Then enter the file name and click OK. To copy, delete, or rename a folder: 1 In the Browser window Folder View, select a folder and right-click to open a context sensitive menu. 2 Copy, delete, or rename the folder as follows: a) To copy the folder, choose Copy Folder To and browse to the directory to which you want to copy the folder. b) To delete a folder, choose Delete Folder. c) To rename a folder, choose Rename Folder to open the Rename Folder dialog. Then enter the new folder name and click OK Rev C /1008

56 50 softworx Suite User's Guide View File Properties You can view an extensive list of properties for files that are in a directory on your file system. For DeltaVision or.tiff files, you can view additional metadata. To view file properties: 1 At the bottom of the browser window, click the Image Properties tab. Then click the General Properties folder. 2 If a DeltaVision file is selected, click the DeltaVision Properties folder to view properties that are specific to the DeltaVision format. Note You can also view all XML metadata associated with images and view file metadata for Adobe PhotoShop or.tiff files Applied Precision, Inc.

57 Using the softworx Browser 51 Send Files to Other Applications You can send files to the Bitplane Imaris application or other applications that you configure. Before you can send files, you will need to configure your SendTo preferences. Examples of SendTo destinations you can set up are Photoshop, Notepad, and Paint. To add an application to the SendTo List: 1 On the Browser menu, choose Edit Preferences to open the preferences dialog box. 2 On the left side of the Preferences window, select the SendTo folder. 3 In the Application type list, choose Generic Application. 4 In the Name field, enter the name that you would like to appear on the SendTo list Rev C /1008

58 52 softworx Suite User's Guide 5 Click Browse and browse to the executable file for the application that you are adding. Then click Add to add the application to the SendTo list. Send a File to an Application To send a file to an application: 1 On the right pane in the Browser window, select a file and right-click to open a context sensitive menu. 2 Choose SendTo and then select which application or view mode to send the file to Applied Precision, Inc.

59 Using the softworx Browser 53 Create and Use a Favorites Folder You can create favorite folders that you can open or copy files to. Creating and using Favorites is the fastest and sometimes the only method of copying files between common locations that you use on a consistent basis. To create a Favorites folder 1 In the Browser window, click the File System tab and select the folder. 2 From the browser window Favorites menu, choose Add Current Location. 3 Select Save on the Add Favorite window. To copy to a Favorite Folder 1 In the Browser window, click the File System tab and select a file or group of files. 2 Right-click on the selected files to open the context menu. 3 Click Copy To Favorites and then select the desired favorite folder Rev C /1008

60 54 softworx Suite User's Guide Connect to a softworx DMS Database Connecting to a New Database Site Before you connect to a new database, you ll need an address for the site, a user name, and password. Check with your microscope administrator for this information. To connect to a new database 1 On the main browser menu, select Database Connect to New Database. The Connect to Database Site dialog box is displayed. 2 In the Address field, enter the site address for the database. 3 In the Shortcut Name field, enter any name that will help you keep track of this database. 4 In the Login section, click the Personal radio button. 5 In the Login and Password fields, enter your user name and password. 6 Select the Connect button at the bottom of the dialog box Applied Precision, Inc.

61 Using the softworx Browser 55 Change Database View Databases can be explored from one of two views: The Project/Dataset/Image view is used to group images in the database logically. The Category Group/Category view is used to view and organize images based on their attributes. To change the database view: Right-click on a connected database and select either View Project/Dataset/Image or View Category Group/Category. A category group is a feature or attribute about the image. A category is the actual description. An example of a category group would be Color, while the categories would be Red, Green, and Blue. You can select only a single category within a category group. For example, an image can be classified as Red or Green, but not both. You can, however, classify an image in several different groups at the same time. For example, a single image could be classified as Color/Red and Size/Small. Create New Project Folder The Project/Dataset/Image view basically describes the view s hierarchy. You can right-click on a database to create a new project folder, or right-click on a project to create a new dataset folder. To create a new project folder: Right-click on the database where you want your new project to appear and select New Folder. Enter a name for your new project folder and click OK. Create New Dataset Folder Rev C /1008

62 56 softworx Suite User's Guide To create a new dataset folder: 1 Right-click the project where you want your new dataset folder to appear and select New Folder. 2 Enter the name for your new dataset folder and click OK. Upload Data To upload data: 1 To upload an image, group of images, or folder, select the FileSystem tab. 2 Select the file(s) you want to upload, right-click and select Copy Folder To <your site name>. The Copy Image to Database dialog box is displayed. Copy Images to Database dialog box 2008 Applied Precision, Inc.

63 Using the softworx Browser 57 Copy Images to Database dialog box (shown divided for viewing purposes) 3 Select the project and dataset where you want to upload the file(s). 4 Select the initial categorization for the files. Categorizing tags an image as having certain characteristics and identifies it as a member of a specific group. You can later search for images that have categorized with certain values. 5 In the dialog box, you can also select the initial annotation (comment tag containing user information, date stamp, etc.) and initial categorization for the selected file(s). 6 When you are satisfied with your selections, click OK to upload the file(s). log files When necessary, it can be helpful to log files to Applied Precision Customer Support. Set up for Log Files To set up for log files 1 On the Browser menu, choose Edit Preferences Rev C /1008

64 58 softworx Suite User's Guide 2 Under User Preferences, choose . 3 In the Server Name field, enter the fully qualified name of your mail server. 4 In the From Address field, enter your address. 5 If authentication is required, enter the information for your account in the User Name and Password fields Applied Precision, Inc.

65 Using the softworx Browser 59 Log Files to Applied Precision To a log file to Applied Precision Customer Support 1 On the Browser Help menu, choose Show Log Files to open the Log Viewer window. 2 On the tabs at the top of the Log Viewer window, select a log file. 3 Click Log Files. Run Batch Jobs You can run batch jobs on several files from the softworx browser. You can also set up and submit several jobs at a time and use the browser to assign priorities to jobs or to delete jobs. After you submit the jobs, you can use the Browser to perform other tasks while the jobs run in the background. To set up a job, you apply a task to a file. A task is a template for a job. The task defines generic options that apply to any file. It does not define options that require specific information about file properties (for example, region of interest, time points, or Z sections). When a task is applied to a group of files, a job is created for each file. The default options for each job are those that are defined in the task. You can modify these job options or select additional job options, based each file's properties Rev C /1008

66 60 softworx Suite User's Guide Create Tasks and Task Chains You can perform a variety of tasks to manage files in the Browser window. You can also set up multiple tasks to be performed in a specified series on your datasets. To create a task: 1 On the softworx browser menu, choose Tasks Create Task to open the Task Editor. 2 In the Task Name field, enter the name for the task. 3 Under Available Actions, select a task (for example, Quick Projection). The Add button becomes active. 4 Click Add to move the task to the Actions in Task list. 5 Click Save to save this as a single-action task Applied Precision, Inc.

67 Using the softworx Browser 61 You can also configure a series of tasks (known as a task chain) in the same general manner used to generate a single task. To create a task chain: 1 On the softworx browser menu, choose Tasks Create Task to open the Task Editor. 2 In the Task Name field, enter the name for the task chain. 3 Under Available Actions, select the initial task for the chain (for example, Quick Projection). The Add button becomes active. 4 Click Add to move the task to the Action list. 5 Repeat Steps 3 and 4 to move additional tasks to the Action list. 6 For each task you add to the list, choose either Selected File or Previous Step s Result in the Data Source field. This field indicates whether to use the original file or the file subsequent to the previous task s results for the next task in the list. Note Actions that produce multi-file results (for example, a folder of several files such as a multi-file.tiff, cannot be used as a data source for another action within a task chain since the result is data dependent. Also, files that contain Z s, T s, or C s could produce multi-file results. This will depend on the particular actions and options you define, and on the source data file. 7 To change the order of the tasks placed into the list, click on the action to highlight it. The Remove, Move Up, and Move Down buttons are activated. Select the desired button for the highlighted task. You can also use the Edit button at the bottom of the Task Editor to make specific modifications to any of the actions within the task chain (see Edit Tasks and Task Chains for more information.) Rev C /1008

68 62 softworx Suite User's Guide 8 When you are satisfied with the setup of your task chain, select Save. Edit Tasks and Task Chains 1 On the softworx browser menu, choose Tasks Edit Task to open the Preferences dialog box. 2 In the Tasks Preferences list, select the task or task chain you want to edit. The buttons to the right are activated. 3 Click the Edit button to view the task or task chain in the Task Editor Applied Precision, Inc.

69 Using the softworx Browser 63 4 Select the action within the task to edit. The Remove, Move Up, and Move Down buttons are activated, as well as the Edit button at the bottom of the screen. If this is a task chain, you can use the positioning buttons to rearrange the various actions in the chain. 5 To edit the task, click the Edit button. Depending on the selected action, a dialog box specific to that action is displayed. For example, if the selected action is Quick Projection, the Quick Projection Action dialog box is displayed. 6 Make the desired changes to the action for this particular task or task chain and select the Save Settings button Rev C /1008

70 64 softworx Suite User's Guide 7 In the Task Editor, click Save to save your changes and click Close on the Preferences dialog box to close the window. Customize Actions You can modify specific actions for tasks and task chains and make adjustments to the default parameters in much the manner used to edit tasks. To customize actions 1 On the softworx browser menu, choose Tasks Edit Task to open the Preferences dialog box. 2 In the Tasks Preferences list, select the action you want to customize. (Save As TIFF is used in the following example.) The buttons to the right are activated. 3 Click the Edit button. The Task Editor is displayed showing the selected action Applied Precision, Inc.

71 Using the softworx Browser 65 4 Highlight the action (in this case, Save As TIFF) in the actions list and click the Edit button at the bottom of the screen. The Save As TIFF Action dialog box is displayed. 5 This dialog box allows you to change the parameters of the Save As TIFF action. Depending on the action selected in the Task Editor, different action dialog boxes will be shown allowing you to modify other active parameters of the selected action (for example, Deconvolution or Quick Projection). Note You can change generic parameters when you are customizing an action. Parameters that require specific file properties are not active when those specific properties are not detected Rev C /1008

72 66 softworx Suite User's Guide 6 When you are satisfied with the changes, click Save Settings to save the updated action. 7 Select Save on the Task Editor and click Close on the Preferences dialog box to close the window. From the Task Editor, you can use the customized action for tasks or task chains in the same way that you would use other actions. Customize the Task Menu To customize the task list menu 1 On the Browser menu, choose Edit Preferences. The Preferences dialog box is displayed. 2 Under User Preferences, select Tasks. 3 Under Tasks Preferences, select a task. The Edit, Delete, Move Up, Move Down, and Insert Separator buttons on the right side of the window are activated. 4 Use the buttons on the right side of the window to change the order of the tasks, delete or edit tasks, or insert a separator between tasks Applied Precision, Inc.

73 Using the softworx Browser 67 5 When you are satisfied with your changes, save and close the open dialog boxes. Run a Job Before you begin the process of running a batch job, it will help you to understand the overall process. The basic steps for running batch jobs are: a. You begin by selecting one or more files, or one or more folders. b. Use your mouse to right-click on the selected files to bring up a popup menu. c. Choose Tasks and then select the type of task you want to perform. d. Next, you ll want to review the list of jobs to remove or edit any entries. e. Select the Start Jobs button to run the batch job(s). The following example procedures show how to run a Deconvolution batch job (Example 1) and a Quick Projection batch job (Example 2). To Run a Batch Job (Example 1 Deconvolution): 1 In the File List, select a group of files. Then right-click on the selected files to open a context sensitive menu and select Tasks Deconvolve. (In this case, Deconvolution is used as an example. You can use Decon1, Save As TIFF, or any of the standard or customized tasks or task chains previously configured.) Rev C /1008

74 68 softworx Suite User's Guide softworx Suite displays the Job List Review dialog box. The Job List Review dialog box indicates that one of the files is ready for processing (as shown by the icon) and one of the files is not ready (as shown by the icon). If the Show Rejected Files button is active, it indicates that at least one file was rejected. 2 If any of the files in the Selected Items list have the icon, you must either remove these files (Step 3) or add information for the files (Steps 4-6) before you run the batch job. 3 To remove a file from the job list, select the Deconvolution folder with the file name (e.g., Deconvolve-Fast2_R3D.dv) and click Remove Applied Precision, Inc.

75 Using the softworx Browser 69 4 To find out why a file is not ready for processing (e.g., NUCLEAR_PORE_R3D.dv), double click the icon under the file name to open the Deconvolution Action dialog box. softworx Suite displays an error message that indicates why the file cannot be processed (e.g., the OTF file could not be found in the library). 5 Click OK to close the message box. 6 To make the file ready for processing, add the missing information (e.g., the OTF file location) in the Deconvolve Action dialog box and click Save Settings. 7 After you add the information, the Job List Review dialog box indicates that the file is ready for processing Rev C /1008

76 70 softworx Suite User's Guide 8 To view a list of selected files that cannot be processed, click Show Rejected Files. Note softworx Suite rejects files if they have a format that is not compatible with the selected task. 9 To change the deconvolution options for any of the jobs in the Selected Items list, click or under the file name to open the Deconvolution Action dialog box. Then change the options to apply to this job and click Save Settings. (These changes apply only to the file above the or icon that you selected.) 10 On the Job List Review dialog box, click Start Jobs. The jobs are displayed on the status bar as they run. 11 To view the actions, click the right icon on the status bar Applied Precision, Inc.

77 Using the softworx Browser 71 To Run a Batch Job (Example 2 Quick Projection): 1 In the File List, select a group of files. Then right-click on the selected files to open a context sensitive menu and select Tasks Quick Projection. (In this case, Quick Projection is used as an example. You can use QuickProjChain, Save As TIFF, or any of the standard or customized tasks or task chains previously configured.) softworx Suite displays the Job List Review dialog box. 2 The Job List Review dialog box indicates that most of the files are ready for processing. If the Show Rejected Files button is active, it indicates that at least one file was rejected. Select Show Rejected Files to view a list of the files and the reasons for their rejection Rev C /1008

78 72 softworx Suite User's Guide The files may have been rejected either because they are not image files or the file type isn t supported for this action (in this case, Quick Projection). Image file will also be rejected for Quick Projection if they do not contain multiple Z sections. 3 Select Close on the Rejected Files List to return to the Job List Review dialog box. 4 When you are satisfied with the jobs on the list, click Start Jobs. The jobs are displayed on the status bar as they run. 5 To view the actions, click the right icon on the status bar Applied Precision, Inc.

79 Using the softworx Browser 73 Set Preferences Use the Preferences dialog box to edit the General settings, Favorites folder, FTP sites, or the SendTo folder. To set preferences: From the Browser menu, choose Edit Preferences to open the Preferences dialog box. On the left side of this dialog box, select which folder to set. Then configure the settings on the right side of the Preferences dialog box Rev C /1008