MScan 2.3 and MView 3.2

The new version of MCS, which includes MScan 2.3 and MView 3.2. has been sent for beta-testing. Aside from improvement in performance and minor bug fixes, the two prgrams introduce new scripting features which will facilitate near real-time processing of imaging data, even in resonant scanning mode.

MScan 2.3 can now export frame data during the OnNewFrames event by using the GetFrameArray method, which returns a variant array which contains the latest frame values of a specific imaging channel. Incoming data can be piped into a workspace in MView for display and processing. What is noteworthy is the possibility to jump outside the boundaries of MScan to pass data to another program in a time-efficient manner. In principle, the result of GetFrameArray should be compatible with Matlab’s PutWorkspaceData. 

The next release of MScan will have a version number matching that of MView. We plan to support additional hardware. In particular, we intend to make MScan compatible with a high-speed, low-cost USB 3.0 video camera for synchronous behavioral recordings. 

MScan 2.2 and MView 3.1 in beta testing.

MScan 2.2 and MView 3.1 are in beta testing at Sutter Instrument.

This release introduces episodic acquisition, a feature available in resonant scanning mode.

MScan 2.2 is now able to simultaneously acquire multiphoton frames with synchronized analog data and video streaming images into stretches called "episodes". Episodic imaging is first armed manually then automatically started by a TTL signal going high. Episodes are stopped automatically either when a pre-set number of imaging frames has been reached or when the TTL signal goes down. Subsequent episodes are re-triggered by the TTL line. Live display of two-photon imaging channels, analog channel voltages and video stream is turned off when episodes are not acquired. In addition, the Pockels cell modulating the ultrafast laser output is set to a minimum between episodes, thus preventing overexposure of the sample during the experiment.

The main advantage of running an experiment using episodic acquisition is to reduce the amount of data to analyze. What makes episodic acquisition unique in MScan is the fact that episodes are sequentially stored in separate "folders" in the same data file. In practice, there is no limitation in the size of each episode, allowing many arbitrarily long bouts of data (i.e., > 4 GB) to be  recorded in one data file. Because the starting time of each episode is written to the file with a 1 ms accuracy, data analysis of discontinuous periods of imaging is greatly facilitated. MView and MCSX have been enhanced to easily handle episodic files.

MScan 2.1. Close-loop scripting benchmarks

MScan 2.1 brings new scripting capabilities to easily develop and run close-loop experiments based on functional imaging with multiphoton microscopy. Particular attention was devoted to optimizing the response time of scripting functions.

The StartDigitalTrain and StartAnalogTrain functions introduced in the previous post are fast enough to be used in non-resonant scanning experiments, but with resonant scanning we recommend using the new scripting methods SetDigitalTrain, SetAnalogTrain, FireDigitalTrain and FireAnalogTrain.

SetDigitalTrain and SetAnalogTrain are quite similar to their counterparts StartDigitalTrain and StartAnalogTrain with the exception that they do not output the train. SetDigitalTrain and SetAnalogTrain can be used for instance in the On Scanning Starts event to set up and arm either a digital or an analog train. Train delivery can be done with minimal latency using FireDigitalTrain or FireAnalogTrain, for instance when processing ROIs in the On New Frames event handler. If an analogy with electronics can be made, the pairs of scripting functions SetDigitalTrain/FireDigitalTrain and SetAnalogTrain/FireAnalogTrain are similar to non-retriggerable, one-shot train stimulators. Resetting the stimulators is automatically performed when the imaging run terminates, regardless of whether the train was delivered or not.

We performed initial benchmarks to measure and optimize the latency of script-triggered delivery of digital trains in resonant scanning mode, which is arguably the most demanding situation to run scripts driven by frame acquisition. The latencies result from delays to:

(1) get the imaging data from the acquisition board to memory,

(2) process frame data (mostly reordering pixels into an image, adding offsets etc…),

(3) signal threads that frame data is available,

(4) activate the scripting interpreter,

(5) execute the user-written code in the On New Frames handler

(6) and deliver the digital train;

The tests were conducted in resonant scanning mode using a protocol involving simultaneous acquisition and real-time display of two imaging channels and two analog channels with each analog channel sampled at 20 kHz. The first analog channel recorded the motion of the “slow” Y mirror to give accurate timing of frame acquisition while the second analog channel was connected to the digital output of the analog board. MScan was set to process every frame individually rather than in batches as soon as frames arrived.

The script executed SetDigitalTrain in the On Scanning Starts event handler to set up a train consisting of ten pulses of 10 ms duration each. The On New Frames executed the user-written code:

If CurrentFrameIndex = 20 Then FireDigitalTrain

to deliver the digital train immediately after the 20th imaging frame was scanned and processed. 

With 512 x 512 frames sampled at 31 fps, the latency from the mirror position at the end of the 20th frame to the beginning of the pulse train ranged from 15 to 17 ms. In comparison, the frame interval was 32 ms. In other words, MScan can react asynchronously to run user-written scripts and deliver stimuli in less time than the sampling interval of two-photon imaging, even in resonant scanning mode. Similarly, we obtained a near real-time latency of only 8-10 ms with frames sampled at 94 fps (512 x 170 frames). We found that most of the latencies in both cases were due to waiting for the device driver of the acquisition board to complete Step 1 described above.

We are looking forward to hear from scientists running cutting-edge, script-based close-loop experiments with the MOM and MCS.

MScan 2.1. New feature: close-loop experiments

Two-photon close-loop experiments with MScan 2.1.

MScan can react in near real time to changes in image intensity to trigger a response. This feature opens the unique possibility to perform close-loop experiments either in brain slices or even in live animals.  Custom code can be easily written using the built-in scripting environment to perform specific actions when certain cells in the field of view become more active. These actions can include for instance the delivery of an analog or a digital stimulation pattern. Scripts allow developing complex experiments easily - you can imagine triggering an optogenetic stimulation when the difference in activity between two or more cells reaches a threshold. It might be even possible to obtain the phase-response curve of an entire neural network imaged by two-photon microscopy. These experiments can be programmed in scripts by using a combination of:

The OnNewFrames event. The OnNewFrames scripting event is triggered each time one or more frames have been received. In MScan 2.1, special care has been taken to ensure that OnNewFrames is called with the lowest latency possible. The code associated with OnNewFrames runs in its separate thread to ensure that it does not slow down frame acquisition while taking advantage of the multicore capability of the processor powering the the MScan computer. The CurrentFrameIndex property returns the current frame index, allowing for instance specific code to be run after waiting for a certain number of frames. A new protocol setting called Process Frames can be set to At Every Frame to ensure that OnNewFrames is called each time a new frame has been acquired.

The ROIs property. Intensity data from Regions Of Interest (ROIs) are now available in scripts in real-time. Arbitrary rectangular, elliptical or polygonal regions can be created around cells in the Viewer window. Intensity values can be used in scripts with the ROIs property, which returns the pixel intensity of a specific ROI averaged across all pixels of the ROI for the latest frame and those preceding it. ROIs(3, 0) will return the intensity of ROI number 3 in the latest frame acquired (0 is the index of the most recent frame in the ROIs buffers).

Analog and digital stimulation. Scripts can now generate analog or digital trains without having to use the Stimulator object. The StartAnalogTrain or StartDigitalTrain methods can be used to specify and deliver analog or digital train in scripts, for instance during the OnNewFrames event. Analog trains can use any of two analog outputs available on the PCIe-6321 board, while digital trains can be delivered on any of the eight digital input/output lines of the board. This gives plenty of flexibility to trigger either inhibitory or excitatory stimuli depending on the functional response of the network imaged by two-photon microscopy. A typical train consists of a delay and a series of one or more identical pulses, each composed of two steps with independent duration and value. For instance, StartDigitalTrain 1000000, 255, 15000, 0, 5000, 100 will deliver 100 pulses consisting first of  a step setting all 8 of the digital lines to 1 (11111111 in binary = 255) lasting 15000 microseconds (i.e., 15 ms) followed by a step where all the lines are back to 0 (000000000 in binary = 0) for a duration of 5 ms (5000 microseconds). The step is preceded by a delay of 1 s (1000000 microseconds) with all lines set to 0. StartAnalogTrain delivers a train consisting of analog values from -10 V to + 10 V on one of two possible analog output channels.

Putting all these elements together in a script is straightforward. In the OnNewFrames code editor, the line:

If ROIs(1, 0) > 1500 Then StartDigitalTrain 0, 255, 10000, 0, 10000, 100

will deliver a digital train each time ROI number 1 will be above a value set to 1500.

We hope far-reaching experiments will be possible with the script-based close-loop features of MScan.

MScan 2.1. New feature: behavioral camera

Concurrent video streaming.

Cutting-edge multiphoton experiments now deal with imaging neurons in awake animals performing a behavioral task. Observing animal actions and timing them accurately with respect to functional imaging is of paramount importance to correlate behavior with neural activity. MCS is well-suited for these kinds of experiments. Information from sensors for touch or licking behavior can be displayed and recorded using the eight analog channels available on the analog input board, a National Instruments PCIe-6321 board which is capable of sampling data at up to 250 kHz.

In addition, MScan 2.1 now supports a second, optional video camera dedicated to filming behavior during scanning. The first camera, also optional, is used for focusing the microscope. The cameras, which are identical, are designated as CSFV90BC3-B from their manufacturer, Toshiba-Teli. They output VGA-style black and white frames with 256 levels of gray (i.e., 640 x 480 pixels with an 8-bit resolution).

MScan 2.1 takes advantage of the fact that Toshiba-Teli FireDragon cameras can be triggered externally, a feature that is seldom found on cameras in that price range. This capability allows accurate hardware synchronization of frames from the camera with those taken by the MOM. Because CSFV90BC3-B  cameras can acquire frames at a rate of up to 90 fps, video streaming can be performed simultaneously even with resonant scanning. Internal frame buffering inside the camer and computer interfacing through IEEE 1394B (i.e., FireWireB), which guarantees data transfer at up to 800 Mbit/s ensure loss-free streaming. In MScan, the video stream is displayed live during two-photon imaging and is stored in parallel with the two-photon imaging frames in the same data file to facilitate analysis with MView. A custom cable is used to convey the Frame Sync signal from the computer to the camera. Initial testing shows concurrent video and two-photon display and streaming with two imaging channels at close to 90 fps.

MView 2.1 has been enhanced to open and display the video stream stored in data files synchronously with the two-photon images. Multiple video stream windows can be opened simultaneously to ease frame-to-frame comparisons. The video stream can be converted into an AVI movie or individual frames can be saved as bitmap files.

MScan 2.1. Enhancements in ROIs

Enhancement of ROI handling

Plotting the intensity of regions of interest (ROIs) in real-time, especially during resonant scanning is one of the most useful features of MScan when performing functional imaging with calcium indicators or other functional dyes. ROIs can be drawn directly on features displayed in the Viewer window as ellipses, rectangles or polygons.

With MScan 2.1, individual ROIs can be moved pixel-by-pixel with with keystrokes (Shift+1,2,3, or 4) or deleted, while all ROIs can be saved or recalled from a *.ROI file which can be used by MView to load ROIs.

ROIs are a key feature of two-photon close-loop experiments (see later post).

MView 2.1. New Features: Frame and line shifting

Manual shifting of images.

One issue with functional imaging is motion correction. This procedure can be handled automatically in MView with the Motion Correction algorithm. However, on occasion, one needs to adjust " by hand" the position of individual frames relative to other frames by shifting pixels in the X or the Y position. MView 2.1 allows users to perform this correction with the Ctrl+1, 2, 3 or 4 keystroke combination to move frames pixel by pixel. The modified frames can be reviewed then saved into a new data file. The modified frames can be reviewed then saved into a new data file.

Scan line aligment.

Another related feature of MView 2.1. is the possibility to cancel or reduce scanning artifacts due to misalignment of scan lines, often seen as “hairs” on images after acquisition. Pixel shifts, which are used to move odd lines horizontally with respect to even scan lines, can be fractional (e.g., ‘4.3’). The integer value of the shift (i.e., 4) moves odd lines by four pixels, while the fractional value of the shift is used to interpolate the values of consecutive pixels in odd lines to provide a sub-pixel positional adjustment. Contrary to manual shifting, scan line alignment applies the same shift to all frames in a file. The modified frames can be reviewed then saved into a new data file.

MView 2.1. New feature: Searching MDF files

Searching MDF files

Multiphoton experiments eventually generate lots of data files. This trend will continue with the use of the MOM in automated high-content screening experiments. Annotation and indexing of data files with relevant meta-data information is one of the strengths of the MOM Computer System. MDF files already store a large number of pre-set tags such as Frame Width, Comments, etc… In addition, users can add arbitrary pairs of Property Name/Property Value such as “Animal Age=21” during acquisition, either

• automatically, by specifying these values when the user logs into MScan; in this case, all data files generated during the current session will be tagged with the same extra meta-data
• manually, by clicking on the File Comments button on the MOM Control Panel
• or programmatically, using the ActiveX Automation feature of MScan which can also be called from within a script.

Finding out if a data file contains a specific Property Name/Property value can be done in several ways:

• Right-clicking on the file, clicking and Properties menu item and choosing the Custom or Details tabs in the Properties window will display the list of Property Name/Property Values 
• In MView, by accessing the Custom Properties tab of the File Properties on the File Manager window
• In MCSX.OCX by using the ReadParameter function.

MView 2.1. provides powerful tools to make data analysis even more efficient.

Metadata in MDF files are now automatically indexed by Windows Search, the  desktop search platform available on any computer running Vista or later versions of Windows. This allows MView users to query Windows to show the list of all MCS files at chosen locations that have specific metadata in their header such as “Animal ID =GCamp6_25” and “Tag1=Grating_45”.

Complex searches using logical operators can be done from MView using Structured Query Language (SQL). In addition, data mining can be made even more efficient by programmatically controlling Windows Search to find MCS files using an application programming interface based on OLE DB/SQL.

MCS 2.1 in testing

MCS 2.1 is a major release which features the following enhancements:

• Concurrent video streaming in MScan
• Enhancement of regions of interest in MScan
• Close-loop experiments in MScan
• Integration with Windows Search in MView
• Minor bug fixes/improvements

We expect MCS 2.1 to be available to our 32- and 64-bit customers very soon. As seen in the diagram below we now provide a comprehensive high-performance computing system to perform and analyze data from the most demanding experiments in multi-photon microscopy using the MOM.

2.0.6.3 in advanced beta testing

MScan and MView 2.0.6.3 32- and 64- bit are in advanced beta testing and should be released soon.

New Features in 2.0.6.3.

Heat display. Functional imaging of  fast calcium transients in live tissue is a very important application of two-photon microscopy.  Monitoring fluorescence changes in real-time provides essential feedback on how the experiment is running. MScan allows plotting the intensity of multiple regions of interest across time even in resonant scanning mode. In release 2.0.6.3, MScan introduces a new way to visualize active areas by displaying a live heat map with “hotter” colors  representing pixel intensities greater than those of a "baseline" frame. The map is superimposed over the current frame. Regions whose activity is below a pre-set threshold will be seen through the heat map. The heat map will facilitate spotting patterns of spatial activity. MView 2.0.6.3 also allows overlaying a heat map above frames, which can lead to the creation of visually appealing movies.

Data file recovery. Programs like MScan or the computer running them can crash unexpectedly, resulting in damaged data files. MView 2.0.6.3 can detect when a file generated by MScan 2.0.6.3 is corrupted and offers the possibility to repair it via a window allowing users to correct or enter missing metadata information.

Minor improvements in MScan 2.0.6.3.

• Increased limit on number of frames that can be averaged during live display or stacks. Up to 200 frames can be averaged on a rolling basis and displayed when taking movies.
• Resonant mode: frame rates of 496 fps (512 x 32 lines) and 565 fps (512 x 28 lines) have been qualified.

Cloud-based storage in MCS 2.0.6: setting up MScan and MView to access the cloud

In MScan and MView, each user (chosen or created from the User window shown when the programs start) has his or her own cloud settings.

Click on the Settings/Cloud Storage Settings menu item on uppermost window of MScan or MView.  

For Amazon S3:

Choose Amazon S3 for the service and  enter the Access key ID and the Secret key ID.

For Microsoft Azure

Choose Microsoft Azure for the service and enter the Storage Account Name and the Primary Access Key.

Cloud-based storage in MCS 2.0.6: introduction to S3 and Azure

Amazon S3 (Simple Storage Service) and Microsoft Azure services are very similar in the way they operate. Their services can be tried for free, either for a limited time or for a certain amount of data transfer. In addition, data files located on the cloud are organized in a similar way (see table below). The the top level is called an account, which would be similar to a disk drive. The account holds either buckets or containers, which are very similar to disk folders or directories. Buckets or containers contain objects or blobs. For all practical intent, objects or blobs are MCS data files. A major difference between a file system on a disk and the S3 or Azure cloud storages is the fact that buckets or containers cannot contain other buckets or containers, only objects or blobs.

Your Amazon S3 Microsoft Azure

computer

Drive Account Storage Account

Folder Bucket     Container

File         Object Blob 

An Azure storage can store up to 200 TB of data. Blobs can be as large as 200 GB.

MScan allows you

• to create new buckets and containers
• and directly upload data files to one of these "folders" at the end of an imaging session.

MView is capable of

• dowloading data files on the cloud to a local folder on your computer
• create new buckets or containers.
• upload files to the cloud
• delete files in the cloud

Cloud-based storage in MCS: setting up your S3 or Azure account

For Amazon S3:

1. You need first to set up an account. Go to:

Amazon S3: http://aws.amazon.com/s3/

2. Once you are activated, you will receive a confirmation e-mail. Follow the instructions in the e-mail to set up Access Identifiers. Use the Web-based AWS Management Console to try creating a bucket, manually upload a file etc… Click on the Security Credentials menu item (under the menu item bearing your user name).

The two most important information to retrieve from your account are:

• Your Access Key ID: it is a 20 character-long string
• Your Secret Key: it is a 40 character-long string

Copy these two values somewhere (on paper, in a text file or in an e-mail) to register later in MScan and MView.

For Microsoft Azure:

1. You need first to set up an account. Go to:

Microsoft Azure: http://www.windowsazure.com/en-us/

This requires an account name and a password.

Log into the Windows Azure Management Portal.

Click on the NEW button at the bottom of the navigation pane 

Click on DATA SERVICES menu item on the left of the window, then click on STORAGE, QUICK CREATE.

Enter a name for the storage account in the URL input box (e.g., jimtwophotonfiles), select a location for the file repository (e.g., West US) and enable/disable geo-replication.

2. Once the storage account is created

Click on the Manage Access Key button at the bottom of the screen 

The two most important information to retrieve from your account are:

• Your Storage account name
• Your Primary Accesst Key

Copy these two values somewhere (on paper, in a text file or in an e-mail) to register later in MScan and MView.

Backing up and archiving your multiphoton data: the MCS 2.0.6 cloud-based solution

Optical imaging instruments such as multiphoton microscopes generate large amount of data. Because MOMs are often used to collect two-photon images many times per second over periods ranging from minutes to hours, typical files can routinely exceed hundreds of megabytes. The trend towards producing tens or hundred of gigabytes of data per day is accelerating with the use of video-rate resonant scanning imaging in behavioral experiments. As a resut, the problem of backing up and archiving terabytes of two-photon datasets is becoming particularly acute. One could use a local file server but this requires funds to buy the hardware, expertise to set up the server and some kind of periodic administration. And of course, when the file server is full, someone will have to take care of the problem.

The computer industry has already a solution, called "cloud storage" to safely store large amount of data without having to invest in a costly infrastructure. In exchange for a small fee, Web behemoths such as Amazon, Google and Microsoft offer disk space on their servers to end-users, provide a Web-based interface to administrate accounts and programming tools to upload or download files. The advantages of cloud storage include:

• virtually unlimited or extremely large storage capacity.
• reliability: the data is usually stored in triplicate and, optionally, at sites that are geographically distinct to prevent losing data in case of a catastrophic hardware failure.
• universal availability through an Internet connection.
• flexible pricing that scales up with the amount of data you store.

MCS 2.0.6 now leverages cloud storage capabilities by allowing:

• in MScan, to systematically upload your newly created data files to a user-specific location on the cloud upon finishing an imaging session. You won't have to back up (or forget to archive...) your data files manually anymore.
• in MView, to download data files from the cloud to your local disk storage to perform analysis. Your data is available anywhere and at all times as long as you have an Internet connection to access your cloud account.

MCS 2.0.6 at present supports two services, Amazon S3 (Simple Storage Service) and Microsoft Azure. If you opt for their fee-based plan, Amazon has no restriction on the amount of data you can store while Microsoft now caps the amount of data per storage to 200 TB. However, you can create as many storage accounts as you want. Maximal file size is 200 GB and 5 TB for Azure and S3, respectively.

There are many other cloud storage companies. Google has a service similar to S3 and Azure called Drive, but files cannot be larger than 10 GB, which could be a problem with data collected in resonant scanning mode. For those who are accustomed to Dropbox, it appears that this company uses Amazon S3 as its underlying infrastructure.

MCS 2.0.5 released soon

MCS 2.0.5 is currently being tested for imminent release.


MScan 2.0.5

New features:
(1) NON-RESONANT SCANNING.  The 3DMap window demagnification can be changed to be less than one (i.e., one can zoom in on views).
(2)  NON-RESONANT SCANNING. Photostimulation targets can now be designated in the 3DMap window with a demagnification < 1.
(3) Time-lapse imaging can now be done with intervals less than 1 s (the interval between frames is now set in milliseconds). You can take frames every 500 ms when your frame duration is less than that (for instance ~ 330 ms at the default frame rate of 3.05 fps).
(4) There is now a zPiezo Automation object (of the Piezo type) that allows outputting voltages to the z-piezo controller during scripts.
Features (3) and (4) allow scripts to move the objective with the piezo in time-lapse mode after taking a frame. The idea is to take a frame and while waiting for the next frame, to move the piezo. The interval between each frame will allow the objective lens to settle when performing large z- changes.
Bug fixes:(6) RESONANT SCANNING. There was a bug in generating the waveform controlling the Pockels cell.(5) NON-RESONANT SCANNING. When imaging a subframe (less than 512 x 512) consecutive images are not flipped anymore (subframes are selected by dragging the mouse over a region inside the display area of the Viewer).


MView 2.0.5

Improvements
- When converting to TIFF files, information is now written as an ASCII string (not as UNICODE).

Bug fixes
- Files taken during photostimaging in modes other than region scans can now be open in MView.

The on-line documentation has been updated.

On avoiding TIFF files

TIFF files.

TIFF (Tagged Image File Format) files are used by several notable two-photon imaging software packages to store frame data. TIFF files appeared in the mid-1980s and the latest update, TIFF 6.0 was issued in 1992. Needless to say, TIFF files are woefully outdated - one of the biggest limitations of TIFF file is their size, which cannot be larger than 4 GB.

With conventional scanners, when imaging 512 x 512 frames at 2 fps on two channels, a TIFF file would be full in about 34 min. As I mentioned earlier, this would happen in a little more than 2 minutes in resonant scanning. Writing files in the BigTIFF format could bypass the 4 GB size limitation, but this new file format is not widespread.

Another disadvantage of TIFF (and BigTIFF) files is their internal organization (or lack of). Frame data can be placed anywhere in the file, thus defeating most streaming strategies. In particular, TIFF readers cannot expect the n-th frame to be located at a predictable location related to the frame index - the entire file has to be read until that frame is found, which is arguably a performance problem with large files.

Lastly, the collection of image tags is not extensible so important two-photon scanning information has to be placed arbitrarily in the image description section of the file.

For those who are accustomed to analyzing data in TIFF files, MView provides MCS to TIFF conversion, either for individual files or for batches of files in the same folder.

Structured Storage files.

MCS uses an advanced file format that completely overcome the shortcomings of TIFF files. Firstly, MCS files are based on the Structured Storage technology available under Windows. Structured storage files are like miniature file systems that contain arbitrary numbers of folders called storages which in turn can hold either other storages or internal files called streams.

An immediate advantage of such files is the ability to store analog data (e.g., electrophysiology) in a separate stream alongside imaging data. Individual streams can be as large as 16 TB, so there is little concern that Structured Storage files will run out of space in the foreseeable future. Writing or reading data to or from  the data file is straightforward, thus efficient, during streaming operations. MView has no difficulty opening and reviewing data files larger than 100 GB. In principle you can think of adding all kinds of parallel streams of data, for instance visual stimuli patterns without disturbing the structure of the file.

Similarly, file properties are stored in an independent stream. MScan writes standard file property / value pairs (e.g., microscope lens resolution, stimulation parameters, etc…) but you can add also your own property names and values to the file (e.g., "Animal Line" = "Wfs1-Tg2-CreERT2 : Ai38").

During analysis by either MView or MCSX, file properties can be queried programmatically for property values. You can also visualize the property name / value list of any file without opening it by right-clicking on the file name in any Explorer window.

Structured Storage is a powerful technology used by many professional Windows programs including Microsoft Office, MSSQL, Dassault Systemes SolidWorks and other CAD programs. By using Structured Storage, MCS provides two-photon experimenters with a whole new level of capabilities during imaging and data analysis.

MCS 2.0: 32-bit and 64-bit versions

The programs in MCS are now either 32-bit or 64-bit.


MScan 2.0

The new MCS 2.0 workstation runs MScan 2.0 64-bit under Windows 7 64-bit Professional Edition. This system, which allows either conventional or resonant scanning, is now the standard computer for new MOM and MCS orders.

We provide a 32-bit version of MScan 2.0 for customers who are running MCS on a 32-bit computer. To allow resonant scanning, we recommend switching to the 64-bit version of MCS.


MView 2.0

MView, the analysis program of MCS and the software component MCSX (which allows, for instance, to read MCS files from Matlab) are free of charge and can be downloaded from the web site of Sutter Instrument (www. sutter.com). They can be installed on any version of Windows starting from XP.

The MCS analysis package is now available in either 32-bit or 64-bit versions. Prior to installation, choose the correct version that matches the "bitness" (32-bit or 64-bit) of your operating system.

MOM and MCS 2.0: now with resonant scanning

Resonant scanning allows video rate two-photon imaging at 31 frames per second, a near 10-fold increase in frame rate over conventional scanning. Sutter Instrument is now proposing its Moveable Objective Microscope with either conventional or resonant scanners.  Current owners of the MOM can also benefit from the advantages of resonant scanning without having to buy a new microscope. The unique design of the resonant scanning unit allows swapping it with conventional scanners in a matter of minutes. The resonant scanning module provides also much needed sound muffling. 

MCS, the computer system of the MOM, has been upgraded in version 2.0 to control either type of scanning from the same Windows 64-bit MCS workstation. There is, by design, much commonality between the hardware and wiring of the two systems. Switching between conventional and scanning mode in MScan 2.0, the acquisition program of MCS, requires only restarting the application.

Notable features of MScan 2.0. operating in resonant scanning mode include the possibility to:

• acquire and display 31 frames per second on two channels with 512 x 512 frames, or even at a higher rate by selecting a subframe (e.g., 124 fps with 128 x 512 frames), while simultaneously
• perform the "Sanderson correction" to linearize the field of view
• acquire up to 8 analog channels
• stimulate the preparation with 2 analog channels and 8 digital channels
• plot intensities of regions of interest in real-time (very useful when doing calcium imaging)
• run JavaScript or VBScript automation programs in the background
• and stream data to disk.

Because resonant scanning generates a large number of frames very quickly, it is a challenge to store the incoming data on file. Many programs other than MScan use TIFF as their main data file format, which is inadequate for resonant scanning due to the 4 GB limitation in size of these files. With two imaging channels, it would take only 2 minutes and 16 seconds to fill a TIFF file to capacity. To allow continuous recordings on a much longer scale, MScan features a high-speed, large capacity disk streaming system. This allows MScan to record more than 100 GB of uninterrupted imaging data in the same file. In addition, a new triggering mode allows starting and stopping imaging and data streaming upon sensing the level of a TTL line. The possibility to perform gap-free resonant imaging for several hours is a major advantage of using MCS in experiments involving behavior.

Welcome to the Sutter MOM blog

The Sutter MOM blog.

You will find news, updates and tutorials related to the hardware and software of the Moveable Objective Microscope from Sutter Instrument.