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  • Imaris V 7.5 Reference Manual

  • © Bitplane 2012

    1 Preface

    This Reference Manual provides a description of all menu entries, display modes, functions and parameters.

    Information in this book is subject to change without notice and does not represent a commitment on the part of Bitplane AG. Bitplane AG is not liable for errors contained in this book or for incidental or consequential damages in connection with the use of this software.

    This document contains proprietary information protected by copyright. No part of this document may be reproduced, translated, or transmitted without the express written permission of Bitplane AG, Zurich, Switzerland.

    For further questions or suggestions please visit our web site at:

    www.bitplane.com

    or contact our support teams:

    [email protected] [email protected]

    Bitplane AG Badenerstrasse 682 8048 Zurich Switzerland

    © May 2012, Bitplane AG, Zurich. All rights reserved. Printed in Switzerland. Imaris Reference Manual V 7.5

    1.1 Getting Familiar

    Today, all optical microscopes commercially available can record several channels simultaneously to produce multi-channel images. Imaris is an application designed to visualize such microscopic data. Imaris uses a special file format to store images with parameters and can incorporate image files for all major microscopes and image acquisition systems. The images can be viewed in several different ways and processed to provide the optimum amount of information from 2D or 3D still images, time series, and animations.

    Once a data set has been loaded into Imaris, individual parameters such as channel colors, geometrical settings or voxel sizes can be adjusted. Imaris has a variety of tools available, such as cropping, threshold cutting and filters for processing the images to bring out the required details.

    It provides 8 different viewing functions for the visualization and production of high quality images for presentation and storage:

    A Slice viewer. A Section viewer for simultaneous viewing along three coordinate axes. A Gallery viewer for slice image overview and selection. The Easy 3D viewer provides a quick image view. The Surpass viewer, which offers numerous tools for data preparation, presentation and manipulation of different types of data display as well as any combination of them and the ability to define, combine and group an arbitrary number of objects out of a set of viewing objects. Animations can be created from the Slice and 3D modes, or with the key frame animator in Surpass. InMotion is a 3D viewing and precise interaction mode. Imaris produces a real 3D impression by a smooth animation of the view.

    http://www.bitplane.com mailto:[email protected] mailto:[email protected]

  • Imaris Reference Manual

    A viewer for Colocalization computation.

    It is easy to navigate within the Imaris modules because the frequently used toolbars, menus, and interactive controls remain the same, and can all be operated with the mouse buttons.

    1.2 Getting Started

    The software is delivered on a standard CD or downloaded from www.bitplane.com. The CD includes a folder containing the necessary manuals, or the manuals can be downloaded.

    Minimum hardware/software requirements are:

    Windows NT 4.0, or a more recent version, Windows 2000, XP, Vista, OS X 10.5.0 (Leopard) or higher CD-ROM Graphics card with 3D accelerator Network facilities for image import from the microscope 512 MB RAM (> 1 GB recommended)

    Bitplane also recommends:

    A database for storing images (e.g., Image Access)

    Installation

    To install the software, please proceed as follows:

    Insert your Imaris CD-Rom in the computer. Follow the instructions on the screen. The installation is completed automatically.

    Licensing

    To run the Imaris system, the appropriate licenses for the required modules, such as the Imaris base (including Surpass), ImarisTime, ImarisColoc or Imaris MeasurementPro. Without licenses, the Imaris can only be run in a restricted mode. In case of any license problems, please refer to the support information on our website www. bitplane.com for detailed instructions.

    Starting Imaris

    Imaris can be started by one of the following methods:

    Double-click on the Imaris icon (we recommend copying the icon to the desktop). Drag the icon of an image or a file to the Imaris program icon. Imaris can be started directly from the Image Access database.

    The software opens with the main screen.

    Supported File Formats

    Imaris (as of version 6.0.0) can read the following file formats, i.e. it can read the image and the parameters.

    Andor: Multi-TIFF series (*.tif, *.tiff) Andor: MM (*.kinetic) Andor: iQimage (*.kinetic) Applied Precision, Inc: DeltaVision (*.r3d, *.dv)

  • © Bitplane 2012

    Biorad: MRC-600, MRC-1024 (series)(*.pic) BioVision: IPLab Mac (*.ipm) Bitplane: Imaris 5.5 (*.ims) Bitplane: Imaris 3.0 (*.ims) Bitplane: Imaris 2.7 Classic/Old (*.ims) Bitplane: Imaris Scene File (*.imx) BMP (adjustable file series) (*.mrc, *.st, *.rec) Carl Zeiss: LSM 510 (*.lsm) Carl Zeiss: LSM 410, LSM 310 (*.tif, *.tiff) Carl Zeiss: Axiovision (*.zvi) Compix:Simple PCI (*.cdx) Image Cytometry Standard: ICS - used by Nikon, Huygens, and others (*.ics, *.ids) Gatan Digital Micrograph (serie):(*.dm3) Leica: TCS-NT (*.tif, *.tiff) Leica: LCS (*.lei, *.raw, *.tif, *.tiff) Leica: series (*.inf, *.info, *.tif, *.tiff) Leica: Image File Format (*.lif) MetaSystem: Meta Viewer (*.imv) Molecular Devices: Metamorph STK (series) (*.stk) Molecular Devices: Metamorph ND (*.nd) MRC: primarily electron density volumes as in cryo-EM (*.mrc, *.st, *.rec) Nikon: ND2 (*.nd2) Olympus: FluoViewTIFF (*.tif, *.tiff) Olympus: 1000 OIF (*.oif) Olympus: 1000 OIB (*.oib) Olympus: Cell^R 1.1/standard (*.tif, *.tiff) Olympus:Virtual Slide Image (*.vsi) Opellab: liff (series) (*.liff) Openlab: raw (*.raw) Open Microscopy Environment XML (*.ome) Open Microscopy Environment TIF (*.tif, *.tiff) Perkin Elmer: UltraView (*.tim, *.zpo) Prairie Technologies: Prairie (*.xml, *.cfg, *.tif, *.tiff) Scanalytics: IPLab (*.ipl) Slide Book (*.sld) TIFF (adjustable file series) (*.tif, *.tiff) TILL Photonics: TILLvisION (*.rbinf)

    Plus it can read general TIFF series (or BMP series) of the format aaaNNN.tif (where a is a character and N is a number).

    2 Menu File

    Open... Ctrl + O Revert to File Ctrl + R Save Save as... Ctrl + S

    Batch Convert... Scene Viewer...

    Batch

    Import Scene... Ctrl + L Export Scene... Ctrl + E

  • Imaris Reference Manual

    Snapshot... Ctrl + T

    Exit Ctrl + Q

    See also: Addendum - Mouse & Keyboard Mac

    2.1 Open

    Data sets can be loaded from various file formats.

    Image File Series

    If the data set consists of a series of images each is stored as an individual file. To open a series of images select the folder and click on Open to open it. This brings up the Image selection window, which allows you to explore your file system. The window contains a preview of all the images as well as the following info: Name, Description, Recording date, Size, Time Points, Channels, Total size and Voxel size. The image series is ordered according to the number, which appears after the file name suffix.

    To open the image select a file name from the list and click Open

    Image Preview Check the box Thumbnail Preview to activate an image preview.

    Search Image name Enter the image name for instant image selection.

    Resampling Open... The Resampling Open dialog box can be used as a preview before loading the data set and allows you to change the resolution of the data (subsampling) and to select only a part of the data set (cropping) by specifying the parameters in the Resampling Open dialog box. Both options reduce the size of the data set, decreasing the time needed to read the file and speeding up any operations on the data. This is particularly helpful/beneficialwhen reading large data sets over a network.

    In the menu select File Open. Select a file name from the list and click Open or double-click on the requested file entry.

    The file is loaded.

    iQ files in Imaris

    To open iQ files in Imaris locate and select the DisckInfo5.kinetic file. Clicking on the Settings button opens a new window with a list of images and image information. Check the box Thumbnail Preview to activate an image preview. Select the required image and click on the OK button. Than click again on the Open button. This will instantly create 3D volume rendered image of the selected data set.

    File Formats

    Format Name Extension Remarks

    Imarisbase

    Bitplane Imaris 5.5 *.ims

    Bitplane Imaris 3.0 *.ims

  • © Bitplane 2012

    Bitplane Imaris 2.7 *.ims

    Bitplane Imaris Scene File *.imx

    Andor iQ Image *.kinetic

    Andor Multi-TIFF *.tif,*.tiff

    MetaSystems MetaViewer *.imv

    TIFF-Series *.tif,*.tiff

    BMP-Series *.bmp

    Imarisreaderdeltavision

    Applied Precision DeltaVision *.r3d,*.dv

    Imarisreaderbiorad

    Bio-Rad MRC *.pic

    Imarisreaderiplab [BioVision purchased IPLab in 2006]

    BioVision IPLab IPM *.ipm Mac

    BioVision IPLab IPL *.ipl Windows

    Imarisreadergatan

    Gatan DigitalMicrograph *.dm3

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