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
