Critical Bug Fixes
Neuropixels workspaces were not properly using the new spikeSortingGroups feature, causing trodesexport to hang. Now fixed so that each probe has its own sorting group.
Minor Changes or Bug Fixes
Small changes to debug log in dropped packets reporting.
Critical Bug Fixes
The Camera Module and StateScript Modules now receive the correct sampling rate from Trodes when using the new ZMQ network
Stimulation commands now have the correct number of pulses (it was doing one more than it should have
Fixed a camera module crash condition when closing, then opening a video recording file
Camera module can save/load all geometry types again (has been disabled)
Minor Bug Fixes
Reduced audio output latency
Export utility displays percent done more reliably
Sorting groups are now used by default when exporting to MountainSort or Kilosort formats. The sorting group for each channel can be modified in the channel map interface of the workspace editor.
Better Red/Green tracking in the camera module makes it usable even if the background is white
Workspace editor now has a feature to split recordings into set file sizes. Commands are sent to modules to also split files at the same time (i.e., video)
Workspace editor now has an LFP subsampling rate interface that is used by the export program and the ZMQ network
Camera module can now reduce the resolution of incoming video frames in order to reduce CPU usage during tracking and video compression.
Critical Bug Fixes
DataLogger GUI has many fixes relating to data extraction and merging
Stability improvement for when multiple nTrodes were selected and their settings were changed together.
Stability improvement when lack of available audio hardware
The merge utility has multiple additions to improve tolerance for less common conditions
A combined export utility (trodesexport) was developed that is used to export multiple types a data at once.
Trodes and the export utilities now use AVX2 to process data if it is available on the machine. This includes filtering, referencing, and spike waveform processing
An API is introduced that allows users to gain access to the data in real time using either c++ or python. This API is based on the ZMQ library.
Neuropixels support, including an interface to select which channels are active
Stimulation control and pulse visualization
Critical Bug Fixes - nTrode menu was not updating correctly as the user clicked on a new nTrode. This issue was introduced in 1.9.0
Audio was not updating properly with CAR referencing changes.
exportLFP was scrambling the channels id’s in the output. This issue was introduced in 1.9.0
Fixed a crash condition in splitRec
Two new export functions were added: exportraw and exportspikeband. These are used to export continuous data from either the raw data band or the spike data band.
CAR groups can now be added from the main Trodes window.
Minor fixes and features
Workspace editor was overwriting the nTrode colors. This is now fixed.
Improved export program help menu
- Data Logger GUI: Updated with a better, more streamlined interface.
Works with new Dock for faster data extractions, charging station, and streaming.
- RF connected device panel: Our new Dock streams DIO/analog like an MCU, and can also
connect to a data logger wirelessly! When connected in Trodes, an RF panel shows up that displays details about the connected data logger, including # of channels, SD capacity, battery remaining, and more.
RMS plot: Plots root-mean-sq of each hardware channel. Useful for noise debugging
Power spectral density plot: Density plot of frequencies of a selected ntrode’s signal. Useful for noise debugging.
- Allied Vision cameras: Using Bayer8 image format (can be set in their VimbaViewer software),
your video frame rate can improve by as much as 2x, because CameraModule now supports Bayer8 to normal RGB24 conversion.
Thanks to Tom and Abhilasha from the Frank Lab!
Updated internal streaming and processing code to be more efficient
Moved create/edit/remove of CAR groups to workspace editor
Renamed quickstart to auto-connect
Version checking and online updater works and can be properly launched from Trodes
Changed names of certain hardware devices to more intuitive names
For wireless logger users: Added specific .trodesconf workspaces for datalogging to SampleWorkspaces/Logger_workspaces
- System clock bug fixes:
export programs can properly deal with sysclock
workspaces with sysclock display DIO data properly
Improved tooltips in ntrode settings dialog
Statescript does simple check if observer language executable is valid
Group referencing is included in export code
Auto-connect that can generate workspaces based on connected hardware
Common Average Referencing
PTP for AVT cameras
System clock in recordings, saved in each packet
Data Logger GUI
Installer and updater tools
1.7.2 (Mar 27, 2018)¶
NTrode selection and settings: Multiple ntrodes can now be selected, by using typical conventions with SHIFT or CTRL and clicking on multiple ntrodes. The ntrode button now creates an ntrode settings panel which applies the changes to all ntrodes selected.
Categories and tags for ntrodes: Ntrodes can be assigned categories and tags in the settings panel. Categories can have any number of tags. Any ntrode can be labeled with a category-tag combination. They are stored in the config file. The categories and tags can also be used to filter and select ntrodes.
Spike display: Unclustered points and waveforms can now be hidden. This is useful when clusters are created and the user wants to hide unclustered points. Both the scatterplot and waveforms plot support this. Individual clusters can also be shown or hidden at the menu from a right-click on a cluster.
Stream display: The user can decide to view a spike stream, LFP stream, or raw unfiltered stream. The LFP stream only displays the designated channel. The filters are separate from the stream display, so the user can view the LFP stream while still enabling the spike filter.
Hardware disconnects: if the hardware briefly disconnects, the system will automatically attempt to reconnect. There is also now an indicator for hardware status.
Moved to Qt5.9: Qt has fixed several of their own bugs and improved features over their releases. We are moving from 5.5.1 to 5.9.1.
Bug fixes from 1.7.0-1.7.2
Critical bug fix in export spikes.
Opening a file on cameraModule on a different machine will result in creating a folder for the recording in the cameraModule’s directory
Switching cameras is now more stable and does not result in random crashes
Monitor switching should no longer cause crashes, was reintroduced by new Qt version 5.9
Fixed GUI on cameramodule that was ambiguous and did not prevent user error
LFP and unfiltered data polarity was mistakenly reversed. They are now normal. Spike polarity is kept as reversed.
Fixed disconnect fault tolerence with USB connection
Export functions bugs and settings fixes
Build script fixed on Linux
1.6.1 (July 6, 2017)¶
We are now a registered Apple developer . This means Mac users will not receive messages about Trodes being from an “unverified developer”
Can now highlight and select multiple channels/ntrodes at a time in the workspace gui using shift click
Workspace GUI has a more intuitive interface
CameraModule can now save and load inclusion/exclusion zone geometries
Workspace GUI highlighting and selecting bug fixes.
Available space in hard drive is back in status bar when recording
CameraModule in playback mode opening in the wrong mode or the wrong files is fixed
Changed video encoding so there isn’t a missing frame at the end of a recorded video file
Merge SD-Rec bugs fixed
1.6.0 (June 7, 2017)¶
Multi waveform plotting. The spike waveform viewer can not display many spikes at once and color them according to sorted spikes.
Workspace editor interface. Workspaces can now be generated and edited using a graphical interface. This eliminates the need to know XML to create or edit workspaces.
File playback improvements. File playback mode now uses a slider bar to allow the user to skip to any part of the file. The camera module will open the accompanying video (if it exists) and synchronize playback with neural data.
Intro menu. Upon startup, Trodes now displays a menu allowing the user to quickly access previously used workspaces or recordings.
Headstage settings dialog. Users can now change headstage settings such as auto settle, smart referencing, and motion sensor on/off states from Trodes.
Improved recording status indicator. Previously, when a file was opened for recording, some users had the assumption that it meant recording had started, because there was no obvious indicator. Now, indicators have been added to make it clear to the user if recording is currently on or not. We added text that states the number of hours and minutes recorded so far, a long status bar that changes color and reads either “Recording Paused” or “Recording Active”, and on the camera module, the file opened and time recorded is displayed at the top of the window
Freeze display. The user can now freeze the continuous stream display by either pushing the Freeze Display button, using the menu, or pressing the space bar.
Hardware serial number and version display. This information is also appended to recordings.
StateScript GUI improvements. Macro buttons can be configured to enter StateScript commands to toggle DIO pins, etc. Also, there is improved labeling of the different panels.
Version update lookup. Trodes will automatically lookup if a newer version is available. In the intro menu, the ‘Information’ box will alert the user if a new version is available for download.
Camera module export additions. The camera module will now export linear track geometries, zone geometries, and scale info (cm per pixel). It will also export linearized position if a linear geometry was enabled during tracking.
If settings are changed to any nTrodes after a recording file is opened, the program will prompt the user to save an updated workspace alongside the recording (since the header at the top of the recording only captures the initial state).
Multiple PETH windows open. The user can open separate PETH windows for multiple nTrodes, which will automatically update when new events occur.
Spike waveform alignment. Spikes are now automatically aligned to the peak. This applies both the Trodes and the exportspikes program.
Audio Off command line argument to disable audio. On some machine, auto driver incompatibilities can cause crashes, so this was implemented to diagnose audio issues.
For two-diode tracking in camera module, users can set if the red diode or the green diode is in the front.
CRITICAL BUG FIXES
MINOR BUG FIXES
Python data extraction program fixed
mergeSDRecording had incorrect error outputs that were removed
Fixed the number of displayed columns to match what is in the workspace.
Digital reference nTrodes are referenced by their in the workspace ID number rather than their index
Camera module now allows user to define which color LED is the ‘front’ using red-green position tracking.
1.5.1 (February 28, 2017)¶
Camera module now does not allow switching cameras once a recording file has been created. File must be closed before the camera can be switched again.
Fixed minor memory leak from PETH windows
Fixed Camera module time rate being recorded as 0 instead of 30000
Fixed bug causing StateScript GUI to crash when in standalone mode and opening the camera module
1.5.0 (February 15, 2017)¶
Added Multi-Plot PETH functionality in spikes window. Users now have the option of seeing a histogram of all spike data points as well as histograms of individual, user-defined cluster plots at the same time. Clicking on specific cluster plots will open a PSTH window containing more specific data bout that cluster. Further, switching to a different nTrode will update the histogram window automatically.
Automated testing system, specifically with regard to command line testing. These tests currently exist: a workspaces test (opens all workspaces and closes them among a set), a file playback test (opens all files in directory and checks to make sure all threads are syncing properly), a hardware connection test (tries communicating with a hardware setup), and a hardware streaming test to make sure data can be streamed from the hardware.
Benchmarking GUI. Basically a settings control panel available in the main Trodes program, the Benchmarking GUI allows the user to edit benchmarking settings at runtime. Along with turning specific benchmarking tests on/off, the user can edit the frequency with which benchmarking statements are being printed (this is to prevent console clogging). These benchmarking settings can now also be saved and loaded via workspace files.
Version information (compile date/time, git commit compiled, Trodes version info) can now be displayed from all modules in their ‘About’ tabs. This information is also saved in recordings and exported using the export utilities.
Linux build system now automatically packages all required files into final build folder. All modules are compiled alongside Trodes main in all OS’s using Trodes_all.pro.
Event system. Events can now be defined and recieved by other modules for user-defined behavior. Current events include spikes from defined units and zone enter/exit events from the camera module.
Warnings are now thrown when opening Trodes if a separate instance of Trodes is detected to be running with an open workspace and Trodes will prevent itself from opening a workspace if this is the case to prevent networking issues.
Trodes debug .txt logs are now automatically created in a folder directly adjacent to the Trodes executable, for windows/linux this is the same location as the binary/exe, and for mac the .app folder.
Debug messages from modules now forwarded correctly to Trodes main on Windows
Camera module auto gain behavior removed for GigE cameras
Switching between two GigE cameras is now more robust to failed connections
Switching from either of the signal generator sources no longer causes the next source to crash the system
Rhythm source turned off by default to prevent crash when selected
Improved button behavior and appearance across OS’s
StateScript GUI now has a separate input widget to type commands to hardware. Users can use the up and down arrows to scroll through command history.
Event System Added
Implemented an event system in Trodes server-client architecture that allows modules to dynamically create and send event messages to all other modules.
Added EventHandler class implementing a GUI menu allowing users to create connections between events and module actions. (e.g. when an event is received, all actions/methods linked to the event will be executed)
This class is highly portable and can easily be added to any module. (see documentation on the Trodes Wiki)
Position data streaming greatly expanded, the following data is now being streamed:
Linear position data (continuous)
Linear track data whenever it is created/edited/moved in a relative scale (0-1) format. (Non-Continuous)
Velocity data received from embedded Python. (Continuous)
See documentation on the Trodes wiki for specific format information
A compatibility mode was added that will either enable, or disable the changes to position data streaming (modules that rely on the previous position data format will not be broken by this update).
SimpleCommunicator is a heavily modified version of SimpleMonitor which should be used as an example for how to set up a module to request and receive data from other modules. (It should go hand-in-hand with the wiki for documentation purposes)
SimpleCommunicator currently supports full communication with Trodes and CameraModule. (Notably, SimpleCommunicator will display CameraModule’s real time position data)
SimpleCommunicator contains a fully implemented EventHandler.
All executables can now be called directly. (I.e you can run Trodes, instead of Trodes.sh) The shell scripts have been removed.
OfflineSorter exporter added to export programs
Added event system support to Trodes main module (it can now send events to other modules)
Added events to Trodes which track when spikes occur in user defied clusters in different NTrodes. These events are created when a new polygon is created in the ‘spike’ dialog menu.
Several event definitions added at module startup (e.g. Zone created, linearization tract created) that can be seen by other modules.
Events added that tell the user when specific zones have been entered and exited by tracked objects.
Zones will now turn blue when entered by tracked objects and revert to clear when left.
Added UI element in Camera Module that brings up an eventHandler menu.
Added a plotLocation method action visible in the event connection menu that plots a point on the currently tracked position
Fixed an issue that would cause a crash if the user tried to create a linear track while tracking was enabled.
Fixed an issue that would cause a crash when double clicking the first node while drawing with either the Linear Track tool or the Range Line tool.
Fixed a bug in the load geometry code which would append a bad node onto the end of loaded linear geometry.
Added debugging tool which prints all function calls as specific IDs in console output (set DEBUG_MODE define to 1 in videoDisplay.h)
Export code can now keep going if an erroneous backwards timestamp is detected with -abortbaddata 0 flag
Fixed an issue where cameraModule would try to track linear position on a rangeLine and cause a crash.
Improved buffering of data to ensure that data are not lost even if the hardrive become inaccessible for over a second. If the buffer is overrun, the system will now recover smoothly after the lost section.
Embedded python in Camera Module. Still a work in progress, but this will be used to allow custom processing of position information
Optimized processing of video frames in Camera Module to reduce CPU load
Added export programs, including ones for Phy Suite and Offline Sorter
Improved graphics plotting in channel streaming window. All done with Open GL.
Camera Module linearization tool to project animal’s position onto a track geometry. Bugs were fixed to allow saving and loading of geometry files.