Volocity Acquisition. Volocity Acquisition part of the Volocity family

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1 Volocity Acquisition Volocity Acquisition part of the Volocity family Volocity consists of four unique, totally integrated products that provide a suite of tools for 3D and 4D imaging. Choose the Volocity products you need for the discoveries you want to make today and add new products when you re ready to move forward. Your Volocity purchase includes a USB key and software for Mac OS X, 32-bit and 64-bit Windows for complete cross platform flexibility, greater productivity and sharing of results. Imaging Computing Server The Imaging Computing Server (ICS) is a partner product for Volocity that harnesses the power of recent advances in computer technology to provide enhanced performance of some key functions of Volocity. The ICS will accelerate image restoration, Ray Tracing, noise removal and 4D measurements (excluding tracking) by using multi-threading and is a scalable solution that can be built around your application and budget. Improvision License Server The Improvision License Server (ILS) provides network access to Volocity for any size group, from a single research lab right up to an entire institution. Using an ILS system with multiple Volocity licenses means that every researcher can share an imaging platform and use the same high quality tools, for a cost effective and resource efficient solution to cellular imaging. Improvision Technical Support Improvision is committed to providing the best in after-sales service. Volocity is supported by a dedicated Technical Support desk, manned by a team of highly trained staff. You can contact our team by or telephone, or use our web-based sources of information that are regularly updated with helpful notes and tips so that you can make the most of your Volocity products. Images reproduced by kind permission of the following scientists: Page 2: Zebrafish development. Courtesy of Dr. Nadine Peyriéras, CNRS-DEPSN, Institut de Neurobiologie Alfred Fessard. Acquired at the MiFoBio meeting, Page 3: Pancreatic islet cell. Sample supplied by Dr. Simon Watkins, University of Pittsburgh, at the Quantitative Fluorescence Microscopy imaging course, MDIBL Improvision, A PerkinElmer Company 940 Winter Street Waltham, MA USA Phone (+1) For a complete listing of our global offices, visit PerkinElmer, Inc. All rights reserved. The PerkinElmer logo and design are registered trademarks of PerkinElmer, Inc. Volocity is a registered trademark of PerkinElmer, Inc. Mac and QuickTime are registered trademarks of Apple, Inc. Windows is a registered trademark of Microsoft Corp. All other trademarks not owned by PerkinElmer, Inc. or its subsidiaries that are depicted herein are the property of their respective owners. PerkinElmer reserves the right to change this document at any time without notice and disclaims liability for editorial, pictorial or typographical errors _01 Printed in the USA

2 high speed, time resolved, 3D image acquisition Volocity Acquisition is designed for high speed, 3D image capture. It provides a flexible capture interface to a wide range of cameras, microscopes and associated hardware, so that you can select the most suitable hardware items for your application without compromise. Capture protocols can be quickly constructed using the clear and easy to use Acquisition dialogue from simple 2D image capture to multi-channel 4D experiments. Time lapse imaging with confidence When using Volocity to acquire images over time, you don t have to wait until the end of the experiment to see the results; you can review the data as soon as the first time point has been captured, so that you can be sure that your protocol is working correctly right away. This means that you don t waste valuable hours acquiring a data set that has failed to develop as expected. Key Features Easy to use, versatile protocol design for 2D, 3D and 4D experiments. Parallel processing for faster image acquisition and simultaneous image processing. Video streaming architecture for high speed image capture direct to disk. Compatible with a range of cameras, microscopes and associated hardware for maximum flexibility. Designed for Mac OS X, 64-bit and 32-bit Windows. Parallel processing and streaming technology for fast acquisition Volocity Acquisition uses parallel processing, which means that data acquisition and online processing of image data is much faster when using Volocity with a computer that has multiple processors. The video streaming architecture is designed to acquire image sequences direct to hard disk at the maximum frame rate possible from each supported camera. This means that with the right combination of hardware, high speed, 3D time lapse experiments can be performed with ease. The direct to disk streaming technology has the additional benefit of continuously saving acquired data, so that if your system should experience a power failure, your images will be preserved up to the time of the failure. Images are acquired directly into an image sequence. For time lapse experiments, the first time point data can be explored as soon as it has been acquired. Flexible protocol design for all your imaging experiments Capture protocols are created using the Acquisition Setup dialog. Once you have correctly configured your hardware in the preferences, simply enter the protocol parameters using the choices offered in the dialog. Your acquisition protocol can include any combination of multiple channels, time points and multiple point scanning on a well plate or slide, all performed in 3D, with Z step control using a motorized focus drive or piezo focus device. You can save your protocols for repeated use and name them so that they can be easily identified by anyone using the system. 2

3 Creating acquisition protocols is quick and easy to do, from simple 2D capture to 4D, multi-point, multichannel acquisition. Image acquisition made easy You can view your sample in the Video Preview before you start to capture images. You have the option to apply a color look-up table and Auto Contrast to both the Video Preview and to the images as they are acquired. Auto Contrast allows you to set a shorter camera exposure without reducing the apparent brightness of the image ideal for fast focusing or very rapid image acquisition. Customize the hardware interface controls on the Video Preview palette to hide items you don t use, so that navigation is easier. Once you have set up your acquisition hardware for a particular task, you can save the settings in the Light Path Manager. Properties that can be saved include filter position, objective turret, camera exposure and binning for use with a particular fluorochrome. This means that when you want to use the same settings again, you can simply click on the appropriate light manager button and they will be restored, saving you time and providing consistency. Multi-parameter protocols Protocols that involve scanning multiple points on a well plate or slide are easy to configure by first creating a Well Overlay of the selected or random points from which you wish to acquire images. Well overlays can be saved for reuse. By selecting the XY Stage in the Acquisition Setup dialog, images will be captured at the points set in the well overlay. The acquisition protocol can include image capture at multiple wavelengths, multiple time points and in 3D at each point you have selected, for complete flexibility. Volocity 3D Acquisition Solutions Volocity Acquisition drives a range of 3D imaging solutions, designed for applications ranging from multichannel fixed cell imaging to 4D live cell confocal imaging using spinning disk technology the UltraVIEW VoX. We can provide a complete hardware and software system, or drive your existing hardware where appropriate, for a cost effective and flexible approach to your imaging requirements. Acquisition controls are integrated into the preview window for convenience. The display can be customized to show only those controls you require. FRAP and Ratio Acquisition Volocity Acquisition can be used to acquire and analyze FRAP and ratiometric imaging experiments, by adding the optional FRAP Plugin and Ratio Plugin to your system. Volocity Quantitation must be included in the Volocity configuration in order to perform analysis. The FRAP Plugin supports the PhotoKinesis Accessory, which is an option to the UltraVIEW VoX spinning disk confocal imaging system. This configuration provides all the tools required to acquire and analyze FRAP images, providing both raw and graphical data. In addition to FRAP experiments, the unit can be used for techniques such as FLIP, photoswitching (photoconversion) and acceptor photobleaching. The Ratio Plugin provides the ability to acquire 2D and 3D ratiometric image pairs, with simultaneous online analysis, or post-acquisition analysis and charting of results. 3

4 Volocity Visualization Volocity Visualization part of the Volocity family Volocity consists of four unique, totally integrated products that provide a suite of tools for 3D and 4D imaging. Choose the Volocity products you need for the discoveries you want to make today and add new products when you re ready to move forward. Your Volocity purchase includes a USB key and software for Mac OS X, 32-bit and 64-bit Windows for complete cross platform flexibility, greater productivity and sharing of results. Imaging Computing Server The Imaging Computing Server (ICS) is a partner product for Volocity that harnesses the power of recent advances in computer technology to provide enhanced performance of some key functions of Volocity. The ICS will accelerate image restoration, Ray Tracing, noise removal and 4D measurements (excluding tracking) by using multi-threading and is a scalable solution that can be built around your application and budget. Improvision License Server The Improvision License Server (ILS) provides network access to Volocity for any size group, from a single research lab right up to an entire institution. Using an ILS system with multiple Volocity licenses means that every researcher can share an imaging platform and use the same high quality tools, for a cost effective and resource efficient solution to cellular imaging. Improvision Technical Support Improvision is committed to providing the best in after-sales service. Volocity is supported by a dedicated Technical Support desk, manned by a team of highly trained staff. You can contact our team by or telephone, or use our web-based sources of information that are regularly updated with helpful notes and tips so that you can make the most of your Volocity products. Images reproduced by kind permission of the following scientist: Page 2: Pancreatic islet cell. Sample supplied by Dr. Simon Watkins, University of Pittsburgh, at the Quantitative Fluorescence Microscopy imaging course, MDIBL Page 2: Zebrafish development. Courtesy of Dr. Nadine Peyriéras, CNRS-DEPSN, Institut de Neurobiologie Alfred Fessard. Acquired at the MiFoBio meeting, Improvision, A PerkinElmer Company 940 Winter Street Waltham, MA USA Phone (+1) For a complete listing of our global offices, visit PerkinElmer, Inc. All rights reserved. The PerkinElmer logo and design are registered trademarks of PerkinElmer, Inc. Volocity is a registered trademark of PerkinElmer, Inc. Mac and QuickTime are registered trademarks of Apple, Inc. Windows is a registered trademark of Microsoft Corp. All other trademarks not owned by PerkinElmer, Inc. or its subsidiaries that are depicted herein are the property of their respective owners. PerkinElmer reserves the right to change this document at any time without notice and disclaims liability for editorial, pictorial or typographical errors _01 Printed in the USA

5 fast, interactive, 4D volume rendering Volocity Visualization is designed to provide rapid, interactive, high resolution volume rendering of multichannel 3D and 4D data sets. This Volocity product puts you in full control of the way that you view your 3D data, offering a choice of rendering methods so that you can achieve the best results. A range of file formats can be imported from wide field and confocal microscopes and snapshots and movies to share and publish can be created quickly and easily. 3D imaging brings a new perspective to your research To truly understand the biology of your samples, you need to view them in 3D. Only when you see your sample from every direction, both inside and out, can you fully appreciate the complex interactions that occur between structures. Morphology that is difficult to comprehend in two dimensions can become clearer when viewed in 3D. Tracking moving objects such as vesicles and relating structure to function in time resolved experiments can give better results in 3D, as the whole volume of the sample can be explored, compared to only one optical Z slice using standard 2D imaging. Volocity Visualization will allow you to achieve this greater understanding quickly and easily, using high resolution rendering techniques. Key Features Interactive, high resolution rendering of 3D and 4D volumes providing new and exciting ways to explore your samples. Choice of rendering options included. Use with a wide range of file formats from confocal and wide field microscopes. Share and publish your results as images, QuickTime, AVI and WMV movies, or QuickTime Virtual Reality movies. Available for Mac OS X, 64-bit and 32-bit Windows. Interactive 3D rendering Volocity Visualization creates a high resolution rendering of your data which is fully interactive. This enables you to rotate, zoom and fly through the rendered object in real time, so that you can interact with and explore the data in new and exciting ways. Simultaneously, the channel controls allows you to vary the contribution of each channel to the rendered view to allow a better understanding of structural relationships within the object. For time lapse data, you can interact with the volume whilst playing through the data at each point, so that temporal changes in structure can be observed in 3D. Interactive 3D and 4D rendering adds a new dimension to your research. Time lapse data, such as this developing Zebrafish embryo sample, can be played through as a 3D rendering that remains fully interactive. 2

6 Choice of renderers Volocity Visualization provides a choice of interactive renderers which allow you to view and interact with your images as 3D objects, in either fluorescence or isosurface mode, so that you can decide how to best display your data. In addition, Volocity Visualization includes the Ray Tracer, a non-interactive renderer which produces very high quality rendered images, with user defined options such as lighting position, shadowing effects and background choices. The results can be spectacular in terms of the final image, although the process is more computationally intensive than the interactive rendering modes. This technique is ideal for producing publication quality images, when only the best will do. Image data can be viewed as orthoganol planes for close examination plane by plane. Bookmarks save a viewing state Using the Ray Tracer can produce very high quality images for publication. The bookmarks feature allows you to save a viewing state (orientation, zoom factor etc.) so that you can easily compare multiple data sets and be sure that you are using the same viewing parameters. Bookmarks can be created for the 3D, XYZ and slice views and provide a quick and easy way to create movies from your data. View your data in XYZ The Image view displays the volume as a series of orthogonal planes in XY, XZ and YZ. Move the cross hair cursor in one plane and the view in the other two planes will automatically update. The Image view is useful for precise location of structural details and you can vary the contribution of each channel as desired. For time lapse data use the playback controls to play through all the time points to see how your sample changes over time. Reslice your data If you find that the XYZ plane in which your volume has been acquired does not provide the best presentation of the structure that you wish to examine, you can reslice the data in a different orientation. You will then be presented with a new set of XYZ planes and your original data is unaffected by the reslicing process. Make movies and snapshots to share and publish your 3D and 4D data. Share and publish your images Volocity Visualization includes features to share and publish your results. The Capture Snapshot command is a convenient way to create images which can be exported from your Volocity library in standard publication ready formats. However, a single image cannot always convey the true 3D appearance of your volume, so why not make a movie that does? Create a collection of bookmarks then drop them into the movie making interface. You can then export the sequence as a QuickTime, AVI or WMV movie to share or publish on the internet. The option to make QuickTime Virtual Reality movies is also provided. 3

7 Volocity Quantitation Volocity Quantitation part of the Volocity family Volocity consists of four unique, totally integrated products that provide a suite of tools for 3D and 4D imaging. Choose the Volocity products you need for the discoveries you want to make today and add new products when you re ready to move forward. Your Volocity purchase includes a USB key and software for Mac OS X, 32-bit and 64-bit Windows for complete cross platform flexibility, greater productivity and sharing of results. Imaging Computing Server The Imaging Computing Server (ICS) is a partner product for Volocity that harnesses the power of recent advances in computer technology to provide enhanced performance of some key functions of Volocity. The ICS will accelerate image restoration, Ray Tracing, noise removal and 4D measurements (excluding tracking) by using multi-threading and is a scalable solution that can be built around your application and budget. Improvision License Server The Improvision License Server (ILS) provides network access to Volocity for any size group, from a single research lab right up to an entire institution. Using an ILS system with multiple Volocity licenses means that every researcher can share an imaging platform and use the same high quality tools, for a cost effective and resource efficient solution to cellular imaging. Improvision Technical Support Improvision is committed to providing the best in after-sales service. Volocity is supported by a dedicated Technical Support desk, manned by a team of highly trained staff. You can contact our team by or telephone, or use our web-based sources of information that are regularly updated with helpful notes and tips so that you can make the most of your Volocity products. Images reproduced by kind permission of the following scientist: Page 3: GFP-positive neutrophil granulocytes. Courtesy of Dr. Stephen Renshaw, University of Sheffield. Improvision, A PerkinElmer Company 940 Winter Street Waltham, MA USA Phone (+1) For a complete listing of our global offices, visit PerkinElmer, Inc. All rights reserved. The PerkinElmer logo and design are registered trademarks of PerkinElmer, Inc. Volocity is a registered trademark of PerkinElmer, Inc. Mac and QuickTime are registered trademarks of Apple, Inc. Windows is a registered trademark of Microsoft Corp. All other trademarks not owned by PerkinElmer, Inc. or its subsidiaries that are depicted herein are the property of their respective owners. PerkinElmer reserves the right to change this document at any time without notice and disclaims liability for editorial, pictorial or typographical errors _01 Printed in the USA

8 a range of tools to find, measure, track and analyze in 3D and 4D Volocity Quantitation provides a comprehensive range of options to analyze structure and function in 3D and 4D image data. Objects can be identified, measured and tracked in 2D, 3D and 4D. Objects and tracks can be viewed as overlays to image data ideal for relating structure to function, especially in time lapse data sets. Volocity Quantitation also includes functionality to analyze colocalization, FRET images and ratioed images. 3D measurements for precise results When using 3D data sets, Volocity Quantitation creates measurements using the entire volume of data. By working with 3D voxels instead of 2D pixels, the precision of your results is improved and you can understand your samples in greater detail. This is particularly important when tracking moving objects which may travel up and down within a sample as well as in X and Y. By analyzing the whole volume of the sample, objects can be tracked over many time points. Key Features Rapid measurement and analysis of objects in 2D, 3D and 4D. Provides automatic tracking of large numbers of objects in time resolved 2D and 3D data. Overlay the measured objects on the image data to better understand your results. Includes features to create charts and graphs as well as to analyze colocalization, ratioed and FRET images. Available for Mac OS X, 64-bit and 32-bit Windows. Step-by-step protocol design Volocity Quantitation works by creating a measurement protocol to detect the objects that you wish to measure or track. The protocol is made step-by-step using a combination of criteria intensity, size and shape are just some of the options you can include. Feedback to your images is displayed in the Measurement view so that you can refine your protocol quickly and easily. Protocols can be saved and applied to multiple volumes as a batch process, which is useful, for example, when working with time lapse data. Objects and tracks can be overlaid with 3D image data to allow a better understanding of results. Measurement protocols are created step-by-step, with automatic feedback to the image data, so that you can immediately see the results. 2

9 Data analysis tools Volocity Quantitation includes a powerful suite of tools to analyze your measurements. The results generated by the measurement protocol are stored in an analysis table. This provides the ability to summarize and extract data from your measurements; for example you may wish to analyze your data for patterns of change in intensity or volume over time at selected points; once the measurements have been made on the sequential volumes, the analysis table will allow the data to be extracted quickly and easily. 3D feedback display Once measured, objects and tracks can be viewed as feedback to the image data, to help you to relate structure to function. If you are working with 3D data and have Volocity Visualization as well, the feedback overlay will be displayed on the 3D volume for a better understanding of events. Create charts for export Creating charts from your measurements and tracking data is quick and easy. Choose from the many options available including bar and pie charts, histograms, and even interactive 3D charts, so that you can display your data using the most relevant method. Analysis of colocalization Objects and tracks can be overlaid to image data in a choice of ways. Movies can be created from this view to share and publish. Measurements can be analyzed and charted and data and charts can be exported for publication. 3D charts can be created for 3D data. 3D object tracking When used to track objects in 2D or 3D over time, Volocity Quantitation provides tracking data including velocity and distance traveled. For convenience each object track is identified by a number and a color in the Measurements table and tracking can be performed both automatically and manually. A choice of tracking models is provided and there are options to automatically join broken tracks, ignore static objects and ignore new objects, so that you can decide what is best for your data. Volocity Quantitation can quickly and accurately track several hundred objects within a data set. Volocity Quantitation can be used to analyze colocalization in pairs of images, by calculating measurement statistics based on the voxels and their intensity. Using voxels ensures that an accurate measurement of colocalization is obtained, although the software can be used with 2D images as well. The Colocalization view shows an extended focus merge of the selected pair of channels as a preview for the current time point and the scatter plot of colocalization. Selecting a region of the scatter plot produces a binary mask on the preview image to allow you to see the position of each selected voxel or pixel. Colocalization coefficients and Pearson s correlation may be calculated for whole volumes or the region of the scatter plot. FRET and ratio imaging FRET analysis allows accurate FRET measurements and generation of net FRET (or corrected FRET) and normalized FRET images for publication. The analysis currently offered by Volocity Quantitation is the 3-image FRET technique. Ratiometric imaging can be performed in Volocity using the Ratio Plugin, which provides the tools required to acquire ratio image pairs and perform simultaneous online ratioing. The Ratio Plugin requires Volocity Acquisition and Volocity Quantitation to function. Volocity Quantitation does however include tools to ratio and analyze image pairs that have been acquired using another system. 3

10 Volocity Restoration Volocity Restoration part of the Volocity family Volocity consists of four unique, totally integrated products that provide a suite of tools for 3D and 4D imaging. Choose the Volocity products you need for the discoveries you want to make today and add new products when you re ready to move forward. Your Volocity purchase includes a USB key and software for Mac OS X, 32-bit and 64-bit Windows for complete cross platform flexibility, greater productivity and sharing of results. Imaging Computing Server The Imaging Computing Server (ICS) is a partner product for Volocity that harnesses the power of recent advances in computer technology to provide enhanced performance of some key functions of Volocity. The ICS will accelerate image restoration, Ray Tracing, noise removal and 4D measurements (excluding tracking) by using multi-threading and is a scalable solution that can be built around your application and budget. Improvision License Server The Improvision License Server (ILS) provides network access to Volocity for any size group, from a single research lab right up to an entire institution. Using an ILS system with multiple Volocity licenses means that every researcher can share an imaging platform and use the same high quality tools, for a cost effective and resource efficient solution to cellular imaging. Improvision Technical Support Improvision is committed to providing the best in after-sales service. Volocity is supported by a dedicated Technical Support desk, manned by a team of highly trained staff. You can contact our team by or telephone, or use our web-based sources of information that are regularly updated with helpful notes and tips so that you can make the most of your Volocity products. Images reproduced by kind permission of the following scientist: Page 2: Meiosis in Drosophila germinarium. Courtesy of Professor Sharon Bickel, Dartmouth College. Improvision, A PerkinElmer Company 940 Winter Street Waltham, MA USA Phone (+1) For a complete listing of our global offices, visit PerkinElmer, Inc. All rights reserved. The PerkinElmer logo and design are registered trademarks of PerkinElmer, Inc. Volocity is a registered trademark of PerkinElmer, Inc. Mac and QuickTime are registered trademarks of Apple, Inc. Windows is a registered trademark of Microsoft Corp. All other trademarks not owned by PerkinElmer, Inc. or its subsidiaries that are depicted herein are the property of their respective owners. PerkinElmer reserves the right to change this document at any time without notice and disclaims liability for editorial, pictorial or typographical errors _01 Printed in the USA

11 4D volume restoration for wide field and confocal image data Volocity Restoration provides a choice of proven restoration algorithms to quickly and easily convert standard wide field fluorescence microscope images into superior confocal quality data, removing out-offocus haze and producing exceptional results. Volocity Restoration is an essential addition to your imaging tools and can be used to improve images from confocal microscopes as well as wide field data. Confocal quality images from a wide field microscope When you acquire image data from a wide field microscope, the images can contain out-of-focus as well as in-focus information, created as a product of the optical properties of the microscope. This unwanted haze can be removed quickly and easily using Volocity Restoration so that you can achieve confocal quality images without using a laser scanning confocal microscope. Key Features Includes Fast Restoration, an ultra-fast routine for improvement of resolution in X and Y. Includes Iterative Restoration, an award winning algorithm for improvement of resolution in X, Y and Z. Calculated PSFs for confocal and wide field microscopes can be created, or use a measured PSF from your microscope. Batch process multiple data sets for convenience. Available for Mac OS X, 64-bit and 32-bit Windows. Includes two restoration algorithms Two options are included in the product; Fast Restoration and Iterative Restoration. Which one you choose will depend on how you wish to use the resulting images. Even if your images were acquired using a laser scanning or spinning disk confocal microscope, the image quality may benefit from applying Volocity Restoration. Volocity Restoration removes out-of-focus haze to produce confocal quality image data. 2

12 Fast Restoration The Fast Restoration algorithm is an ultra-fast routine developed by Improvision, which uniquely uses every voxel in the volume in a single pass process to improve both the visual quality and the precision of the result. This feature is extremely fast to compute and produces superior results when viewed in XY. Fast Restoration will significantly improve the visual quality of your images, to reveal details that would otherwise be obscured, allowing you to successfully explore your data in 2D or in 3D using Volocity Visualization. Iterative Restoration The Iterative Restoration algorithm is an award winning restoration algorithm developed by Improvision from published Maximum Entropy techniques. It uses a restorative technique that reassigns out-of-focus haze rather than subtracting it from the data. Iterative Restoration is a more computationally intense process and therefore takes longer to produce results than Fast Restoration. However, it will not only provide an improvement in resolution in X and Y, but very importantly, also in Z. The resultant images can be used for making intensity and morphological measurements as well as for visualization purposes. Volocity for 64-bit Windows a faster option for restoration Volocity Restoration is available for Mac OS X, 64-bit and 32-bit Windows. The 64-bit version of Volocity is designed to take advantage of a recent development in computer technology, Windows XP Professional x64 Edition. This operating system was created specifically for applications such as Volocity that use large amounts of data. Benchmark tests have confirmed that processes including Iterative Restoration are significantly faster using the 64-bit version of Volocity. Volocity Restoration can be used with wide field and confocal image data. These images were acquired with a wide field system and are shown before and after deconvolution with Fast Restoration. 3