CMOS-MEA-Tools

Features:

• [Network Explorer] Delete units manually using keyboard or toolbar button
• [Network Explorer] The Network Explorer works only on selected sensors

 

Bug fixes and improvements:

• [Spike Explorer] Refactor StartStopProcess
• [Spike Sorter] Load results SpikeSorter -> Change threshold and apply changes
• [Network Explorer] Show progress when reanalyzing
• [Network Explorer] Reanalyze data -> remove units -> crash
• [Network Explorer] Unit selection in network view doesn't work
• [Network Explorer] Load results SpikeSorter - NetworkExplorer fails
• [Network Explorer] Flexible Axon representation, save and load axon path
• [General] Simplify Batch Mode -> clean up, Optional Analysis Label

Features

• The new Network Explorer is an advanced STA Explorer with new functions. Based on the electrical activity of neurons the path of the axons is extracted to build a map of the interconnection of the active neural network.
• The Spike Explorer now performs an automatic peak detection after spike detection to find locations of higher activity. This feature reduces the overall processing time and memory needs dramatically, because the following Network Explorer just analyses the activity at the interesting locations.
• Improved path handling for opening files dialogs.
• Simplified Batch Mode and repaired some minor bugs
• Added new color map and interpolation to Sensor Array View.
• Option to perform offset correction when loading raw data.
• Adjusting y-axis to signal amplitude when loading new data into the chart.
• Improved Roi handling in Sensor Array Views.

Fixed Bugs:

• Spike Sorter: Fixed Memory leaks
• Events aren't shown in SummaryTool, Raw Data Explorer and Spike Explorer after reanalyzing file
• RawData Explorer: Resizing a roi with a endpoint outside the sensor array crashes. This also happens in the other sensor array displays.
• SummayTool didn't saved its data to the result file.
• Batch Analysis: crash when canceling before applying

Features

• Compartibility release, due to the new COMS-MEA-Control version
• All tools can handle multiple Roi data
• [SpikeTool] Extended Raster Dot display so that the complete data is shown
• [SummaryTool] Move through data with forward and backward buttons

Bugfixes

• [SummaryTool] Reset spike count if rerunning
• [StaTool] Repaired crash when switching STA sensor/unit while the movie is running
• [General] Repaired crash when loading a result file with connected STA tool

This release consists mainly of improvements suggested by useres and some bug fixes.

• New feature: menu control to access online help files.
• New feature: Data Analysis feature extended by Load/Save settings.
• New feature: Allow nV range for Voltage SensorArray displays.
• New feature: SpikeExplorerTool export spikes to CSV file.
• New feature: Add button to re-run RedundancyRemoval of the SpikeSorter.
• Improvement: Improve open/save dialog, Optimize scanning of result files and Open File via extension.
• Improvement: Set Batch Out folder as default when opening result files.
• Improvement: Open File resets all tools.
• Improvement: Rework batch analysis dialog for easier use.
• General: bug fix to load Event data.
• Spike Sorter: Delete Chip Overview Spike Count display when reanalyzing data.
• Spike Sorter: IndexOutOfRange Exception in SumThresholdFilter.
• Spike Sorter: Change unit of RoiSTAs to nV.
• Export bug fix: export selected Unit/Sensor in StaExplorerTool.
• Export: SpikeSorter unit channels are exported in nV unit.
• Export: Added Unit of data when exporting STAs from STA Explorer.

• New Spike sorter tool: Automatic sorting of detected spikes.

• Run Spike sorter clients on other machines on the network to reduce processing time.

• STA Explorer:  Select input for averaging: Spikes or sorted units.

• New file formats and extensions. All output files are saved in a hirarchical data format (HDF5) which is supported by many commercial and non-commercial software platforms, including Matlab and Python.

  • Results (*.cmtr) saved in HDF5 file format.

  • Templates (*.cmtt) saved in HDF5 file format.

  • Export (*.cmte) saved in HDF5 file format.

Important:
New file formates were introduced to increase the file transfer rates, and provide a easier way to access the data by other applications. The speed up is mandatory to save spikes along with the raw data, and in offline mode it reduces the time needed to process the data dramatically. Therefore, the CMOS-MEA-Tools version 2 can only open HDF5 file created by CMOS-MEA-Control version 2. Files recorded by older CMOS-MEA-Control versions can be converted to the new file formate using our Multi Channel DataManager.

Also the format for template files has changed, so that it is not compartible with previous template files. Therefore, old template files has to be replaces by new ones.

New Features:

• Batch Mode: Additionally to the analysis of small segments (Explore Mode) and a whole file (ProcessFile Mode) now many files can be selected to be analyzed in a single run. Several different analyzer settings can be defined.
• Video Recorder for RawData Explorer and STA Explorer: The activity over the sensor array can be recorded in different resolutions and frame rates to a MP4 file.
• Summary Tool now uses filter pipeline for the extraction of spikes.
• Spike Explorer was refactured in preparation to the planned Spike Sorter. New improved methods for sensor selection. Keep selected sensors also when reprocessing the data.

Bugfixes:

• STA Explorer: Crash when selecting sensor while Processing file.
• Summary Tool: Navigation with Roi display error when start time < 0.

New Features:

• Added new display to show recorded events, for example stimulation events or digital port events.
• The user can select one to many event types to be used for navigation through the raw data.
• Show analysed region in the summary display. When processing data the amount of processed data is depicted. If loading a result file the displayed region represents the raw data intervals for which the results were obtained.
• Added display and controls to navigate through raw data using the recorded events.
• Added user interface to represent processing chain and states. The display can be used to enable/disable tools when precessing data. A progress bar within the tool icons represents the processing progress.
• Improved sensor selection for the Spike Explorer tool.

Bugfixes:

• Crash when loading files larger than 20s.
• Spike Explorer: Zooming raster plot fails.
• Recordings shorter than 1s causes display problems.