Data Logger GUI
The Data Logger GUI was developed to provide a convenient way to download neural data recorded during an untethered experiment from SpikeGadgets’ data loggers and merge that data with a simultaneously recorded environmental record.
It can be used in conjunction with the SpikeGadgets’ Logger Dock or Main Control Unit (MCU). The Data Logger GUI can be opened directly, or from Trodes using the “Merge with logger data” menu item under “File” when an environmental record is opened in playback mode.
Mounting SD Card
figure 1: Data Logger GUI with SD card mounted in MCU
Once you have finished your recording, you need to download the data to your computer. To start this process, insert the SD card into the Logger Dock or MCU. The Logger Dock or MCU should be turned on and connector to your computer via a USB connection. After opening the Data Logger GUI, The SD card will be listed with the control unit you are using under “Detected Storage Devices”. If your control unit does not appear on this list, click the refresh list button, and it should appear.
NOTE: The MCU must be running firmware version 3.19 or later to be used with the DataLoggerGUI.
The SD card will appear in the device list under the “Type” heading of your control unit, with information about card size and status listed. If data has been recorded on the SD card, the right-hand Headstage Setting panel will populate with information about the recording, and the card status will indicate that the card is “Not enabled for recording”. This is a safety feature to prevent accidental erasing of data before it had been downloaded to your computer. After you have downloaded the data, you will need to enable the card for recording before it can be used to record with a SpikeGadgets datalogger again. This is done by clicking the “Enable for recording” button.
Updating Control Unit and Headstage Settings
The DataLoggerGUI can also be used to update control unit and headstage settings such as radio frequency (RF), sampling rate and session ID for untethered recording. The MCU must be running firmware 3.19 or later to update MCU settings or headstage settings, with the exception of the ML32, which can be plugged into the Logger Dock directly.
Updating control unit settings: Control unit settings can be updated by selecting the desired control unit (Logger Dock or MCU) from the Detected Storage Device list, then clicking the Edit device settings button above.
Updating data logger configuration: For some data loggers, configuration settings can be updated by selecting the desired data logger from the Detected Storage Devices list, and clicking Edit logger config. To do this, your data logger must be connected to the MCU via HDMI tether or docked on the Logger Dock.
Extracting Data and Merging With Environmental Record
Most users will have two recordings that were simultaneously recorded during an untethered experiment: 1) the neural recording on the SD card, and 2) environmental recording (.rec file) taken by the Trodes software, which may be linked to other files such as video.
These 2 files are aligned and merged into a single
.rec file using the radio frequency (RF) sync
pulses embedded in each file. These RF sync pulses are transmitted from the control unit with a 10-second
interval (for most setups) and are recorded by both devices. More information about Untethered
Data Synchronization can be found here.
To merge the neural data with the environmental data, make sure the checkbox
next to “Merge logger data with environmental data” under the “Export” tab is checked. If you opened
the DataLoggerGUI application from Trodes, the path to the environmental recording
will already be populated. If you opened the application directly, you will need
to browse to the relevant environmental
Next, you will need to select the “Final Trodes workspace” file. This workspace file will be appended to your recorded data, and will include the relevant header data for your neural recording. Importantly, this is not the workspace file used to record your environmental data, but rather a workspace containing all the settings that would have been used if the neural data was acquired using a tethered recording, such as channel count, nTrode assignment, etc.
Often the easiest way to generate this workspace is to simply save the workspace used when applying settings to your headstage while setting up your experiment. Just be sure to include any custom nTrode mapping when doing this. Otherwise, simply create and save a new workspace with the relevant settings.
For more information about workspace creation, see the Workspaces subsection of the Trodes wiki.
Finally, you will need to specify a filename for the merged data file. The DataLoggerGUI will create a default filename, which can be seen under “Extracted file name,” but this can be edited to meet your needs.
Click the “START” button to begin the extraction and merging process.
Notes: - If you are not merging with an environmental record, uncheck the corresponding checkbox at the top of the Extract tab. The “Final workspace” will simply be appended to the extracted file without merging the data.
If you have previously extracted a file from an SD card and the resulting
.datfile is already on your computer,
this data can be extracted and/or merged by selecting the “Browse existing .dat” button below your device list. When using this approach, the extraction step will be skipped and the
.datfile data will be used instead.
When the START button is pressed, the extraction process will begin. The “Console” window will display the output of the process, with percentage complete indications and potential errors or warnings displayed. For large files, this process may take several hours.
When the extraction process is complete, the extracted file will be saved to your computer in the same folder as the designated output file. This is to expedite any subsequent merge processes.
Next, the merge process will begin. This process is generally fairly fast. Percent
complete will be shown in the console window, along with errors and warnings. If the
process completes without errors, the merged
.rec file will be saved to your computer
automatically. Please review the “Console” output of the merge process to check for any errors
or warnings that may need your attention:
Excessive drift During the ongoing merge process, every time a synchronization signal is detected the program will display how far apart the two files have drifted. It is normal for the two files to drift a few dozen samples every ten seconds. However, drift in the thousands of samples points to a larger problem that needs to be addressed.
Excessive dropped data Every time data are dropped in either the environmental file or the neural data file, a warning will be printed to the console displaying how may packets were dropped. A few hundred packets here and there is generally not a problem, but excessive drops will also need to be addressed, and likely indicates that the SD card was not fast enough to record the number of channels used on the headstage.
All alignment corrections (due to drift or dropped packets) gives priority to the neural recording. Data are either filled in or taken out of the environmental recording to accomplish the alignment. When data are filled in, the last digital or analog values are repeated.
Once extraction and merging are complete, if you opened the DataLoggerGUI from Trodes, clicking
the “Close” button at the bottom right of the window will trigger Trodes to automatically open
the resulting merged
.rec file in playback mode for inspection.
SD Card Enable
Once a SD card has been used to record data, it must be re-enabled before it can be used to record again. This prevents data on the SD card from being accidentally overwritten. This must also be done when using a SD card for the first time. The SD card can be enabled either using the DataLoggerGUI, or the MCU (if running firmware 3.19 or later).
DataLoggerGUI: Mount the SD card to either the Logger Dock or MCU (if running firmware 3.19 or later), select this relevant device from the device list in the DataLoggerGUI, then select the above “Enable for recording” button.
MCU: Mount the SD card to the MCU, then press and hold the left button on the MCU. The left LED will rapidly flash red for a few seconds while the card is being enabled. Once the card has been enabled the LED will return to solid green and the button can be released.