CellExplorer is a graphical user interface, a standardized processing module and data structure for exploring and classifying single cells acquired using extracellular electrodes.
Home Page: https://cellexplorer.org/
License: BSD 3-Clause "New" or "Revised" License
Is there a way to upload sorted data from ultramegasort2000 mat files into cell explorer?
ultramegasort2000 github
https://github.com/danamics/UMS2K -
example mat files of ultramegasort sorted spikes:
https://drive.google.com/file/d/1h7VBAiu2oFu9pDtBcFjpI8EA9E4uJA1Z/view?usp=sharing
spikes =
struct with fields:
params: [1×1 struct]
info: [1×1 struct]
waveforms: [12907×45 single]
spiketimes: [1×12907 single]
trials: [1×12907 single]
unwrapped_times: [1×12907 single]
assigns: [1×12907 double]
labels: [8×2 double]
when cell_metrics is run for several intervals, only the last summary figure is saved because the name under which those figures are saved is the same. i.e. the name tag of the interval is not carried over to the name under which the summary figure is saved.
not urgent, but useful to save the summary figures with distinct names
Hello Peter,
I am trying to prepare my data to be read into the cellexplorer data structure. I understand that the raw dat file should also be in the basepath. However, I have multiple Neuropixels probes per session and thus more than one raw dat file.
Maybe also, what is the rawdata file used for? Can I leave it out?
Thanks for your help!
Best
Yangfan
Hi there,
I have successfully downloaded CellExplorer and am trying to run CellExplorer with the provided example data (cell_metrics_batch.mat) that comes with the installation, however I am running into an error. I am following the instructions on the 'Getting Started' page of CellExplorer but run into the following error message:
Attempt to execute SCRIPT CellExplorer as a function:
C:\Users\User\Documents\AJ\Data\MATLAB-20210304T193031Z-001\MATLAB\CellExplorer.m
Error in CellExplorer (line 10)
CellExplorer('metrics',cell_metrics)
I have added the appropriate path and I am running R2020 version of MATLAB, windows 64-bit. Is there something I am missing?
Why the fitting equation in fit_ACG.m is slightly different from the one in the website (parenthesis after the first parameter c (decay amplitude))?
fit_ACG.m -> max(c*(exp(-(x-f)/a)-d*exp(-(x-f)/b))+h*exp(-(x-f)/g)+e,0)
website -> max(c*exp(-(x-f)/a)-d*exp(-(x-f)/b)+h*exp(-(x-f)/g)+e,0)
'getBasenameFromDir' which is called in 'basenameFromBasepath' is missing from the repo
Operating system
Windows11
Matlab version
matlab2021a
Describe the bug
I load kilosort rez.mat into cellexplorer and get a basename.session.mat. Then I try to use neuroScope2 to run sleepScore and it come an error said no basename.sessionInfo.mat. I wonder if there is some option to get basename.sessionInfo.mat from basename.session.mat
Matlab error log
NeuroScope2('session',session)
Scoring Recording: bandpass_diference
Warning: could not find file bandpass_diference.sessionInfo.mat running LoadParameters instead..
In bz_getSessionInfo (line 53)
In SleepScoreMaster (line 209)
In analysis_tools.states.run_SleepScoreMaster (line 23)
In NeuroScope2/analysis_wrapper (line 6647)
In uiwait (line 81)
In NeuroScope2 (line 161)
Warning: Escaped character '\B' is not valid. See 'doc sprintf' for supported special characters.
In LoadParameters (line 40)
In bz_getSessionInfo (line 55)
In SleepScoreMaster (line 209)
In analysis_tools.states.run_SleepScoreMaster (line 23)
In NeuroScope2/analysis_wrapper (line 6647)
In uiwait (line 81)
In NeuroScope2 (line 161)
Error using LoadParameters (line 40)
No .xml in FatterDocument
Error in bz_getSessionInfo (line 55)
sessionInfo = LoadParameters(basePath);
Error in SleepScoreMaster (line 209)
sessionInfo = bz_getSessionInfo(basePath,'noPrompts',noPrompts);
Error in analysis_tools.states.run_SleepScoreMaster (line 23)
SleepScoreMaster(data.session.general.basePath);
Error in NeuroScope2/analysis_wrapper (line 6647)
out = analysis_tools.states.(function1)('ephys',ephys,'UI',UI,'data',data);
Error while evaluating Menu Callback.
Operation terminated by user during uiwait (line 81)
In NeuroScope2 (line 161)
uiwait(UI.fig);
Hi Peter,
I have a bad channel on the probe and labeled it in the session metadata as 'Bad'.
However, this channel is still used for the waveform extraction and because the large noise amplitude, is selected as the channel with largest waveform amplitude for display in CellExplorer.
Are there any extra steps to do in order to avoid this during the creation of the sessionInfo or is it a bug?
best,
Noam
Hello,
I am trying to use CellExplorer for my own dataset. Although on the website, it is mentioned that XML files are not required, Matlab gives me an error when I do not include the XML files in the clustering path.
Undefined function or variable 'xml'; Error in loadSpikes (line 201) spikes = GetAllWaveformsFromDat(spikes,xml,basepath,basename,LSB,session)
We are using the OpenEphys system for recording which gives an XML file and I included that into the clustering path but then other errors appear.
Reference to non-existent field 'AnatGrps'. Error in loadSpikes>GetAllWaveformsFromDat (line 569) if isfield(xml.AnatGrps,'Skip')
I am using Klusta for spike sorting. Is there any suggestion for how this might be fixed?
Also, can you provide details on what the required XML filed should contain?
Hi! When testing your powerful toolkit with your example dataset, I noticed that computations regarding behavioral trials are not yet implemented. The file Peter_MS22_180629_110319_concat.trials.behavior.mat is never loaded into memory and metrics about behavior is not calculated. Therefore plots using trials as variables (e.g. the default spikes_pos_vs_trials) are not available (see screenshot). Would you be so kind to have this feature supported in the near future?
Matlab version
R2021b
Describe the bug
Behavioral trials not yet supported
Matlab error log
Session struct
Peter_MS22_180629_110319_concat.session.mat from example dataset.
Screenshots
Additional context
Matlab setpath
Operating system
Windows 11 Enterprise
64-bit operating system, x64-based processor
Matlab version
R2023b Update 4 (23.2.0.2428915)
Describe the bug
I just run "session = sessionTemplate(pwd,'showGUI',true);", but it showed error.
I would like to clarify if CellExplore is exclusively compatible with iOS. Because I only saw in the iOS platform in website of CellExplore and videos of YouTube.
Upon visiting the website "https://cellexplorer.org/#getting-started", I noticed indications that it might also be compatible with Windows 64-bit systems.
Matlab error log
If relevant, please provide your session Matlab struct (basename.session.mat) by zipping it and dragging it into this text field. This will ease the troubleshooting.
I haven't use any data
Matlab setpath
MATLABPATH
C:\Users\ttsai\Documents\MATLAB
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addon_enable_disable_management\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addon_updates\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons\cef
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons\fileexchange
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons\supportpackages
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_common\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_desktop_registration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_install_location\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_product
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_product_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_registry\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addons_sidepanel\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addressbar_plugins\browse_for_folder_button\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\addressbar_plugins\cd_up_one_dir_button\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appcontainer
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\appdesigner
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\appdesigner\interface
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\appdesigner\runtime
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\appdesigner_api
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\comparisons\mldesktop_m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\appdesigner\matlab_integration\cfb\cfb
C:\Program Files\MATLAB\R2023b\toolbox\matlab\apps
C:\Program Files\MATLAB\R2023b\toolbox\matlab\audiovideo
C:\Program Files\MATLAB\R2023b\toolbox\matlab\automation\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\bigdata
C:\Program Files\MATLAB\R2023b\toolbox\matlab\bluetooth
C:\Program Files\MATLAB\R2023b\toolbox\matlab\buildtool\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\buildtool\ext
C:\Program Files\MATLAB\R2023b\toolbox\matlab\capabilities
C:\Program Files\MATLAB\R2023b\toolbox\matlab\cefclient
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codeanalysis\analyzerrpt\backend
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codeanalysis\reports\analysis
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codeanalysis\tools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codetools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codetools\embeddedoutputs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codetools\embeddedoutputs\DataToolsRegistration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\codetools\liveapps
C:\Program Files\MATLAB\R2023b\toolbox\matlab\configtools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\binary
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\common
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\configuration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\connector
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\editor
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\figures
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\http
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\interpreter
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\logger
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\messageservice
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\mgg
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\nativebridge
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\restmatlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\session
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\shadowfiles
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\webwindow\m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\connector2\worker
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datafun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datamanager
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datastoreio
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\datatoolsservices\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\desktop_variableeditor\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\desktop_workspacebrowser\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\editorconverters\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\import_livetask
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\importtool\matlab\peer
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\importtool\matlab\server
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\inspector\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\inspector\registration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\matlab_integration\cfb\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\media_widgets\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\peermodel_mcos\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\plotstab\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\preprocessing
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\uicomponents\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\variableeditor\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\widgets\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatools\workspacebrowser\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\applyfuns
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\calendarDuration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\categorical
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\cell
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\cell_nonlibmatlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\codegen\categorical
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\codegen\datetime
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\codegen\duration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\codegen\tabular
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\datetime
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\datetime_nonlibmatlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\dictionary
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\duration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\missing
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\shared\codegen
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\shared\matlab_datatypes
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\struct
C:\Program Files\MATLAB\R2023b\toolbox\matlab\datatypes\tabular
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dataui
C:\Program Files\MATLAB\R2023b\toolbox\matlab\ddux
C:\Program Files\MATLAB\R2023b\toolbox\matlab\debugger
C:\Program Files\MATLAB\R2023b\toolbox\matlab\demos
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\analysis
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\app
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\attribute
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\comparisons\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\refactoring
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\report
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\widget\progress
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\widget\progress_web
C:\Program Files\MATLAB\R2023b\toolbox\matlab\dependency\widget\window
C:\Program Files\MATLAB\R2023b\toolbox\matlab\depfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\editor_actions\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\editor_open_action\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\matlabcode_filename_validation\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\matlabcode_filepreview\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\matlabcode_filetype_icons\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor\cfb_integration\matlabcode_filetype_labels\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor_addons\fixedpoint_data\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor_addons\matlab_unit\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\editor_addons\system_object\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\elfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\elmat
C:\Program Files\MATLAB\R2023b\toolbox\matlab\embeddedoutputs\figureoutputs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\embeddedoutputs\outputs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\embeddedoutputs\outpututilities
C:\Program Files\MATLAB\R2023b\toolbox\matlab\embeddedoutputs\variableoutputs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\engines\codegen\common
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\engines\codegen\cpp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\engines\codegen\csharp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\engines\engine_api
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\cpp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\dotnet
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\java\jmi
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\json
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\python
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\webservices
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\webservices\http
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\webservices\restful
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\interfaces\webservices\wsdl
C:\Program Files\MATLAB\R2023b\toolbox\matlab\external\mex
C:\Program Files\MATLAB\R2023b\toolbox\matlab\file_chooser\service\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filebrowser
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\default_filetype_plugins\file_icon_plugin
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\default_filetype_plugins\folder_icon_plugin
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\default_filetype_plugins\folder_label_plugin
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\default_filetype_plugins\folder_preview_plugin
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\matlab_filetype_filters\filetypefilters
C:\Program Files\MATLAB\R2023b\toolbox\matlab\filesystem\services\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\findfiles\m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\funfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\funfun\examples
C:\Program Files\MATLAB\R2023b\toolbox\matlab\general
C:\Program Files\MATLAB\R2023b\toolbox\matlab\git
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graph2d
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graph3d
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphfun\codegen
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\annotation
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\axis
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\chart
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\color
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\function
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\hg
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\illustration
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\legacy
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\maps
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\math
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\objectsystem
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\obsolete
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\primitive
C:\Program Files\MATLAB\R2023b\toolbox\matlab\graphics\printing
C:\Program Files\MATLAB\R2023b\toolbox\matlab\guide
C:\Program Files\MATLAB\R2023b\toolbox\matlab\hardware\shared\sensors
C:\Program Files\MATLAB\R2023b\toolbox\matlab\hardware\stubs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\helptools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\helptools\help_static_content_deferred_services
C:\Program Files\MATLAB\R2023b\toolbox\matlab\helptools_js\link_click_handling_docservice\m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\helptools_js\matlab_colon_docservice\m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\htmlviewer
C:\Program Files\MATLAB\R2023b\toolbox\matlab\icons
C:\Program Files\MATLAB\R2023b\toolbox\matlab\images
C:\Program Files\MATLAB\R2023b\toolbox\matlab\imagesci
C:\Program Files\MATLAB\R2023b\toolbox\matlab\import_sci_livetasks
C:\Program Files\MATLAB\R2023b\toolbox\matlab\indentcode\m
C:\Program Files\MATLAB\R2023b\toolbox\matlab\indexing
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\archive
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\arrow
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\common
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\array
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\common
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\file
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\fileset
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\image
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\keyvalue
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\legacy
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\parquet
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\range
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\spreadsheet
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\tall
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\datastore\text
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\filesystem
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\filter
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\ftp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\functions
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\html
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\interface
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\json
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\parquet
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\spreadsheet
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\struct
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\text
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\word
C:\Program Files\MATLAB\R2023b\toolbox\matlab\io\xml
C:\Program Files\MATLAB\R2023b\toolbox\matlab\iofun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\iot
C:\Program Files\MATLAB\R2023b\toolbox\matlab\iot\connectivity
C:\Program Files\MATLAB\R2023b\toolbox\matlab\lang
C:\Program Files\MATLAB\R2023b\toolbox\matlab\licensing
C:\Program Files\MATLAB\R2023b\toolbox\matlab\login
C:\Program Files\MATLAB\R2023b\toolbox\matlab\mapreduceio
C:\Program Files\MATLAB\R2023b\toolbox\matlab\maps
C:\Program Files\MATLAB\R2023b\toolbox\matlab\matfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\matlab_preferences\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\matlab_suggestion_models
C:\Program Files\MATLAB\R2023b\toolbox\matlab\mex
C:\Program Files\MATLAB\R2023b\toolbox\matlab\mpm
C:\Program Files\MATLAB\R2023b\toolbox\matlab\mvm
C:\Program Files\MATLAB\R2023b\toolbox\matlab\network
C:\Program Files\MATLAB\R2023b\toolbox\matlab\networklib
C:\Program Files\MATLAB\R2023b\toolbox\matlab\networklib\apps\tcpclientapp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\notifications\notifications_center_ui\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\object_serialization_customization
C:\Program Files\MATLAB\R2023b\toolbox\matlab\ops
C:\Program Files\MATLAB\R2023b\toolbox\matlab\optimfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\optimfun\gui
C:\Program Files\MATLAB\R2023b\toolbox\matlab\oss
C:\Program Files\MATLAB\R2023b\toolbox\matlab\parallel
C:\Program Files\MATLAB\R2023b\toolbox\matlab\pathtool
C:\Program Files\MATLAB\R2023b\toolbox\matlab\pathtool_sidepanel\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\plottools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\plottools\inspector
C:\Program Files\MATLAB\R2023b\toolbox\matlab\polyfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\preferences\addonspanel
C:\Program Files\MATLAB\R2023b\toolbox\matlab\preferences\figurecopyprefspanel
C:\Program Files\MATLAB\R2023b\toolbox\matlab\preferences\fonts
C:\Program Files\MATLAB\R2023b\toolbox\matlab\preferences\variablesprefpanel\variablesprefpanel-ui
C:\Program Files\MATLAB\R2023b\toolbox\matlab\preferences\workspaceprefpanel\workspaceprefpanel-ui
C:\Program Files\MATLAB\R2023b\toolbox\matlab\profileviewer
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\api
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\cfbfileinfoplugin\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\comparison
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\comparisons\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\creation\fromarchive
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\creation\fromfile
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\customtasks
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\dependency
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\examplesetup
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\java
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\preferences
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\refactoring
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\unsavedchanges
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\upgrade
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\action_web\project-action-ui\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\customtasks
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\customtasks_web\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\file
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\labels
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\references
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\unsavedchanges
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\upgrade
C:\Program Files\MATLAB\R2023b\toolbox\matlab\project\views\util
C:\Program Files\MATLAB\R2023b\toolbox\matlab\randfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\registration_framework\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\remotedata\hdfs
C:\Program Files\MATLAB\R2023b\toolbox\matlab\remotedata\s3
C:\Program Files\MATLAB\R2023b\toolbox\matlab\remotedata\wasb
C:\Program Files\MATLAB\R2023b\toolbox\matlab\reports
C:\Program Files\MATLAB\R2023b\toolbox\matlab\resources_folder
C:\Program Files\MATLAB\R2023b\toolbox\matlab\richcontent_preview\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_clike_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_java_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_js_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_mlike_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_python_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_tlc_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_verilog_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_vhdl_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\rtc_addons\rtclanguagesupport\rtc_xml_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\scribe
C:\Program Files\MATLAB\R2023b\toolbox\matlab\scribe\obsolete
C:\Program Files\MATLAB\R2023b\toolbox\matlab\serial
C:\Program Files\MATLAB\R2023b\toolbox\matlab\serialport
C:\Program Files\MATLAB\R2023b\toolbox\matlab\serialport\apps\serialportapp
C:\Program Files\MATLAB\R2023b\toolbox\matlab\sparfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\specfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\specgraph
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\matlabdrive
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\mldrivedesktop
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\mldrivejsplugins\matlabdrive_js\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\mldrivejsplugins\share_folder_preview\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\mldrivejsplugins\sharing_actions\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\storage\mldrivejsplugins\tripwire_button\matlab
C:\Program Files\MATLAB\R2023b\toolbox\matlab\strfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\strfun\pattern
C:\Program Files\MATLAB\R2023b\toolbox\matlab\strfun\validators
C:\Program Files\MATLAB\R2023b\toolbox\matlab\supportpackagemanagement
C:\Program Files\MATLAB\R2023b\toolbox\matlab\system
C:\Program Files\MATLAB\R2023b\toolbox\matlab\system\editor
C:\Program Files\MATLAB\R2023b\toolbox\matlab\taskpool
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\measurement\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\measurement\ext
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\mock\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\mock\core\masked
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\obsolete
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\performance\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\performance\ext
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\shared\testbrowser\testbrowser-mi
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\testbrowser\testbrowser-mi
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\ui\toolstrip
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\uiautomation
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\uitest
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\unittest\core
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\unittest\core\masked
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\unittest\ext
C:\Program Files\MATLAB\R2023b\toolbox\matlab\testframework\unittest\parallel
C:\Program Files\MATLAB\R2023b\toolbox\matlab\timefun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\timeseries
C:\Program Files\MATLAB\R2023b\toolbox\matlab\toolbox_packaging
C:\Program Files\MATLAB\R2023b\toolbox\matlab\toolboxmanagement\matlab_api
C:\Program Files\MATLAB\R2023b\toolbox\matlab\toolstrip
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents\databrowser
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents\graphics
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents\plugin\appdesigner
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents\style
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uicomponents\uicomponents\uicontrol
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uitools
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uitools\mofigurehelperfunc
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uitools\obsolete
C:\Program Files\MATLAB\R2023b\toolbox\matlab\uitools\uicomponents\components
C:\Program Files\MATLAB\R2023b\toolbox\matlab\updateinstaller
C:\Program Files\MATLAB\R2023b\toolbox\matlab\urlmanager
C:\Program Files\MATLAB\R2023b\toolbox\matlab\validators
C:\Program Files\MATLAB\R2023b\toolbox\matlab\verctrl
C:\Program Files\MATLAB\R2023b\toolbox\matlab\webcam
C:\Program Files\MATLAB\R2023b\toolbox\matlab\winfun
C:\Program Files\MATLAB\R2023b\toolbox\matlab\xmlfun
C:\Program Files\MATLAB\R2023b\toolbox\local
C:\Program Files\MATLAB\R2023b\toolbox\simulink\configset\derived
C:\Program Files\MATLAB\R2023b\toolbox\simulink\configset\m
C:\Program Files\MATLAB\R2023b\toolbox\simulink\multisim\design
C:\Program Files\MATLAB\R2023b\toolbox\simulink\online\server\m
C:\Program Files\MATLAB\R2023b\toolbox\simulink\protected_model\core\core
C:\Program Files\MATLAB\R2023b\toolbox\simulink\runtime_callbacks
C:\Program Files\MATLAB\R2023b\toolbox\simulink\simulink_data_dictionary\matlab
C:\Program Files\MATLAB\R2023b\toolbox\simulink\simulink_data_dictionary\sldd
C:\Program Files\MATLAB\R2023b\toolbox\simulink\slsa\parametertuning
C:\Program Files\MATLAB\R2023b\toolbox\stateflow\sf_file_preview_plugin\matlab
C:\Program Files\MATLAB\R2023b\toolbox\rtw\rtw
C:\Program Files\MATLAB\R2023b\toolbox\rtw\targets\connectivity
C:\Program Files\MATLAB\R2023b\platform\pf_matlab_impl\m
C:\Program Files\MATLAB\R2023b\toolbox\classdiagram\app\core
C:\Program Files\MATLAB\R2023b\toolbox\classdiagram\app\mcos
C:\Program Files\MATLAB\R2023b\toolbox\coder\codedescriptor_core
C:\Program Files\MATLAB\R2023b\toolbox\coder\coderapp\common\ml
C:\Program Files\MATLAB\R2023b\toolbox\coder\coderapp\emlwhich\ml
C:\Program Files\MATLAB\R2023b\toolbox\coder\coderapp\screener\ml
C:\Program Files\MATLAB\R2023b\toolbox\coder\coderapp\screener_globallist\ml
C:\Program Files\MATLAB\R2023b\toolbox\coder\coderapp\utils\ml
C:\Program Files\MATLAB\R2023b\toolbox\coder\compile
C:\Program Files\MATLAB\R2023b\toolbox\coder\compile\codebuildtests
C:\Program Files\MATLAB\R2023b\toolbox\coder\compile\tools\registry
C:\Program Files\MATLAB\R2023b\toolbox\coder\connectivity
C:\Program Files\MATLAB\R2023b\toolbox\coder\connectivity_core
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\build\tools\registry
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\templates
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\tfl
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\tfl\AUTOSAR\AUTOSAR4p0\IFL
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\tfl\AUTOSAR\AUTOSAR4p0\IFX
C:\Program Files\MATLAB\R2023b\toolbox\coder\foundation\tfl\gui
C:\Program Files\MATLAB\R2023b\toolbox\coder\profile
C:\Program Files\MATLAB\R2023b\toolbox\coder\rtiostream
C:\Program Files\MATLAB\R2023b\toolbox\coder\targetreg
C:\Program Files\MATLAB\R2023b\toolbox\coder\trace
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\binary\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\cfb\action_ui\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\folder\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\mat\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\rptgen_shared
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\text\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\text\view\rptgen\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\view\edits
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\view\web3\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\zip\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\comparisons\zip\utilities\matlab
C:\Program Files\MATLAB\R2023b\toolbox\da
C:\Program Files\MATLAB\R2023b\toolbox\diagram\editor\web\m
C:\Program Files\MATLAB\R2023b\toolbox\diagram\layout\treelayout
C:\Program Files\MATLAB\R2023b\toolbox\dig\src
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsp
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsp\compiled
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsphdl
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsphdl\dsputilities
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\crl
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\dspinit
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\dspmex
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\dsptoc
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\dsptransform
C:\Program Files\MATLAB\R2023b\toolbox\dsp\dsputilities\dspupgrade
C:\Program Files\MATLAB\R2023b\toolbox\dsp\filterdesign
C:\Program Files\MATLAB\R2023b\toolbox\dsp\halidesim
C:\Program Files\MATLAB\R2023b\toolbox\dsp\samples
C:\Program Files\MATLAB\R2023b\toolbox\dsp\templates
C:\Program Files\MATLAB\R2023b\toolbox\eml\eml
C:\Program Files\MATLAB\R2023b\toolbox\experiments\custom_templates\experiments
C:\Program Files\MATLAB\R2023b\toolbox\experiments\experiments
C:\Program Files\MATLAB\R2023b\toolbox\experiments\matlab_templates\experiments
C:\Program Files\MATLAB\R2023b\toolbox\fixedpoint\fixedpoint
C:\Program Files\MATLAB\R2023b\toolbox\hdlcoder\hdllib\ml_lib
C:\Program Files\MATLAB\R2023b\toolbox\livecode\comparisons\mldesktop\matlab
C:\Program Files\MATLAB\R2023b\toolbox\parallel
C:\Program Files\MATLAB\R2023b\toolbox\parallel\array
C:\Program Files\MATLAB\R2023b\toolbox\parallel\bigdata
C:\Program Files\MATLAB\R2023b\toolbox\parallel\cluster
C:\Program Files\MATLAB\R2023b\toolbox\parallel\cluster\discovery
C:\Program Files\MATLAB\R2023b\toolbox\parallel\distcomp
C:\Program Files\MATLAB\R2023b\toolbox\parallel\gpu
C:\Program Files\MATLAB\R2023b\toolbox\parallel\gpuapi
C:\Program Files\MATLAB\R2023b\toolbox\parallel\lang
C:\Program Files\MATLAB\R2023b\toolbox\parallel\mpi
C:\Program Files\MATLAB\R2023b\toolbox\parallel\mpi\profilerviewer
C:\Program Files\MATLAB\R2023b\toolbox\parallel\parallel
C:\Program Files\MATLAB\R2023b\toolbox\parallel\parallel\util
C:\Program Files\MATLAB\R2023b\toolbox\parallel\user
C:\Program Files\MATLAB\R2023b\toolbox\parallel\web
C:\Program Files\MATLAB\R2023b\toolbox\parallel\web\plugins\runasbatchjob\matlab
C:\Program Files\MATLAB\R2023b\toolbox\parallel\web\preferences\src
C:\Program Files\MATLAB\R2023b\toolbox\physmod\simscape\language_editor\m
C:\Program Files\MATLAB\R2023b\toolbox\rptgen\xmlcomp
C:\Program Files\MATLAB\R2023b\toolbox\shared\adlib
C:\Program Files\MATLAB\R2023b\toolbox\shared\advisor
C:\Program Files\MATLAB\R2023b\toolbox\shared\appdes\services
C:\Program Files\MATLAB\R2023b\toolbox\shared\asam\mdf
C:\Program Files\MATLAB\R2023b\toolbox\shared\asynciolib
C:\Program Files\MATLAB\R2023b\toolbox\shared\audio\signallabeler
C:\Program Files\MATLAB\R2023b\toolbox\shared\bigdata\bigdata
C:\Program Files\MATLAB\R2023b\toolbox\shared\blelib
C:\Program Files\MATLAB\R2023b\toolbox\shared\cgxe\cgxe
C:\Program Files\MATLAB\R2023b\toolbox\shared\cmlink\api
C:\Program Files\MATLAB\R2023b\toolbox\shared\cmlink\preferences
C:\Program Files\MATLAB\R2023b\toolbox\shared\cmlink\view\action_web\cmlink-action-ui\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\cmlink\view\core
C:\Program Files\MATLAB\R2023b\toolbox\shared\codeinstrum\core_mi\core_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\coder\coder
C:\Program Files\MATLAB\R2023b\toolbox\shared\coder\coder\lib
C:\Program Files\MATLAB\R2023b\toolbox\shared\coder\reportinfo
C:\Program Files\MATLAB\R2023b\toolbox\shared\codergui\codergui
C:\Program Files\MATLAB\R2023b\toolbox\shared\comparisons
C:\Program Files\MATLAB\R2023b\toolbox\shared\computils\mockfilechooser\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\configset
C:\Program Files\MATLAB\R2023b\toolbox\shared\configset_model\configset
C:\Program Files\MATLAB\R2023b\toolbox\shared\configset_view\m
C:\Program Files\MATLAB\R2023b\toolbox\shared\controllib\estimation
C:\Program Files\MATLAB\R2023b\toolbox\shared\controllib\general
C:\Program Files\MATLAB\R2023b\toolbox\shared\controllib\graphics
C:\Program Files\MATLAB\R2023b\toolbox\shared\controllib\graphics\plotoptions
C:\Program Files\MATLAB\R2023b\toolbox\shared\controllib\graphics\utils
C:\Program Files\MATLAB\R2023b\toolbox\shared\coverage_data\coverage_data
C:\Program Files\MATLAB\R2023b\toolbox\shared\cxxfe\parser_mi\parser_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\cxxfe_mi\cxxfe_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\dastudio
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\datagenerator
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\task
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\task\codegenerator
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\task\interface
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\task\ui
C:\Program Files\MATLAB\R2023b\toolbox\shared\datacreation\uicomponent
C:\Program Files\MATLAB\R2023b\toolbox\shared\deviceplugindetection
C:\Program Files\MATLAB\R2023b\toolbox\shared\diagnostic
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\dialog
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\filterdesignlib
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\filterdesignlib\filterbuilder
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\float2fixed
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\hdl
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\matlab\utilities
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\matlab\utilities\init
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\matlab\utilities\mex
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\matlab\vision
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\simulink\utilities
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\simulink\utilities\mex
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\vision\simulink\vision
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\dspwebscopesutils
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\mlarrayplot
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\mlfiltervisualizer
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\mlspectrumanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\mltimescope
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\slarrayplot
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\slfiltervisualizer
C:\Program Files\MATLAB\R2023b\toolbox\shared\dsp\webscopes\slspectrumanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\shared\dspblks\dspblks
C:\Program Files\MATLAB\R2023b\toolbox\shared\dspblks\dspmex
C:\Program Files\MATLAB\R2023b\toolbox\shared\experimentmonitor
C:\Program Files\MATLAB\R2023b\toolbox\shared\gpu
C:\Program Files\MATLAB\R2023b\toolbox\shared\gpucoder\gpucoder
C:\Program Files\MATLAB\R2023b\toolbox\shared\hadoopserializer
C:\Program Files\MATLAB\R2023b\toolbox\shared\hotpluglib
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwconnectinstaller\common
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwconnection
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\clientapp
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\devicedata
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\devicedetection
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\devices
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\hwmgr
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\hwsetup
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\plugins
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\providers
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\scopes
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwmanagerapp\shared
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwservices\hwinfo
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwsetup
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwsetup\hwtemplates
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwsetup\hwwidgets
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwsetup\launch
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\hwsetup\thirdpartytools
C:\Program Files\MATLAB\R2023b\toolbox\shared\hwmanager\logger
C:\Program Files\MATLAB\R2023b\toolbox\shared\image_io\imageio_builtins
C:\Program Files\MATLAB\R2023b\toolbox\shared\imageio
C:\Program Files\MATLAB\R2023b\toolbox\shared\images_datatypes
C:\Program Files\MATLAB\R2023b\toolbox\shared\instrument
C:\Program Files\MATLAB\R2023b\toolbox\shared\io\general
C:\Program Files\MATLAB\R2023b\toolbox\shared\labelutils\labelutils
C:\Program Files\MATLAB\R2023b\toolbox\shared\m3i
C:\Program Files\MATLAB\R2023b\toolbox\shared\maputils
C:\Program Files\MATLAB\R2023b\toolbox\shared\matlab\testframework\baselines
C:\Program Files\MATLAB\R2023b\toolbox\shared\matlab\testframework\baselines_sdi
C:\Program Files\MATLAB\R2023b\toolbox\shared\measure
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlarrow
C:\Program Files\MATLAB\R2023b\toolbox\shared\mldatx
C:\Program Files\MATLAB\R2023b\toolbox\shared\mldatx\file_icon_plugin\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\mldatx\file_label_filter_plugin\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\mldatx\file_preview_plugin\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlearnlib
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\dom
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\dom\dom
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\dom\dom\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\fop
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\ppt
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\ppt\ppt
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\ppt\ppt\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\re\re\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\rpt
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\rpt\rpt
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\utils
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\widgets\equation\matlab
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\xml\xml\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\xml_transform\xml_transform\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreportgen\xml_xpath\xml_xpath\help
C:\Program Files\MATLAB\R2023b\toolbox\shared\mlreq
C:\Program Files\MATLAB\R2023b\toolbox\shared\multimedia
C:\Program Files\MATLAB\R2023b\toolbox\shared\networklib
C:\Program Files\MATLAB\R2023b\toolbox\shared\parseutils
C:\Program Files\MATLAB\R2023b\toolbox\shared\pegparserlib\pegparser
C:\Program Files\MATLAB\R2023b\toolbox\shared\performance
C:\Program Files\MATLAB\R2023b\toolbox\shared\polyspace\codeinsight_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\polyspace\configure_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\polyspace\utils_mi
C:\Program Files\MATLAB\R2023b\toolbox\shared\pslink
C:\Program Files\MATLAB\R2023b\toolbox\shared\rptgen
C:\Program Files\MATLAB\R2023b\toolbox\shared\rptgen\udd
C:\Program Files\MATLAB\R2023b\toolbox\shared\sdi
C:\Program Files\MATLAB\R2023b\toolbox\shared\sdi_matlabunit
C:\Program Files\MATLAB\R2023b\toolbox\shared\sdi_visuals
C:\Program Files\MATLAB\R2023b\toolbox\shared\seriallib
C:\Program Files\MATLAB\R2023b\toolbox\shared\siglib
C:\Program Files\MATLAB\R2023b\toolbox\shared\signal_featureextraction\signalfeatureextraction
C:\Program Files\MATLAB\R2023b\toolbox\shared\signallabelutils\signallabelutils
C:\Program Files\MATLAB\R2023b\toolbox\shared\signalwavelet\signalwavelet
C:\Program Files\MATLAB\R2023b\toolbox\shared\signalwavelet_deep
C:\Program Files\MATLAB\R2023b\toolbox\shared\sigwebappsutils\src
C:\Program Files\MATLAB\R2023b\toolbox\shared\simtargets
C:\Program Files\MATLAB\R2023b\toolbox\shared\simulink\simulation_data
C:\Program Files\MATLAB\R2023b\toolbox\shared\sl_async_streaming
C:\Program Files\MATLAB\R2023b\toolbox\shared\slcc_cov\slcc_cov
C:\Program Files\MATLAB\R2023b\toolbox\shared\spc\src_ml
C:\Program Files\MATLAB\R2023b\toolbox\shared\spc\src_sl\simulink\dsp
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\applications
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\logicanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\matrixviewer
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\slwebscopes
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\slwebscopespbcproxyreg
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\unifiedscopes
C:\Program Files\MATLAB\R2023b\toolbox\shared\spcuilib\webscopes
C:\Program Files\MATLAB\R2023b\toolbox\shared\spreadsheet
C:\Program Files\MATLAB\R2023b\toolbox\shared\stateflow
C:\Program Files\MATLAB\R2023b\toolbox\shared\statslib
C:\Program Files\MATLAB\R2023b\toolbox\shared\statslib\gpu
C:\Program Files\MATLAB\R2023b\toolbox\shared\statslib\sensitivity
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportpkgservices\installedapi
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportpkgservices\installservices
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportpkgservices\legacysupportpkginfo
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportpkgservices\supportpackageroot
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportsoftware\launcher
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportsoftware\services
C:\Program Files\MATLAB\R2023b\toolbox\shared\supportsoftware\upgrade
C:\Program Files\MATLAB\R2023b\toolbox\shared\system\coreblocks
C:\Program Files\MATLAB\R2023b\toolbox\shared\system\sfun
C:\Program Files\MATLAB\R2023b\toolbox\shared\system\simulink_block
C:\Program Files\MATLAB\R2023b\toolbox\shared\template_core
C:\Program Files\MATLAB\R2023b\toolbox\shared\testmeaslib\apps
C:\Program Files\MATLAB\R2023b\toolbox\shared\testmeaslib\general
C:\Program Files\MATLAB\R2023b\toolbox\shared\testmeaslib\hwutils\vnt
C:\Program Files\MATLAB\R2023b\toolbox\shared\transportapp
C:\Program Files\MATLAB\R2023b\toolbox\shared\transportclients
C:\Program Files\MATLAB\R2023b\toolbox\shared\transportlib
C:\Program Files\MATLAB\R2023b\toolbox\shared\viewmodel\viewmodel
C:\Program Files\MATLAB\R2023b\toolbox\shared\virtualfileio
C:\Program Files\MATLAB\R2023b\toolbox\signal\deep
C:\Program Files\MATLAB\R2023b\toolbox\signal\edffileanalyzer\src
C:\Program Files\MATLAB\R2023b\toolbox\signal\gpu
C:\Program Files\MATLAB\R2023b\toolbox\signal\sigappsshared
C:\Program Files\MATLAB\R2023b\toolbox\signal\signal
C:\Program Files\MATLAB\R2023b\toolbox\signal\signalanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\signal\signallabeler
C:\Program Files\MATLAB\R2023b\toolbox\signal\sigtools
C:\Program Files\MATLAB\R2023b\toolbox\signal\sptoolgui
C:\Program Files\MATLAB\R2023b\toolbox\sl3d\rtc_plugins\rtc_vrml_language_support\matlab
C:\Program Files\MATLAB\R2023b\toolbox\stats\anomaly
C:\Program Files\MATLAB\R2023b\toolbox\stats\bayesoptim
C:\Program Files\MATLAB\R2023b\toolbox\stats\bigdata
C:\Program Files\MATLAB\R2023b\toolbox\stats\blocks
C:\Program Files\MATLAB\R2023b\toolbox\stats\blocks\classregblks
C:\Program Files\MATLAB\R2023b\toolbox\stats\blocks\clusteringblks
C:\Program Files\MATLAB\R2023b\toolbox\stats\blocks\incblks
C:\Program Files\MATLAB\R2023b\toolbox\stats\builtins
C:\Program Files\MATLAB\R2023b\toolbox\stats\classreg
C:\Program Files\MATLAB\R2023b\toolbox\stats\clustering
C:\Program Files\MATLAB\R2023b\toolbox\stats\distributed
C:\Program Files\MATLAB\R2023b\toolbox\stats\featlearn
C:\Program Files\MATLAB\R2023b\toolbox\stats\gpu
C:\Program Files\MATLAB\R2023b\toolbox\stats\hypothesis
C:\Program Files\MATLAB\R2023b\toolbox\stats\incremental
C:\Program Files\MATLAB\R2023b\toolbox\stats\livetasks
C:\Program Files\MATLAB\R2023b\toolbox\stats\mlearnapps
C:\Program Files\MATLAB\R2023b\toolbox\stats\responsible
C:\Program Files\MATLAB\R2023b\toolbox\stats\semisupervised
C:\Program Files\MATLAB\R2023b\toolbox\stats\stats
C:\Program Files\MATLAB\R2023b\toolbox\stats\statsdata
C:\Program Files\MATLAB\R2023b\toolbox\stats\timeseries
C:\Program Files\MATLAB\R2023b\toolbox\target\shared\asyncioplugins
C:\Program Files\MATLAB\R2023b\toolbox\target\shared\devicedrivers_coder
C:\Program Files\MATLAB\R2023b\toolbox\target\shared\embedded_utilities\common
C:\Program Files\MATLAB\R2023b\toolbox\target\shared\ioserver
C:\Program Files\MATLAB\R2023b\toolbox\target\shared\svd\common
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\data\dmsi\matlabonly
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\matlab
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\model\foundation\matlab
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\model\target\matlab
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\plugins\legacyconnection\matlabprovider\matlab
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\user\commandline\matlab
C:\Program Files\MATLAB\R2023b\toolbox\targetframework\utilities\supportpackage
C:\Program Files\MATLAB\R2023b\toolbox\textanalytics\BERT\matlab
C:\Program Files\MATLAB\R2023b\toolbox\textanalytics\livetasks
C:\Program Files\MATLAB\R2023b\toolbox\textanalytics\textanalytics
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\apps\imageanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\apps\mra\src
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\apps\timefrequencyanalyzer
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\apps\waveletsignaldenoiser\src
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\apps\wv1Danalyzer\src
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\compression
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\deep
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\wavelet
C:\Program Files\MATLAB\R2023b\toolbox\wavelet\wmultisig1d
C:\Program Files\MATLAB\R2023b\ui\desktop-default-plugins\matlab
Hi,
Unfortunately Kilosort GUI does not work when CellExplorer is added to Matlab path. When I try to run Kilosort3 in Matlab, I get the following error:
>> kilosort
Error using uiextras.Panel
Cannot define property 'Enable' in class 'uiextras.Panel' because the
property has already been defined in the superclass
'matlab.ui.container.Panel'.
Error in ksGUI/build (line 112)
obj.H.logPanel = uiextras.Panel(...
Error in ksGUI (line 47)
obj.build(parent);
Error in kilosort (line 18)
h = ksGUI(f);
>> which uiextras.Panel
C:\Users\dmagyar\Documents\Matlab_toolboxes_DM\CellExplorer\toolboxes\GUI Layout Toolbox 2.3.4\layout\+uiextras\Panel.m % uiextras.Panel constructor
I have to remove CellExplorer from the path every time I use Kilosort3. Do you have any suggestions how to solve this problem?
Thank you,
Daniel
Hi Peter,
I was trying to compile mex on my mac and XCode 15(the only version MacOS14 can open) is not supported by MATLAB. So running the mex line generates following error.
I'm wondering if it's possible for you to compile a CCGHeart with mexmaca64 format. Any other possible solutions are appreciated.
Operating system
MacOS Sonoma 14.0
Matlab version
R2023b
Matlab error log
Building with 'Xcode with Clang'.
Error using mex
/Users/tomyi/Research/CellExplorer-master/calc_CellMetrics/mex/CCGHeart.c:195:3: error: call to undeclared library function
'memcpy' with type 'void *(void *, const void *, unsigned long)'; ISO C99 and later do not support implicit function
declarations [-Wimplicit-function-declaration]
memcpy(mxGetPr(plhs[1]), (void )Pairs, PairCntsizeof(unsigned int));
^
/Users/tomyi/Research/CellExplorer-master/calc_CellMetrics/mex/CCGHeart.c:195:3: note: include the header <string.h> or
explicitly provide a declaration for 'memcpy'
1 error generated.
Screenshots
Hey Peter,
The image below has a cell with an ACG that looks like a pyramidal cell but is classified as a narrow interneuron. The monosynaptic connections also show a lot of classified interneurons giving excitatory input to other cells. Not sure if it helps, but this recording is from the retrosplenial cortex.
Hi there,
I have successfully downloaded CellExplorer and am trying to run CellExplorer with the provided example data (cell_metrics_batch.mat) that comes with the installation, however I am running into an error. I am following the instructions on the 'Getting Started' page of CellExplorer but run into the following error message:
Error using strfind
PATTERN must be a string scalar or character vector.
Error in contains (line 88)
tf = ~cellfun(@isempty, strfind(s, pattern));
Error in CellExplorer/initializeSession (line 10936)
table_fieldsNames(find(contains(table_fieldsNames,UI.params.tableOptionsToExlude)))=[];
Error in CellExplorer (line 217)
initializeSession
I have added the appropriate path and I tried R2019b and R2021b version of MATLAB, windows 64-bit, however both MATLAB version met the same error. Is there something I am missing?
Thanks for your help!!
Operating system
Windows 10
Matlab version
2018a
Describe the bug
In the "deep-superficial by ripple polarity reversal" chunk of 'ProcessCellMetrics', the session struct is being overwritten. Specifically, session.extracellular.chanCoords.verticalSpacing = 20 is being changed to []. Even when being manual input into the session before running 'ProcessCellMetrics'. This then causes an error in the 'classification_DeepSuperficial' function.
Matlab error log
Error using *
Incorrect dimensions for matrix multiplication. Check
that the number of columns in the first matrix matches
the number of rows in the second matrix. To perform
elementwise multiplication, use '.*'.
Error in classification_DeepSuperficial (line 275)
deepSuperficial_ChDistance3 =
deepSuperficial_ChDistance3 * VerticalSpacing;
Error in ProcessCellMetrics (line 848)
classification_DeepSuperficial(session);
Session struct
m50_190724_181515_HPC.session.zip
Screenshots
N/A
Additional context
Add any other context about the problem here.
Matlab setpath
A common problem is interferences with other toolboxes. If possible, please provide your search path by typing path in Matlab.
Hi Peter,
I am a PhD student at George Mason University utilizing the CellExplorer MATLAB GUI, and have ran into an issue with loading a session via the function db_load_sessions (using a Windows 10 PC). First off, I am able to successfully load the example session as delineated here. However, I receive an error when setting the session when following step 4 of the database tutorial. Following the database tutorial, for public access we can ignore steps 1-3 -- if I do so, then I receive an error that the repository in db_local_repositories is empty, which makes sense. However, when I set it to the repository path for Windows in db_local_repositories, I get the error of "db_set_path: Unable to change directory to basepath: Z:\Buzsakilabspace\Datasets\PetersenP\MS13\Peter_MS13_171129_105507_concat".
Can you point me in the right direction as to solving this error? I'm thinking I may have missed something obvious, or perhaps the path to the database changed? I'm also happy to send screenshots if necessary.
Thank you for your time and for creating this wonderful tool alongside your colleagues in the lab.
Best,
Jeffrey Kopsick
Hi Peter
First of all, Many thanks for such an amazing tool.
I am trying to use Cellexplorer with some example data, but i am not able to identify this error i usually get with some files.
i am all the time doing the same. converting from Spike2 smrx format to .bin. then sorting with kilosort2 and manual curation in phy2, however while with some files Cellexplorer works perfectly fine, with some others i get the following error:
Error using plot
Vectors must be the same length.
Error in getWaveformsFromDat (line 240)
plot(time,wfF2), hold on, plot(time,wfF2(:,maxWaveformCh1),'k','linewidth',2),
xlabel('Time (ms)'),title('All channels'),ylabel('Average filtered waveforms across
channels (\muV)','Interpreter','tex'),hold off
Error in loadSpikes (line 871)
spikes = getWaveformsFromDat(spikes,session,'showWaveforms',parameters.showWaveforms);
Error in ProcessCellMetrics (line 271)
spikes{1} =
loadSpikes('session',session,'labelsToRead',preferences.loadSpikes.labelsToRead,'getWaveformsFromDat',parameters.getWaveformsFromDat,'showWaveforms',parameters.showWaveforms);
Thank you very much in advance
Best
Jesús
Operating system
Ubuntu 21.10
Matlab version
R2019b
Describe the bug
I tried using the "Extracellular/Generate common coordinates" function in the Session GUI, after having defined probe implants under the Animal Subject. I noticed two problems in the process:
In generateCommonCoordinates.m Line 29, it seems to me that the line should be changed from
nChannels = session.animal.probeImplants{i}.nChannels; to nChannels = session.animal.probeImplants{i}.nChannel;, since the name of the corresponding variable in session.animal.probeImplants is nChannel.
In bregma_to_CCF.m, a function named "rodrigues_rot" is used multiple times for performing Rodrigues Rotation. This function is not available either in cellExplorer repository or MATLAB in general. Is that due to the version of the MATLAB I am using? Or am I missing some packages? After a quick Google search, I found this script with the name rodrigues_rot.m. If that is the one you are using, maybe it would be helpful to add it into the CellExplorer repository.
Many thanks for this great resource you have developed!
Best regards,
Baran
Is your feature request related to a problem? Please describe.
I'm always frustrated when I cannot evaluate the average voltage trace corresponding to events as i am evaluating them for accuracy in NS2 after detection.
Describe the solution you'd like
I'd love a plot inset into the GUI showing the mean +/- SEM and/or STD of all of the events. Bonus would be a customizable time window range around said events and an easy way to enter or omit certain events like is done with the channel tags. Essentially a PSTH with some stats baked in.
Describe alternatives you've considered
extracting events in matlab and plotting manually - not ideal to see in real time how each event impacts average.
Additional context
Add any other context or screenshots about the feature request here.
Hi
Thank you again for creating this amazing tool.
Is there an option to add support for waveclus aswell?
https://github.com/csn-le/wave_clus
The output of Wave_clus is times_[filename].mat containing the following variables:
par (parameters used for clustering)
spikes (a matrix with the spike shapes)
inspk (a matrix with the features of the spike shapes)
cluster_class (a matrix with the clustering results).
The variable cluster_class has 2 columns and nspk rows (nspk is the number of spikes).
The first column is the cluster class, with integers denoting the clusters membership and a value of 0 for those spikes not assigned to any cluster.
The second column is the spike times in ms.
output files example:
https://drive.google.com/file/d/1PCrOGmbOFkEvO5QyqxqrwAI96I6c1Kkc/view?usp=sharing
data files:
https://drive.google.com/file/d/1NrsHZ_MdUYPUgdfTnSLjruAmrp7fSJ9u/view?usp=sharing
either way thank you
Hi Peter,
I hope you're doing well. First let me thank you again for the great tool you created. I installed the latest version of Cell Explorer and now when I look at the refractoryPeriodViolation, the values are way off. Then I checked the code and I saw that in the formulation, the value is multiplied by 1000. Shouldn't it be 100 if it's meant to convert it to percent? Or maybe I'm missing something? When I calculated the RPVs myself (total number of spike intervals < 2ms divided by total number of spikes), I get the same value but of an order of magnitude smaller than what cell explorer gives me. I checked the spike times from cell explorer and they are correct.
cell_metrics.refractoryPeriodViolation(j) = 1000*length(find(diff(spikes{spkExclu}.times{j})<0.002))/spikes{spkExclu}.total(j);
Windows 10
Matlab R2018b
Is your feature request related to a problem? Please describe.
The script CCG.m assumes a default value of 20KHz for the sampling rate. Many labs record at 25KHz or 30KHz. This needs to be generalized. To generalize it, we need to add an extra input parameter for the function that calls CCG.m: ce_MonoSynConvClick.m
Describe the solution you'd like
I am attaching the updated ce_MonoSynConvClick.m so that you can make the appropriate change. I have added an extra input parameter for the sampling rate.
Hi Peter, there's a minor bug upon trying to load datasets with different sampling rates (e.g. 20 & 30 kHz) into the same session, due to a mismatch in the length of 'waveforms'. Could potentially be resolved by up- or downsampling one of the waveform sets or by storing them in a cell array.
Hi Peter,
Thank you for this awesome tool; it's working great so far!
When trying to save my cellMetrics to nwb with saveCellMetrics2nwb, I encounter this error:
Unrecognized function or variable 'generateExtension'.
I can't seem to find this function in the repo or embedded in saveCellMetrics2nwb.
Thanks,
Patrick
Operating system
Linux - Fedora 35
Matlab version
2021a
Describe the bug
Small typo was identified during the input parser part of the ce_MonoSynConvClick.m file. Lines 87 to 90
The lines read:
validationDuration = @(x) assert(isnumeric(x) && length(X) == 1 && X>0, 'Duration must be numeric and positive');
validationBinsize = @(x) assert(isnumeric(x) && length(X) == 1 && X>0, 'Binsize must be numeric and positive');
validationEpoch = @(x) assert(isnumeric(x) && (size(x,2) == 2), 'Epoch must be numeric and of size nx2');
validationIncludeInhibitoryConnections = @(x) assert(isnumeric(x) || islogical(x), 'Epoch must be numeric and of size nx2');
But 'X' should be replaced with 'x' in lines 87 and 88. Thanks. Please fix this minor typo.
Hello,
sorry for posting here again (in addition to the googlegroups), but I think I can now provide a more detailed assessment of my error.
I am trying to run the ProcessCellMetrics pipeline with neuropixel 1.0 data that has been spike sorted using Kilosort3. The data has been recorded using openEphys and nothing else is being done to the data.
In the validation of the session metadata, it tells me that "electrodeGroups channel count is not equal to extracellular.nChannels".
When I run the cell metrics pipeline, it does run and imports waveforms nicely (I am seeing the plots). However, midway, it stops and I receive the following error
loadSpikes: Loading Phy data
Importing 638/1269 clusters from phy
Saved variable 'noiseLevel' to Y:\Staging\Yangfan\yp012\yp012_220211\yp012_2022-02-11_14-26-53\Record Node 102\experiment1\recording1\continuous\Neuropix-PXI-100.2\continuous.noiseLevel.channelInfo.mat
Getting waveforms from dat file (nPull=600). Bandpass filter applied: 500 - 8000 Hz. No bad channels detected.
Index exceeds the number of array elements. Index must not exceed 85.
Error in getWaveformsFromDat (line 225)
nChannelFit = min([16,length(goodChannels),length(electrodeGroups{spikes.shankID(ii)})]);
Error in loadSpikes (line 855)
spikes = getWaveformsFromDat(spikes,session,'showWaveforms',parameters.showWaveforms);
Error in ProcessCellMetrics (line 271)
spikes{1} =
loadSpikes('session',session,'labelsToRead',preferences.loadSpikes.labelsToRead,'getWaveformsFromDat',parameters.getWaveformsFromDat,'showWaveforms',parameters.showWaveforms);
Error in CellExplorer_Tutorial (line 19)
cell_metrics = ProcessCellMetrics('session', session);
After diving into it, I suspect that it has something to do with Kilosort3 putting out fewer channels than 384. I only have 374 channels in the rez structure. I am not sure why it does that and I have opened a report for this on the kilosort repo: MouseLand/Kilosort#482
The extracellular tab indicates that there are only 374 spikeGroups and 374 electrodeGroups. However, when I set the number of channels to 374 in the GUI, it messes up the import of the waveforms: all the waveform are just noise, I think the channel mapping gets shifted.
So my question is:
Thanks so much for your help! Very eager to use this amazing tool!
Best
Yangfan
Matlab version
2021b
at the moment, setting the forceReload to True in ProcessCellMetrics is not passed on to the loadSpikes function.
when in fact, I need to read the spikes from the Phy results again, because I have changed the manual clustering (e.g. merged or removed a noisy cluster)
by using this command: ProcessCellMetrics('session', session, 'forceReload',true);
the forceReload parameter value is not passed on to loadSpikes and hence in line 66 the parameter is set to false.
and the conditional statement in line 108 is not True because all the required fields exist. so it doesn't assume "spikes.mat not up to data" and reloads the existing spikes.
is there a separate parameter that I should define for it? or perhaps a fix is required.
Hey Peter,
First off I want to say thank you for this awesome package!! It's helped loads!
Going through the website, your tutorial on the session metadata video had a field for "electrodes" in the extracellular tab. I am on windows and it doesn't show up for me, and I pulled the most recent updates to the code this morning.
Not being able to specify electrode and measurements is giving me this error.
Any help would be great, and thank you again!
Best,
Kaiser
Hi Peter,
I would like to plot multiple manipulations that have different duration. (e.g. 1 ms vs 10 sec)
Timestamps of different manipulations are stored in the timestamps fields of basename.eventName.manipulation.mat structs.
I also provide duration in the duration fields like it is suggested on the website.
When I run cell_metrics = ProcessCellMetrics('session', session); the program ignores the duration fields, instead loads a hard coded duration value from preferences = preferences_ProcessCellMetrics(session); .
Would it be possible to use those duration values that I provide in the duration fields of the basename.eventName.manipulation.mat structs? In this case, PSTHs of different manipulations could have different length and bin size.
Thank you,
Daniel
I'm really excited to use CellExplorer, but I'm having an issue running it with the example data provided. Below is the following error message I receive when I run CellExplorer('metrics',cell_metrics)
I do have 'CellExplorer\exampleData\cell_metrics_batch.mat' loaded into the workspace, fyi
Thanks
>> CellExplorer('metrics',cell_metrics);
Failed to find basepath files
[15-11-2021 23:06:28] Initializing session
[15-11-2021 23:06:28] Initializing dimensionality reduction plot
Error using CellExplorer>@(X)X(1:end-2)
Too many input arguments.
Error in CellExplorer/initializeSession (line 11213)
customPlotOptions = cellfun(@(X) X(1:end-2),customPlotOptions.m,'UniformOutput', false);
Error in CellExplorer (line 219)
initializeSession
>>
Is your feature request related to a problem? Please describe.
When running "loadCellMetricsBatch" the output doesn't contain the transmission probabilities from the individual session cell_metrics.
Describe the solution you'd like
Within the batch cell_metrics.putativeConnections have matrixes containing the transmission probabilities of the corresponding putative connections.
Operating system
Ubuntu 18.04
Matlab version
2019a
Describe the bug
There is a mismatch between size of cell_metrics.excitatory and cell_metrics.excitatoryTransProb variables.
Screenshots
Hello, my name is Collin, I'm a grad student at Johns Hopkins. I've just started working with CellExplorer and have run into an issue regarding ACG fit. While running CellMetrics, MatLab returned this error while fitting the triple exponential:
It seems like there is not a 'ydata' variable defined prior to line 75 in fit_ACG as needed here:
CellExplorer/calc_CellMetrics/fit_ACG.m
Line 75 in 31562ec
Hi Peter,
For some reason the MonoSyn routine doesn't identify inhibitory cells, even in cases where the inhibition is very clear (see attached image)
On the other hand, the algorithm occasionally identifies cells that are classified as interneurons as 'excitatory', which could be due to some rebound effects (see second image).
Any idea how to fix these issues? should these CCGs be deselected?
Another issue is, when I try to save a classification as a new file I get the following error:
Reference to non-existent field 'spikeSortingID'.
Error in CellExplorer/saveDialog (line 6819)
if length(unique(cell_metrics.spikeSortingID)) > 1
Error using uiwait (line 81)
Error while evaluating Menu Callback.
at what point is this field 'spikeSortingID' generated? does it depend on what program I used for the sorting? (it happens both with sessions that were manually curated with phy and klusters)
thanks in advance,
Noam
Operating system
Windows 10 Pro
Matlab version
R2023a
Describe the bug
There is an error when trying to save cell metrics as an .nwb file through the GUI.
Matlab error log
In saveCellMetrics2nwb (line 18)
In saveCellMetrics (line 23)
In CellExplorer/saveMetrics (line 9961)
In CellExplorer/saveAsDialog (line 9930)
In uiwait (line 81)
In CellExplorer (line 392)
In main_CellExplorer (line 18)
Unrecognized function or variable 'generateExtension'.
Error in saveCellMetrics2nwb (line 18)
generateExtension('ndx-cell-explorer.namespace.yaml');
Error in saveCellMetrics (line 23)
saveCellMetrics2nwb(cell_metrics,file);
Error in CellExplorer/saveMetrics (line 9961)
saveCellMetrics(cell_metrics,file);
Error in CellExplorer/saveAsDialog (line 9930)
saveMetrics(cell_metrics,fullfile(SavePath,file));
Error while evaluating Menu Callback.
Screenshots
Additional context
Add any other context about the problem here.
I am trying to load data collected using UCLA silicon probes (128DN) and sorted using kilosort2 and phy. I followed the guidelines mentioned in the General tutorials. But when I run the cell_metrics = ProcessCellMetrics('session', session);, I run into issues with the loadSpikes and getWaveformsFromDat functions.
The script loads the first few waveforms correctly, and then the following unit waveforms aren't real waveforms and look like noise. It seems like a channel map/ spike group/ or electrode group definition related problem to me. Can you please point me to the instruction to define either of those things? Or let me know if my question is unclear. Thank you!
Hi Peter,
I tried to use the new version of CellExplorer, loading the data and metadata and calculating all metrics including mono_res works fine. However, when launching the CellExplorer viewer I get the following error
"Identifier 'fig' is not a function or a shared variable. To share 'fig' with nested function, initialize it in the current scope. For more information, see Sharing Variables Between Parent and Nested Functions."
Could it have something to do with the MATLAB version? I'm using 2019b.
thanks!
Hi Peter,
first of all, thank you for this amazing tool and all the effort you put into it and for sharing it with the community.
As I was going through the tutorials and explanations, I fount one contradiction regarding how the cells were classified in the section datastructure/standard-cell-metrics/ , more precisely regarding narrow vs wide interneurons. I guess all interneurons are classified without any restriction on the trough to peak time, then they are split into the two classes based on this criterion. It would be great if this was clarified on the website.
Thanks in advance and keep up the good work.
Greetings,
Ruxandra
Hi ,
I managed to get the monosynaptic connection between a group of neurons using the following command:
mono_res = ce_MonoSynConvClick (spikes,'includeInhibitoryConnections',true,'epoch',epochs);
I was wondering if there is an easy way to just plot the connectivity graph using the mono_res structure output. I noticed in the main script (https://github.com/petersenpeter/CellExplorer/blob/master/CellExplorer.m), you make some sort of adjacency matrix (A) followed by a function call to digraph and finally plotting it in the GUI.
Thanks
Hello @petersenpeter,
Thanks for putting together this awesome CellExplorer package. I just went through all of the tutorials on the site and the software seems pretty straight forward. I tried loading my preliminary data that was sorted with Kilosort and "viewed" in Phy, but the GUI outputs an error when trying to load spikes from rez.mat or from phy (see error below) when running ProcessCellMetrics. Any help would be greatly appreciated.
Error in loadSpikes (line 265)
disp(['Importing ' num2str(numel(spikes.times)),'/',
num2str(length(dataArray{1})),' clusters from phy'])
Error in ProcessCellMetrics (line 270)
loadSpikes('session',session,'labelsToRead',preferences.loadSpikes.labelsToRead,'getWaveformsFromDat',parameters.getWaveformsFromDat,'showWaveforms',parameters.showFigures);`
Operating system
Linux - Fedora
Matlab version
2021a
Describe the bug
Mex file called FindInIntervals is not working located in CellExplorer/calc_CellMetrics/mex/
Execution of script FindInInterval as a function is not supported:
Matlab error log
Execution of script FindInInterval as a function is not supported:
Hi Peter,
I have received this error while installing the toolbox. I have installed Xcode which has a c compiler by default.
Operating system
Mac
Matlab version
2021B
Describe the bug
Error using mex
/Volumes/Projects/CellExplorer-master/calc_CellMetrics/mex/CCGHeart.c:195:3: error: implicitly declaring library function 'memcpy'
with type 'void *(void *, const void *, unsigned long)' [-Werror,-Wimplicit-function-declaration]
memcpy(mxGetPr(plhs[1]), (void )Pairs, PairCntsizeof(unsigned int));
^
/Volumes/Projects/CellExplorer-master/calc_CellMetrics/mex/CCGHeart.c:195:3: note: include the header <string.h> or explicitly
provide a declaration for 'memcpy'
1 error generated.
Error occurs in getting started section, when running the command CellExplorer('metrics',cell_metrics).
Stack trace:
[08-05-2023 09:28:08] Initializing session
[08-05-2023 09:28:08] Initializing dimensionality reduction plot
Error using CellExplorer>@(X)X(1:end-2)
Too many input arguments.Error in CellExplorer/initializeSession (line 11267)
customPlotOptions = cellfun(@(X) X(1:end-2),customPlotOptions.m,'UniformOutput', false);Error in CellExplorer (line 217)
initializeSession
Matlab version: R2023a Update 1 (9.14.02239454)
OS: MacOS Monterey 12.5.1, Intel Core i5
Hello Peter,
Sorry to bother you again. In my latest import from kilosort3 (neurpixels) I have weird oscillations in the waveform, see attached image. Do you know where these could be coming from? The raw data looked fine, is it an issue of kilosort3 or is the getwaveform function of cellexplorer the reason? I would appreciate any advice. Thanks!
Best
Yangfan
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
Django
The Web framework for perfectionists with deadlines.
Laravel
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft
Open source projects and samples from Microsoft.
Google
Google ❤️ Open Source for everyone.
Alibaba
Alibaba Open Source for everyone
D3
Data-Driven Documents codes.
Tencent
China tencent open source team.