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Synapse Tech Notes

Help links don't work in Adobe Reader DC 2020

TN2001

Product: Synapse, RPvdsEx
Version: 94
Date Added: 2020-02-19

Issue

When clicking on the help link in Synapse, or for an RPvdsEx component, the PDF manual opens but does not jump to the correct page. This is observed with Adobe Reader DC 2020 only.

Workaround

Download the latest TDTToolBox.dll, copy it into C:\TDT\lib and C:\TDT\Synapse (if using Synapse), replacing the file that is there.

Solution

Upgrade to the latest version of Synapse.

Fiber Photometry Response Data Has Oscillation Artifact

TN0991

Product: RZ5P, Synapse
Version: All
Date Added: 2019-07-12

Issue

The issue typically is seen as a low-frequency oscillation in the demodulated data streams.

Solution

Find the minimum DC Offset, as recommended per the Fiber Photometry User Guide, then make sure to at least double that value. The distortion between the signals levels off at about twice the minimum DC Offset. If you have an LED driver that has low power mode, then we recommend using this setting.

TDT recommends using attenuating patch cords between the LEDs and the Doric Minicube (or light filters). This will allow the RZ5P DACs to be driven at a higher voltage range. This is also beneficial in general because the step resolution for LED driving current is much finer.

Note that if you were not seeing any oscillatory issues before, then there was not a problem in the data. In most cases, even if some distortion was present, the effect is at least an order of magnitude smaller than typical GCaMP activity so there would be no issue in analysis.

RV2 or RS4 can't be reached on network

TN0990

Product: RS4, RV2, Synapse
Version: All
Date Added: 2019-01-10

Issue

If you can see the RS4/RV2 in zBusMon but are having problems mapping it as a network drive, reaching it from Windows Explorer, or problems retrieving an image from the RV2 camera in RVMap, it is likely a compatibility issue with the server protocol the RS4/RV2 uses.

Solution

You can enable support for SMB1 on your machine in the Turn Windows features on or off dialog (part of Add or Remove programs).

More information on the topic can be found at this link.

RS4 High Channel Count Streaming

TN0989

Product: RS4, Synapse, RPvdsEx
Version: 90
Date Added: 2018-10-15

Issue

Improvements to the RS4 firmware have improved stability when streaming high channel count data to multiple ports on the RS4. This requires updates to the software (Synapse and RPvdsEx macros) and RS4 firmware.

Solution

Users streaming high channel count data to multiple RS4 ports require an additional setting. The "Use Larger Buffer Size" option allows more DSP memory to hold the data destined for the RS4, which improves reliability during the data transfer. The RS4 must be updated to v1.19 firmware to most effectively use this setting (more on that below).

In Synapse, this option is in the RS4 options:

If using OpenEx, this option is in the v90 Stream_Server_MC macro In RPvdsEx:

RS4 v1.19 Firmware Update:

It is recommended that all RS4 users update to the latest RS4 firmware. With the RS4 connected to the internet, go to the Config tab and select "Update Firmware". The updates are incremental, so you may need to repeat this step several times until the version number at the top of the Ports tab says "v1.19".

In v1.19, the RS4 saves a log text file within each recording folder that tracks the starting and ending sample of each stream. It also makes audible beeps when a recording starts and stops, or if there is a transfer error during the recording.If there is a gap in the saved data stream (typically this would be caused by a physical problem with the fiber optic connection between the RZ2 and RS4), this will also be indicated in the log file, so the data can be aligned in post processing. If the gap is long enough, the RS4 will assume the recording has stopped and start new files when data comes in. This allowable gap is controlled by the "Rec Stop Timeout" setting on the Config tab Settings.

Issue streaming 32-bit data to RS4 in v90

TN0988

Product: RS4, Synapse
Version: 90
Date Added: 2018-10-15

Issue

32-bit data recorded by the RS4 in v90 Synapse is all zero.

Solution

Users streaming 32-bit data to the RS4 who have already updated to v90 Synapse must install a new patch to fix a potential data transfer issue. With the Synapse computer connected to the internet, go to Menu → About → Check for Updates to install the latest version. This issue was resolved in Synapse v90.0.39174.

Recorded frames from USB Camera don't match number of timestamps in the block

TN0987

Product: Synapse
Version: All
Date Added: 2018-06-11

Issue

The number of frames in the avi video file is greater than the number of timestamps in the block of data.

Solution

The camera timer runs in software, specifically on the Cam1 tab that you see during a Synapse recording. This has two noticeable effect:

  1. At the beginning of the recording, the frame timer doesn't start until the interface is created, which can happen after the hardware trigger initiates recording. You can give the interface more time to create before the recording begins by setting the Persistence Load Delay option longer in the Menu → Preferences → Advanced tab. You should see a shorter delay between when the recording starts and when the camera triggers begin.

  2. At the end of the recording, the hardware stops receiving data, but the camera tab is still open for a short time and is still collecting frames, which creates extra frames at the end.

The frame timestamps that you have in your TDT recorded block will always match the frames recorded in the video, starting from the first frame and timestamp. If a frame was missed during the recording, there won't be a timestamp in the tank for it either. There may be some extra frames in the video but these will always occur at the end.

USB Camera only shows black frames or no frames

TN0986

Product: Synapse
Version: All
Date Added: 2018-05-10

Issue

Third party software can block certain applications from accessing the camera.

Solution

If using Kaspersky software, follow this webpage https://support.kaspersky.com/11157#block1. Go to the 'Application Management' settings page, then right click on Synapse.exe → Restrictions → Trusted to add it to the 'Trusted' group.

PZn data is low pass filtered in Synapse

TN0984

Product: Synapse
Version: 84.0.34769
Date Added: 2017-06-12

Issue

If using a PZ2, PZ3, or PZ4, there is an erroneous 1kHz low pass filter applied to the signal.

Solution

Update to the latest version of Synapse from the downloads page.

Timing issues with media players

TN0981

Product: RV2, OpenEx, Synapse
Version: All
Date Added: 2016-08-22

Issue

Media players do not provide synchronized playback for viewing or scoring recorded data. Because media players use time rather than frame number, playback will inherently lag behind data playback and this lag becomes longer over time. This happens because the frames per second (FPS) value is always rounded to an integer while the TDT clock runs at 24414.0625 Hz. If you select an RZ sample rate of 30 Hz, the actual sample rate is the corresponding fixed or realizable sample rate. For example: A rate of 24414.0625 / 30fps = 813.8 samples per frame. This gets rounded to 814. When stimulation is triggered at 24414.0625 / 814 = 29.9927 fps, which is the real FPS that the RV2 is triggered at and the video is stored at. When viewing in a media player that thinks the video is recorded at exactly 30fps, the time difference after 1 minute is [(30 / 29.9927) * 60000 ms/min] - 60000 = 14.6 ms.

Solution

Use the Video Viewer in OpenScope for synchronized data scoring. For more information of this feature, OpenEx users see: OpenEx User Guide, p. 258 Synapse users see: OpenEx Supplement for Synapse, p.43

Note Options menu not available in OpenScope

TN0978

Product: OpenScope, OpenEx, Synapse
Version: < OpenEx 2.24 / Synapse 84
Date Added: 2016-08-13

Issue

After opening an existing XSP file, the Note Options shortcut menu can't be displayed. When creating a new XSP file, the Note options are available, but changes can't be saved.

Solution

Upgrade to the latest version of OpenEx or Synapse.

Experiment interrupted by Windows Update on Windows 10 PC

TN0964

Product: OpenEx, Synapse
Version: All
Date Added: 2015-09-09

Issue

Long or overnight experiments might be interrupted by Windows Update on PCs running Windows 10.

Workaround

In Windows 10, non-enterprise editions, Windows Update is set to automatic updates by default and the only way to inhibit updates is to disable the service.

Important

If you use this workaround, you will need to return to the Services regularly and turn it on to update your copy of Windows. To be able to install the newest updates, you must install each available update in turn, from oldest to newest. When your computer has no more updates to install, remember to turn off the Windows Update service again.

We don't recommend disabling automatic Windows Update in Windows 10 unless you are making long/overnight recordings or are experiencing problems with automatic updates.

To turn off Windows Updates:

  1. Right-click the Windows Start icon on the desktop.

  2. Click Control Panel.

  3. Click Administrative Tools.

  4. Click Services.

  5. In the Services window, scroll down then right-click the Windows Update process and click Properties.

  6. Next to Startup type, select Disabled.

  7. Click OK.

Group Policy

If your Windows 10 computer uses a Group Policy, you can also change some settings using the Group Policy Editor. Run gpedit and navigate to the following policy setting:

  1. Computer Configuration | Administrative Templates | Windows Components > Windows Update.

  2. On the right side, double-click Configure Automatic Updates and change its setting to suit your requirements.

Tank cache errors and timing

TN0963

Product: OpenEx, Synapse
Version: All
Date Added: 2015-09-09

Issue

OpenEx or Synapse stops recording and displays a "Trouble saving data to Tank" or "Tank unable to cache events" error message.

Solution

Errors related to data storage and timing can occur when saving high rates of data, your PC's hard drive is busy or full, or communication between your PC and your TDT system fails. To narrow the possibilities, look at the timestamp comparison located at the end of the error line in the messages window.

A timestamp comparison of:

  1. "-6.x vs 6" tells you that OpenWorkbench/Synapse can't store the data fast enough.

    1. If you don't need access to the tank data right away, increase the Cache Delay to the maximum (30 seconds). In OpenWorkbench, this option is found in File → Preferences menu. In Synapse, this option is found in Menu → Preferences → Advanced.

    2. Try increasing the Target Bus Loading setting to ~80%. This puts more resources towards storing the data and less on distributing it to applications that are viewing the data, like OpenController or the Synapse run-time interface. In OpenWorkbench, this setting is in the Setup → Polling and Performance menu. In Synapse, this setting is Menu → Preferences → Run-time Ops → Data Read Limit.

  2. "-18.x vs 6" (or similar, where the first number is ~3x larger than the second number) tells you there is a problem saving data to disk. This may be because:

    1. The hard drive is close to capacity or something else, like a virus scanner, is demanding heavy access.

    2. Check your hard drive storage capacity. If that is not the problem, try turning off auto virus scans, update, or other auto-process including Superfetch (aka prefetch) and Indexing. See Tech Note #0237 for more information on optimizing to avoid errors.

    3. The hard drive is failing.

      1. Tool to test hard drive can be downloaded here:

        http://crystalmark.info/download/index-e.html

        http://crystalmark.info/redirect.php?product=CrystalDiskInfo

      2. Note the following 5 best Self-Monitoring, Analysis and Reporting Technology (SMART) hard drive stats that indicate impending disk drive failure as reported by Backblaze:

        SMART 5 - Reallocated_Sector_Count
        SMART 187 - Reported_Uncorrectable_Errors SMART 188 - Command_Timeout
        SMART 197 - Current_Pending_Sector_Count
        SMART 198 - Offline_Uncorrectable

        SMART is a monitoring system included in computer hard disk drives (HDDs) and solid-state drives (SSDs) that detects and reports on indicators of drive reliability, with the intent of enabling the anticipation of predictable (40%) hardware failures.

        Any other values are usually indicative of a communication failure.

    4. Try reseating the fiber optic cables on both the RZ and PC sides. If errors continue to occur, contact Support.

Data Stores Have Different Durations

TN0957

Product: TTankX, OpenEx, RS4, Synapse
Version: All
Date Added: 2015-09-02

Issue

When comparing different data elements saved with the TDT system you may see different total recorded lengths. The TDT data storage methodology emphasizes and guarantees data synchronization across all data sampled on a TDT system, independent of sample rate or data format - even across different devices within the system.

In software, continuous data is stored as a timestamp and a chunk of points that starts and remains synchronized, sample for sample, for the entire recording session. You see different total recorded lengths on different data elements saved with the TDT system because the data Stores are saved to the tank in evenly sized chunks and only full chunks are written. This chunk size is user settable or set automatically in software depending on the sampling rate. By default, chunk sizes run anywhere from 100ms to 500ms. For example, the default chunk size is 2048 samples when sampling at 24414.0625 Hz. You can see the exact chunk size in the Storage Specification table when Workbench is in 'Idle' mode, under 'Store Description'.

When recording ends, sampling stops, and any incomplete chunks are not saved to disk. The start time for each store will always line up precisely, but the recorded duration of each data store will likely be different.

The RS4 works differently. Data is saved sample-by-sample while the software is recording, so its chunk size is effectively one and thus it will always have more data than stores with 'chunked' data.

All data across the tanks and RS4 will be synchronized from the onset of the recording, but each store might have a different recorded duration.

Here is a graphical depiction of what is happening:

RS4 files named incorrectly, RV2 not identified by OpenEx/Synapse, zBusMon or Synapse can't identify RS4/RV2, or UDP communication failure

TN0939

Product: RV2, RS4, RZ-UDP, Synapse, OpenEx, zBUSmon
Version: All
Date Added: 2011-12-06

Issue

OpenEx, Synapse, and zBusMon use UDP packets to broadcast to or receive information from an RS4, RV2 or RZ with UDP on a local network. If these packets are blocked for any reason, the software can't communicate with them and no packets can be received.

When using the RV2, this will cause any attempt at communication with the device to fail.

When using an RS4, the data is still streamed but tank and block file naming information are lost and the RS4 names the data incorrectly.

When using an RZ with a UDP, UDP communication will fail.

When using zBusMon (version 80 or later), the devices are not displayed in the device diagram. Because this problem occurs with zBusMon, but not Windows Explorer, zBusMon serves as a good tool for confirming the source of problems first identified in OpenEx/Synapse Rig Editor.

Solution

The UDP packets may be blocked for any of several reasons.

If you are using OpenEx version 2.12 or earlier, upgrade to the latest version of OpenEx to avoid any related issues resolved in OpenEx version 2.14.

If you are using version 2.14 or later, packets might be blocked either by a Windows Firewall or by firewalls in place on your institutions network.

If your system is connected to your institution's network, TDT strongly recommends getting a small network switch, such as the one found at:

http://www.newegg.com/Product/Product.aspx?Item=N82E16833166061

and connecting all devices to the switch instead. This should resolve the problem. If this isn't feasible, contact your IT department for assistance.

If your system is not connected to your institution's network and you are still having a problem, it is likely that a Windows Firewall is in use on your PC (and a user may have clicked "block" the first time the system tried to communicate across the firewall). To resolve this issue, add a firewall exception for zBusMon and Synapse (or OpenWorkbench for OpenEx users) on port 41257.

Known Third Party Software Conflicts

TN0937

Product: OpenEx, RPvdsEx, Synapse
Version: All
Date Added: 2014-08-15

Issue

Some programs that make background memory calls on a PC create fatal errors and force TDT software, such as OpenEx or RPvdsEx, to shutdown.

Error Message: The TDT application may or may not give an error message, such as: The RPC server is unavailable.

Problem Behavior: Software crashes.

Known program conflicts:

  1. HP Security Manager (Tech Note #0908)

  2. CrashPlan Backup Software on Windows 7

  3. Dell Data Protection

Solution

Remove or disable the software causing the conflict.

The Microsoft Process Explorer (found here: http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx) can be a useful tool for determining the source of the conflict.

Restoring a corrupted block of data in an OpenEx data tank

TN0935

Product: OpenEx, Synapse
Version: All
Date Added: 2014-08-04

Issue

If a block is damaged or corrupted, the stored data may not be selectable. The block name may be visible in the Tank window, but no events/stores will be listed, and data cannot be exported or plotted.

Solution

For 64-bit machines or files larger than 2-3GB, download and run: TankRestore64.exe

For 32-bit machines, download and run: TankRestore32.exe

The Data Tank Utilities window launches:

  1. Click Next.

  2. Choose your Tank and Block then click Next.

    Note

    If you can't select the corrupted block, move the corrupted block into an empty tank and try again. Sometimes the corrupted blocks will not display correctly in a list.

  3. Under Modify Tank, select Re-create Index File and click Next.

The operation should complete in under a minute. This makes a backup copy of the TBK file (if it exists) and then creates a new one based on the block data. You should be able to access your data after this operation.

BoxSort not using all sorting windows

TN0930

Product: OpenController, SpikePac, Synapse
Version: All
Date Added: 2013-11-15

Issue

The BoxSort sorting algorithm does not work beyond 30 samples. Any boxes beyond the 30th sample in the waveform will not be used to classify the waveform during hardware sorting.

Workaround

Make sure no boxes extend beyond the 30th sample or shorten your window width to 32 points. In v78 and above the maximum window width is 32 samples.

Relocated tanks not recognized by TTankInterfaces

TN0907

Product: OpenEx, Synapse
Version: All
Date Added: 2012-09-19

Issue

TTank is the database server used by OpenEx and Synapse to store data. Data is stored as groups of blocks inside of specified tanks. Each block consists of a set of files that share the block name (.Tbk, .Tdx, .Tev, .Tsq, etc) while an additional file is always 'desktop.ini'. Each tank is a root folder for a group of blocks and has a 'desktop.ini' file. The 'desktop.ini' file is a necessary hidden system configuration file that TTankInterfaces uses to determine if a folder is a valid block or tank.

Because it is hidden, it is often overlooked by Windows during the relocation of bulk file sets.

Note

TTankX, TDT2mat, and TDTbin2mat do not use .ini files to access tanks and blocks.

Solution

To properly move blocks and tanks, you must include the desktop.ini file:

To ensure the desktop.ini file is included when you move block and tanks, you'll need to configure the Folder Option prior to moving the folders. To do this, make sure Show hidden files and folders is set true (checked) and Hide protected operating system files is set false (unchecked).

To enter Folder Options in Windows 7, select the Organize tab in Windows Explorer and then Folder and search options.

The Show hidden files, folders, and drives option and Hide protected operating system files options are listed under the View tab of the Folder Options dialog.

Note

If you have already moved your files and cannot easily recopy them, the linked Tank and Block desktop.ini files can be used by unzipping and copying them into the proper folders.

Sometimes when moving files from a network location, Windows sets the file attributes such that TTankInterfaces can't read the ini file to see if it is a valid tank; it shows a regular folder icon instead of the tank icon. TTankInterfaces v2.14 corrects this attribute issue for you automatically. For prior versions of OpenEx, you can fix this on the command line by setting the read attribute for the block folder like this:

C:\> attrib +r C:\TDT\OpenEx\Tanks\DEMOTANK2\Block-1\

RPvdsEx update macro

TN0860

Product: TDT Drivers, SpikePac, Synapse
Version: All
Date Added: 2009-07-09

Issue

When an existing circuit is opened, RPvdsEx checks to see if any of the macros contained within the circuit are out-of-date by comparing the build date with the circuits last modified date. RPvdsEx will prompt a dialog that asks the user if they wish to update any out-of-date macros.

Long recordings interrupted by antivirus utilities

TN0211

Product: OpenEx, Synapse
Version: All
Date Added: 2006-08-21

Issue

Many antivirus programs, such as Symantec Norton Antivirus, automatically scan the hard drives on the PC at fixed times. As a result, antivirus software may interrupt long recordings.

Solution

Communication to the PC controlling the TDT hardware should be limited to pertinent applications during data acquisition. We strongly recommend closing unrelated programs and disabling virus protection during data acquisition. Once an acquisition is stopped users can then access other applications.