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README.md

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NETCAL: An interactive platform for large-scale, NETwork and population dynamics analysis of CALcium imaging recordings

NETCAL is a MATLAB-built, dedicated software platform to record, manage and analyze high-speed high-resolution calcium imaging experiments. Its ease of use, interactive graphical interface and exhaustive documentation is aimed to wet-lab researchers, but it will also meet the needs of any experienced data scientist through its plugin and scripting system. We have developed a large set of tools and incorporated state-of-the-art algorithms and toolboxes for large-scale analysis of network and population dynamics. Analyses include: automated cell detection (both static and dynamic); trace and population sorting through machine learning, clustering and pattern recognition; bursting dynamics; spike detection; network inference (from functional networks to causal relations); and many more. Several of these tools are also available in real-time, e.g. cells and spikes can be monitored during the actual recording, giving the researcher extensive feedback on the progress of the experiment.

Installation instructions

  • You can find here the latest installation instructions.
  • Install additional MATLAB toolboxes: Go to the installDependencies folder and execute the mltbx files (or drag and drop in MATLAB). NOTE: In MATLAB r2017a+ you might need to download the GUI Layout Toolbox from the Add On Explorer yourself.
  • Change default MAT-Files version: Go to MATLAB Preferences -> General -> MAT-Files to v7.3
  • To be able to export figures to pdf and eps you need ghostscript installed.
  • To be able to use any of the python modules you need python installed and available to MATLAB

Requeriments

  • Matlab 9.1+ (2015a or higher) - 2017a or higher recommended. Seriouslly, upgrade.

MATLAB Tolboxes

  • Bioinformatics Toolbox (4.5.1) [bioinfo]
  • Curve Fitting Toolbox (3.5.1) [curve fit]
  • Econometrics Toolbox (3.2) [econ]
  • Global Optimization Toolbox (3.3.1) [globaloptim]
  • System Identification Toolbox (9.2) [ident]
  • Image Processing Toolbox (9.2) [images]
  • Neural Network Toolbox (8.3) [nnet]
  • Statistics and Machine Learning Toolbox (10.0) [stats]
  • Computer Vision System Toolbox (6.2) [vision]

Change Log

[8.6.0] - 2018-10-08

Added

  • Tutorials / Documentation section
  • Ability to change the default average image (useful for ROI detection)
  • ROI detection using a contour image

[8.5.0] - 2018-09-29

Added

  • Working on full compatibility with MATLAB R2018b

[8.4.5] - 2018-09-27

Attention

If you are upgradint to MATLAB R2018b make sure to update the GUI Layout Toolbox too! (Version 2.3.2 minimum)

Added

  • Support for MATLAB R201b (experimental)

Fixed

  • Findjobj required an update tow ork wiht r2018b
  • Spatial kernel on CellSort ROI detection was only being applied on the second dimension

[8.4.4] - 2018-09-26

Fixed

  • Leftover errors on the denoiser when using too large blocks

[8.4.3] - 2018-09-26

Modified

  • Small changes to the denoiser output

[8.4.1] - 2018-09-10

Modified

  • Added warnings in case the drift correction returns an unquared mask

[8.4.0] - 2018-09-08

ATTENTION

Hey! Due to some mailing issues, if you ever sent me a question/request to javierorlandi@javierorlandi.com or *@itsnetcal.com and never got answered. Please send it again to javiergorlandi@gmail.com or javier.orlandigomez@ucalgary.ca . Thanks! (I believe those mails have not been functioning properly for the last year)

Added

  • Several options to automatically import ROI from files and experiments to multiple experiments at once
  • Redesigned export movie pipeline function (so it also works ok with drifft corrected movies)
  • Added big tiff export support
  • Pipeline mode: help window to provide a small description of any selected available function
  • Most pipeline statistics functions are now available on the single and batch mode menus
  • Several pipeline functions added to the main menus
  • Option to export inferred networks to GEPHI (with any additional network statistic you might think of)

Fixed

  • Error when ROI with and without weights coexisted
  • Error when trying to plot fluorescence burst statistics from the bursts GUI

[8.3.0] - 2018-09-07

Added

  • Complete overhaul of the drift correction. Now it should be compatible with the denoiser and cell sort
  • Option to automatically add custom pipeline functions (any m file inside the plugins/pipeline folder is a candidate)

Modified

  • AutoLevels is now based on (iterative) accurate percentile calculations. Not on fixed pixel values

Fixed

  • Many issues with 32 bit images

[8.2.8] - 2018-09-05

Added

  • More features to the drift correction (mostly for in vivo recordings)

Modified

  • Quit accelerator is now Ctrl+Q And Clear Log is Ctrl+X

[8.2.7] - 2018-09-04

Added

  • Drift correction preprocessing feature. For samples that move around: badly fixed coverslips, human intervention, in vivo recordings, etc. You can find it in preprocessing -> drif correction. Uses MATLAB image registration features. For now only rigid body and translation transformations. Once run, it will automatically be applied everytime a frame is captured. So should be compatible with any preexisting function. However, consider it an EXPERIMENTAL feature.

[8.2.6] - 2018-09-04

Modified

  • Added verbose output to fast ICA analysis

Fixed

  • Autolevels function not working on 32 bit images

[8.2.5] - 2018-09-03

Fixed

  • Updater issues

[8.2.4] - 2018-09-03

Modified

  • Statistics plots now run much faster (when multiple statistics are selected)

Fixed

  • Bug when UnivarScatter would enter in an infinite loop
  • Bug when trying to arrange inexistent figures

[8.2.3] - 2018-08-31

Fixed

  • FastICA was only available on the development branch

[8.2.2] - 2018-08-30

Fixed

  • New .TIF or .TIFF could not be added from the load Experiment menu

[8.2.1] - 2018-08-29

Added

  • Plot statistics now shows the # experiment being processed
  • Clustering coefficient measures for directed networks
  • Bunch of new network statistics measures
  • Treatment based network statistics

Modified

  • Now any network plots requires an active network to be set
  • New option to set the active network (adjacency matrix) based on some inference measure

Fixed

  • Tif files without metadata are now being loaded correctly
  • DenoiseRecording was using the transposed image in some instances
  • Small bug fixes

8.2.0 - 2018-08-14

Added

  • Network inference: fast estimator of Generalized Transfer Entropy with significance estimators (fully working)
  • Many network measures (from the brain connectivity toolbox)
  • Full Brain Connectivity Toolbox
  • sigstar allows negative p values (will display # instead of *)
  • Burst statistics. Added high and low bursting rate measures (those that recruit above and below 20% of the population respectively)

8.1.3 - 2018-07-20

Added

  • Global Firing Rate to spike statistics plots
  • Option to automatically export data to csv when generating statistics figures
  • Option to plot several burst spike statistics within the same pipeline call
  • Hardcoded transparency effects on UnivarScatter bars (to fix exporting issues)
  • Option to not use weights when displaying ROIs with weights
  • Option to circumvent pipeline errors when using updated functions.

Modified

  • Right click ROI sorting is now accessible when viewing the average of current ROI within the view Traces window (not only when viewing the movie anymore).

Fixed

  • Multigap subplot had transposed output
  • Issue when cloning experiments with missing fields
  • Small bug fixes

[8.1.2] - 2018-07-08

Added

  • New view recording plugin (2) for fast viewing of recordings (specially for HIS files). Allows drag and drop of the movies and switching between different movies within the same window

Fixed

  • Several files were not being uploaded to the repository due to a faulty .gitignore
  • Several small bug fixes

[8.1.1] - 2018-06-26

Added

  • Univarscatter module to plot statistics functions

8.1.0 - 2018-06-26

Added

  • New features for visualizing defining and sorting schmitt-based inference
  • Statistics plots from schmitt inference features
  • Ability to define more threshold on schmitt inference (minum sizes and durations)
  • More options to measure differences across treatments

Fixed

  • Bug when importing experiments from existing projects with duplicate names would result in the existing experiments being overriden by the new one
  • Improved renaming of existing files when renaming or importing experiments
  • Substantial speed-up when processing statistics across many experiments

8.0.7 - 2018-06-20

Added

  • Option to directly compute p-values on the treatment statistics for each experiment pair (ttest2, Mann-Whitney, Kolmogorov-Smirnov)
  • minimum event size and duration for schmitt-based inference
  • Several new observables for schmitt-based inference

Modified

  • Length of patterns during selection in the pattern-based classification is now limited to the sampling range

Fixed

  • Warning while loading experiments with bigtiff and TIFF_LONG8 datatypes

8.0.6 - 2018-06-18

Added

  • Extra feature list on schmitt trigger based inference
  • Visualization of schmit events on the view traces menu

Fixed

  • Error when identifying similarities in traces if only 1 trace was present
  • Several typos

[8.0.5] - 2018-06-18

Added

  • Transfered many of the new plot statistics options to the treatment version. Exports, significance, etc.

Fixed

  • Improved support of big tiff files
  • Speed up on statistics plots when a large number of labels exist

8.0.4 - 2018-06-11

Added

  • Option to show the standard error of the mean on all plot Statistics functions
  • Speed-up of plot Statistics functions when many labels are present

[8.0.3] - 2018-06-07

Fixed

  • Issue when the project export would get the wrong file list if any experiment was missing some of the bigFields
  • Shortened project names in the recent projects list
  • Error on the denoiser when the number of ICA components was lower than the PCA ones (due to degeneracies)
  • Removed the 'no changes were made' after closing GUI windows
  • Fixed a bunch of issues on the plotStatistics function when the number of groups was bigger than 1
  • Fixed errors due to the Holm-Bonferroni correction on several fringe cases

8.0.2 - 2018-06-06

Fixed

  • Issue when the experiments were not being correctly saved after importing a windows project on a nix system on pipeline mode

8.0.1 - 2018-06-06

Fixed

  • recent projects list not displyaing correctly when using samba shares. Now it should work seamlessly on win and nix systems

[8.0.0] - 2018-06-06

Added

  • Full implementation of CellSort-like (Mukamel 2009) activity-based ROI detection. Selects ROIs after a PCA/ICA dimensionality reduction. Implemented within the denoiser and the pipeline -> fluorescence -> cellsort. Guide coming soon!
  • Pattern count classifier now also creates intersection groups (if pattern overlapping is allowed). Example: you can now end up with traces that belong to both neuron and glia populations in a new subgroup
  • New project export feature. You can export the project to a new folder with only a subset of experiments and a subset dditional data (traces, denoisedData, etc) for reduced project size. Useful to share with collaborators
  • On the traces window you can now sort traces by some ROI properties. Size, position, etc.
  • Option to disable saving the experiment on some figure plots. This will result in a speed up on the pipeline when you are only interested in just plotting stuff.
  • Added fast mode for trace extraction (not recommended, only useful for cellsort ROI detection).
  • Ability to view the PCA and ICA temporal components on the traces menu (after denoising).

Modified

  • Several ROI visualization options now work with weighted ROIs. Weighted ROIs only appeear in the cellsort ROI detection (for now).
  • Simplified the saveProject file.
  • Lots of changes to the denoiser. Now ICA is always performed after PCA.

Fixes

  • Lots of small bug fixes

7.4.1 - 2018-04-16

Added

  • Batch change of framerate for multiple experiments
  • Batch change of multiple experiment handles
  • Batch change of number of frames for multiple experiments
  • Unpaired two-tailed t-test statistic

Fixed

  • Refine ROI threshold was using old progress bar code
  • Movie export profile was not being correctly assigned in some cases
  • Rate-based spike conflict fixing was asking for unecessary variables

7.4.0 - 2018-04-03

Added

  • Option to remember selected FPS on avi and btf files
  • Option to move one ROI at a time (or random) on Spike Inference Training

Modified

  • Option to redo ROI index list is now on the Modify ROI menu
  • loadTraces now tells you what is loading (sometimes)
  • Default range of preprocessing temporal subset (from 600s to inf)

Fixed

  • Bug when training with OASIS failed due to the ncbar not being present

[7.3.4] - 2018-04-03

Fixed

  • Small bug fixes

[7.3.3] - 2018-03-07

Added

  • Additional options can now be passed to the raster plot through an external .m file. Will be rolling this feature to all plots in the near future

[7.3.2] - 2018-03-06

Added

  • Continuous version checker (every hour)

Modified

  • Raster plot function can now plot multiple groups together (using different colors)

7.3.1 - 2018-03-06

Added

  • New spike-based group classifier (identify ISI). Will group spikes with similar ISI statistics (uses two-tailed KS as similarity measure)

Fixed

  • Small bug fixes

7.3.0 - 2018-03-05

Added

  • Support for mj2 files
  • Options to detect spike conflicts based on rate

Modified

  • Major rework on statistics plots. New significance options and distributions features
  • Overhaul of export movie features
  • Color of log headers

Fixed

  • Many small bug fixes

[7.2.6] - 2018-02-16

Modified

  • Added options for spike train exports

[7.2.5] - 2018-02-06

Added

  • X-based burst detection

7.2.4 - 2018-02-05

Added

  • Suprise-based burst detection

7.2.3 - 2018-02-02

Added

  • Semi-automatic burst detector based on ISI_N

[7.2.2] - 2018-02-01

Modified

  • ISI_N burst detection: now each burst is plotted in a different color
  • ISI_N burst detection explorer: now shows the estimated positon of maximums and minimums of the distribution

Fixed

  • New options were not being stored within the experiments after a succesful parallel pipeline run

[7.2.2] - 2018-01-31

Fixed

  • Small bug fixes on KCL analys and ISI_N burst detectors

[7.2.1] - 2018-01-30

Added

  • Option to store traces with single precision (EXPERIMENTAL)

7.2.0 - 2018-01-30

Added

  • Bivariate gaussian kernel density estimation functions
  • nhist for prettier histograms
  • Option to plot multiple statistics simultaneously (spikes and KCl for now)
  • Option to tile (most) pipeline-generated figures

Modified

  • Completely redesigned several options on acute treatments analyses

Fixed

  • Export KCl features now works with the new data

Bugs

  • PCA analysis with KCl features is now broken

7.1.10 - 2018-01-29

Added

  • spike bursts statistics plots now have the option to plot all statistics simultaneously

Modified

  • Forced option to copy files when renaming experiments

7.1.9 - 2018-01-25

Added

  • Option to show signififcance level (stars) on statistics plots. Mann-Whitney and Kolmogorov-Smirnov for now.

Fixed

  • Bug when importing ROIs from an external file would result on their centers being transposed (has no effect on anything other than exporting ROI positions). Added pipeline function to recalculate centers based on the actual pixel values.

7.1.8 - 2018-01-24

Added

  • Pipeline function to create a new population based on firing neurons (those with a minimum number of spikes)

Fixed

  • Jitter option was always on on the ISI_N burst detector

7.1.7 - 2018-01-24

Modified

  • Changed ROI factor name for event in statistics plots
  • Changed amplitude for number of spikes (and a normalized option) for spike-based burst statistics

Fixed

  • Bug when loading/saving pipelines was not working if they contained deep structures with table-like lists

7.1.6 - 2018-01-23

Added

Modified

  • Previous spike burst detector is now called rate detector. Also added option to plot (or not) its results

7.1.5 - 2018-01-23

Added

  • Peeling spike inference now has several new options to allow more customization (as in the original paper)
  • Cartesian coordiantes export of ROI centers
  • Export ROI coordinates button to the view ROI GUI

Modified

  • ROI centers export on the pipeline now has its own section (ROI)
  • Spike inference modes are now in the same order as in the training window

7.1.4 - 2018-01-22

Modified

  • Moved Trace Fixer to the end of the View menu to avoid user missclicks

7.1.3 - 2018-01-22

Fixed

  • Spike inference: Schmitt trigger should correctly display detected events and thresholds in the training window

7.1.2 - 2018-01-22

Added

  • exportROIcenters: pipeline function to export ROI centers of a given group (groups: exports)

7.1.1 - 2018-01-22

Added

  • viewROI now accepts power spectrum images
  • peak detector to detect peaks in traces (will be used to refine pattern-based classifiers)
  • module to detect dying cells (those with step-like changes in fluorescence levels)
  • view traces available in batch mode
  • Several new features on the KCl analyis module
  • Spike-based burst detection method
  • Power-spectrum based preprocessing (obtain different average images based on power-spectrum bands)
  • More spike features (spikes in bursts)
  • More options for MLspike inference
  • Cross-correlation measures
  • New raster plots with average activity on top
  • Options to multiply or divide all frames using an external file (to correct uneven light fields)

Modified

  • Updated CaImAn repository
  • Updated CellSort repository and fully integrated it within NETCAL (GUI pending)
  • Schmitt trigger now admits point to point thresholds
  • Substantial speed up on automatic ROI detection (quick_dev and split modules)

Fixed

  • Renamed brick montage to avoid conflicts
  • Some files where not being copied when importing/cloning exsting .EXP files
  • Some statistics were not being correctly exported

Removed

  • Several consistency checks on trace fixer

Known Bugs

  • There is an ongoing bug where several pipeline functions are not being correctly loaded from their json files

7.0.0 - 2017-11-12

Added

  • Open beta release

Known Bugs

  • There is an ongoing bug where several pipeline functions are not being correctly loaded from their json files

[6.3.0] - 2017-11-03

Modified

  • Clean slate preparing for OpenBeta release

[6.2.1] - 2017-11-02

Added

  • Introduced Development mode to distinguish between dev builds and the open beta
  • Preparing repository for open beta release

Modified

  • Increased menus responsiveness when switching between experiments
  • Added error handling for incomplete video files

Other

  • Moved several functions into the new development folders (will only be avilable on the private/testing repository)

Removed

  • Links to old trunk versions in the repository

[6.1.2] - 2017-10-30

Added

  • Option to define the type of averages when computing the statistics (mean or median)

[6.1.1] - 2017-10-29

Added

  • Option to change bar group order in statistics plots (both normal and treatments)

Fixed

  • Cell-array-type options can now (hopefully) be correctly saved and loaded from pipeline files

[6.1.0] - 2017-10-29

Modified

  • Complete rework of the optionsWindow GUI (again)

Fixed

  • Issue when data tables inside options were not being correctly saved

Fixed

  • Small bug fixes

[6.0.13] - 2017-10-25

Added

  • Option to remove a background image on every frame-acquisition operation
  • Metadata is now displayed on the experiment info tab
  • External files to load patch clamp data
  • External files to correctly read xml for future graphpad output

Fixes

  • Some bug fixes on the plot statistics options

[6.0.12] - 2017-10-24

Added

  • Treatment statistics for bursts

[6.0.11] - 2017-10-24

Added

  • Treatment statistics now fully working for both population and spike statistics

[6.0.10] - 2017-10-24

Added

  • Complete treatment statistics class. Implemented population statistics as first test

Bugs

  • Currenlty the set of labels inside the projectPipleine are not saved when moving through the options

[6.0.9] - 2017-10-24

Added

  • Many pipeline statistics plots merged and integrated into a cohesive structure. Currently working: populations statistics, fluorescence bursts, spike statistics, permutation entropy/complexity
  • Detailed warning incase the pipeline cannot be saved
  • optionsWindow substructures working much better

Modified

  • boxPlot to accept multiple colors

[6.0.8] - 2017-10-23

Added

  • DEBUG tag for pipeline functions. These functions won't be uplodaded to the production version but will appear on the pipeline
  • Unified grid-like ROI addition. With option to reset or append new GRIDs

Modified

  • Pipeline functions now are sorted by name and children.
  • baseOptions class now accepts structures
  • optionsWindow help class generation accepts structures

Fixed

  • camControl new experiments were not being updated on the projectTree
  • producedFields was missing on spikeDetectConflicts

[6.0.7] - 2017-10-20

Fixed

  • Bug when the ROI screen could not be opened

[6.0.6] - 2017-10-19

Added

  • Tononi complexity measure

[6.0.5] - 2017-10-19

Added

  • Drag and drop a project onto the experiment list to load it
  • Option to append a ROI file to a preexisting ROI list on the viewROI menu

Fixed

  • Issues with acute protocols and PCA analysis

[6.0.4] - 2017-10-18

Added

  • Full rework on how to plot 1D statistics using a new class

Modified

  • viewRecording and viewROI menus now have a minimum width and height to deal with very one-dimensional recordings
  • Redefined several observables for the acute protocols
  • Number of (total/selected) ROIs now appear in the viewROI and viewTraces window

Fixed

  • Experiment info window was not always being updated after changes
  • Sometimes new movies could not be generated from the viewRecording menu

[6.0.3] - 2017-10-17

Added

  • Spike statistics for inter-experiment treatments (icomplete)
  • Spike statistics now allows grouping by any kind of labels
  • complexity-entropy curves with global spike trains
  • Dissimilarity and complexity measures on the spike featurse (trivial implementation, not really useful as of now)

[6.0.2] - 2017-10-16

Added

  • Several features to the acute stimulation protocols
  • PCA Analysis with features from stimulation protocols

[6.0.1] - 2017-10-16

Fixed

  • Some .avi files were not correctly being displayed on the viewRecording window

[6.0.0] - 2017-10-15

Added

  • Entropy, ISI fano factor and ISI coefficient of variation as new spike features
  • Analysis and statistics for acute stimulation protocols related to fluorescence transients (KCl for now)
  • New experiment list tree (now with drag and drop functionality)
  • MLspike now has options
  • Experiments can have multiple (comma separated) labels. Also option to modify or add labels on the experiment list
  • Options menu to change default/global options on a project
  • Current pipeline functions can be copied by pressing control while dragging the function

Modified

  • Experiment and project pipelines fused into one
  • Changelog only displayed on succesful updates in a new window
  • Trees should have a consistent look now
  • Project menu is now called File
  • Switching between experiment mode and pipeline is now much faster

Removed

  • xlwrite support - it was a pain and was buggy for large exports. Use CSV instead

Fixed

  • Bug when moving functions/experiments on very large trees
  • Lots of small fixes

TODO

  • Graphad export support
  • Complexity measures

[5.3.14] - 2017-10-10

Fixed

  • Removed debug lines on plotSpikeFeatures

[5.3.13] - 2017-10-10

Added

  • traceFixer now also works on smooth traces, new correction method works much better on single traces.
  • Procedures for the analysis of acute stimulation protocols

Fixed

[5.3.11] - 2017-10-03

Fixed

  • Lots of small bugs
  • traceFixer should also work with smoothed traces now

[5.3.10] - 2017-09-29

Fixed

  • Another issue when loading BTF files

[5.3.9] - 2017-09-29

Fixed

  • Updated OASIS to the latest remote commit. New models available

[5.3.8] - 2017-09-28

Fixed

  • Issue when opening the stream on BTF files

[5.3.7] - 2017-09-28

Added

  • Support for BTF files

[5.3.6] - 2017-09-28

Added

  • Manual option for the new trace fixer
  • Trace fixer options are now also stored

[5.3.5] - 2017-09-26

Added

  • OASIS integration
  • pipeline: plotPopulationStatistics
  • Lots of undocumented changes (sorry!)

[5.3.2] - 2017-08-16

Added

  • New option to remove conflictive spike (those that pattern matching detected as something else)
  • Valid patterns are now stored in a separate file to speed-up loading times

[5.3.1] - 2017-07-12

Fixed

  • New try/catch mechanism for log messages

[5.3.0] - 2017-07-09

Added

  • Pipelines: Run & Check buttons below the pipelines current function list
  • Pipelines: Right click on any function in the available functions list to display its help
  • Pipelines: project info is now also displayed on the pipeline modes
  • Plot spike statistics function on the pipeline
  • Added new options to the pattern count classification

Fixed

  • Small bug fixes

[5.2.1] - 2017-07-05

Added

  • Relative threshold for foopsi spike infernece (works much better)
  • Option to delete all patterns before a new import
  • New options class for raster plots

Fixed

  • Lots of small bug fixes

[5.2.0] - 2017-07-04

Added

  • Pipeline functions now support any number of parents and nested parents. Use colons to separate nested groups in the file header
  • Pipeline functions for pattern-based group classification
  • Pipeline functions for HCG detection
  • Automatic detection and correction of corrupted HIS files
  • Several new options to plot and export qCEC curves

Modified

  • Reestructured pipeline functions

[5.0.4] - 2017-06-27

Added

  • Pipeline functions for burst detection
  • Pipeline functions to load external pattern file
  • View traces: when simultaneously viewing movie and traces, ROIs can be sorted by distance from a given point (by right clicking)
  • camControl: same roi sorting functionality as in view traces
  • camControl: better webcam support
  • Font sizes can be changed from the main preferences menu (experimental)

Modified

  • Completely redesigned burst analysis menu to fully implement pattern-based burst detection

Fixed

  • Several bug fixes

[5.0.3] - 2017-06-21

Fixed

  • Several bugs on the view traces menu due to the new fast loading of the traces

[5.0.2] - 2017-06-20

Added

  • Youtube channel! Subscribe to stay up to date https://www.youtube.com/channel/UCQ8j9oytnMe34Ros_xV4x-w
  • View traces: now when creating the HCG, two new groups will appear (one excluding the largest HCG and another excluding all HCG members)
  • Improved burst statistics export
  • Improved traces export

Fixed

  • Many small bug fixes

[5.0.0] - 2017-06-19

Added

  • Denoiser to clean and generate new recordings
  • Denoised movies are compatible with most primary functions, i.e., roi selection, trace extraction, smoothing...
  • Speedup most functions by only loading the required traces and big fields at any given time
  • Data cursors can now be enabled on many windows
  • Percentile-based preprocessing
  • viewTraces: option to sort ROIs by distance from pointer when visualizing movie and traces simultaneously

Modified

  • New smoothing option (v2), simplified and more accurate (in theory)

Fixed

  • Serval bug fixes

[4.1.6] - 2017-06-13

Added

  • Compatibility for RIKEN VDAQ files
  • Updater now skips user modified files that contain % MODIFIED in the header

[4.1.2] - 2017-06-08

Added

  • View traces: ROI index now appears on the view positions menu
  • qCEC: Option to show aggregated results by label

Fixed

  • Small bug fixes

[4.1.0] - 2017-06-07

Added

  • Trace/event/manual training: You can select multiple training elements by pressing shift
  • View Traces: You can move through the traces both with the arrowkeys and WASD. You can also move through training groups by pressing the appropiate number key
  • View Traces: You should be able to move through the traces with the mousewheel

Fixed

  • Several bug fixes

[4.0.10] - 2017-06-07

Added

  • Patterns: Impot/export feature
  • Highly correlated groups: automatic search of optimal threshold

Fixed

  • Several bug fixes

[4.0.9] - 2017-06-07

Fixed

  • Bug when saving the times after cuting the traces
  • Added option to rebase time

[4.0.8] - 2017-06-07

Added

  • Completed q-CEC pipeline functions. Added option to work on the raw traces instead

Fixed

  • More bug fixes

[4.0.7] - 2017-06-06

Fixed

  • Weird bug on burstAnalysis

[4.0.6] - 2017-06-06

Fixed

  • Error on PCA k-means

[4.0.5] - 2017-06-05

Added

  • Automatic event classification
  • q-complexity-entropy measure and sorting option
  • Added pattern-based burst detection

[4.0.4] - 2017-06-04

Added

  • Option to color the PCA results by experiment, label or cluster index
  • Added subset option to export spikes
  • Added option to plot raster in the pipeline
  • Speedup of experiment saves

Fixed

  • loadExperiment with old quick_dev formats
  • Loading experiment where the traces file could not be located anymore
  • Several bugs with the new progressbar

[4.0.3] - 2017-06-03

Fixed

  • Several bugs with the new progressbar

[4.0.2] - 2017-06-01

Added

  • New robust smooth traces option

[4.0.0] - 2017-05-28

Added

  • Completely redesigned progressbar, now it doesn't get stuck anymore while performing disk writes. There still might be compatibility issues with the old one. Hence the change in version major.
  • Completely redesigned event-based trace classification - almost production-ready
  • New default 'ask' option for updates
  • Started integration of mlspike
  • Black colormap

Modified

  • Considerable speedup on experiment saves - now traces and big folders are only saved if they are modified

Fixed

  • Lots of small bug fixes

[3.3.14] - 2017-05-10

Added

  • camControl .bin files are fully supported

Fixed

  • Improved trace export feature

[3.3.13] - 2017-05-09

Added

  • New button to load ROI for compatibility issues

[3.3.12] - 2017-05-09

Fixed

  • Reverted the use of isstring due to compatibility uses with prior matlab versions

[3.3.11] - 2017-05-08

Added

  • Experiments are now backed up after every save and one hour apart, so previous versions can be recovered
  • Full export of burst statistics populations

Fixed

  • camControl now can handle importing all previous ROI files
  • Issue with the trace smoothing where the spline could overshoot at the end of the recordings

Removed

  • Removing xls support on several export optionsk, since csv works much better and can directly be imported into excel

[3.3.10] - 2017-05-08

Added

  • Export spikes pipeline

Fixed

  • Issue where the pipeline was being incorrectly saved (or not saved at all)
  • Improved pbar reliability
  • Improved trace loader

[3.3.9] - 2017-05-04

Added

  • Pipeline option to export burst features

[3.3.8] - 2017-05-03

Added

  • Zoom level is now preserved when browsing through traces
  • Added alpha-channel slider when viewing the positions of the current traces
  • Dual monitor setups are better supported when it comes to window positioning
  • Option to clear the current log
  • Option to import experiment from the workspace

Fixed

  • Several camControl issues when loading and saving ROIs

[3.3.7] - 2017-05-01

  • Missing

[3.3.6] - 2017-04-24

Added

  • Pipeline option to export fluroescence traces features

Fixed

  • Small bugs on camControl

[3.3.5] - 2017-04-24

Added

  • Plugin to import experiment from workspace

[3.3.4] - 2017-04-24

Fixed

  • small bugs on camControl

[3.3.3] - 2017-04-24

Fixed

  • small bugs on camControl

[3.3.2] - 2017-04-21

Added

  • Java-based multithreading for file writing

Fixed

  • Comptability issues with new newline function
  • Spurious java warnings

[3.3.1] - 2017-04-21

Added

  • Started the detailed documentation for every function
  • macvideo support on camControl

Fixed

  • Old glia analysis now conforms to the new call system

[3.3.0] - 2017-04-19

Added

  • Options to deal with incomplete .HIS files
  • Full integration of new generation camControl files
  • Option to add and edit information in the experiments (metadata)
  • viewTraces now conserves zoom while changing modes
  • new automatic ROI detection mode (combines the previous two)
  • Ability to generate .bin files with a raid-like structure
  • Several new pipeline functions
  • camControl now supports any winvideo-based camera
  • Direct option to integrate experiments within MATLAB workspace

Fixed

  • Several bugs with json files in windows systems
  • Disabled zero-padding on fft smoothing
  • Lots of small bug fixes
  • camControl is now a lot more robust

[3.2.12] - 2017-04-10

Added

  • Option to resize all ROI
  • Full integration of camControl within netCal. Now recorded videos will directly appear onto the current project

Modified

  • Moved several buttons from viewROI to the menubar

Fixed

  • Several errors when trying to load incomplete experiment files

[3.2.11] - 2017-04-05

Added

  • camControl can now record experiments movies and traces simultaneouslly. Almost ready for production

[3.2.10] - 2017-04-03

Added

  • Several functions to camControl

Fixed

  • New issue when loading old exported ROI files

[3.2.9] - 2017-03-30

Fixed

  • Issue with overlapping paths due to oasis dependencies

[3.2.8] - 2017-03-30

Added

  • The viewRecording plugin now remembers the last used folder
  • Oasis spike inference (only in training for now)
  • Barebones cam control (camControlRedux)

Fixed

  • Bug with some HIS files where the last frames would appear out of place

[3.2.7] - 2017-03-17

Added

  • Option to reset ROI IDs
  • Ability to compare experiments with different number of ROIs (will only compare equal IDs)

Fixed

  • Bug when exporting ROI lists that were moved around

[3.2.6] - 2017-03-16

Added

  • Pipeline modes for plotting and exporting spectrograms
  • Ability to preload experiment options in the pipeline functions

[3.2.5] - 2017-03-15

Added

  • Spectrogram to the viewTraces menu
  • Analysis of avalanches exponents
  • Automatic ROI deletion when moving all ROIs simultaneously

Fixed

  • Removed hardcoded robuboost trainer when only 2 populations existed
  • Changed from pcolor to imagesc on fluorescence rasters for 1:1 representation

[3.2.4] - 2017-03-09

Added

  • Several avalanche analysis functions

Fixed

  • Drift of spike times when the frame rate was fractional
  • Baseline in oopsi

[3.2.3] - 2017-02-28

Fixed

  • Several fixes to the new pbar structure

[3.2.3] - 2017-02-22

Added

  • New options on experiment comparison

[3.2.2] - 2017-02-22

Added

  • New option for batch experiment comparison

Fixed

  • Several bugs fixes

[3.2.1] - 2017-02-21

Fixed

  • Several bugs with the new pbar

[3.2.0] - 2017-02-16

Added

  • Redesigned progressbar and its calls standarizing implementation
  • Several new pipeline functions
  • Parallel (asynchronous) running of the pipeline (1 experiment per thread)
  • Experiment-specific validation of function options initial values
  • Transition plots now have trasnparency and count type options
  • Transition plots now have a minimum bar size to avoid issues with nearly empty populations

Fixed

  • Several bugfixes

[3.1.7] - 2017-02-13

Added

  • More options for automatic import of multiple experiments
  • Option to directly import CRCNS datastes (MEA)
  • More pipeline functions

Modified

  • Faster load of multiple experiments

Fixed

  • Memory leak on spike feature extraction for very large spike trains
  • Bug when displaying spikes form non-fluorescence experiments

[3.1.6] - 2017-02-13

Added

  • Much better handling of the options window in pipeline mode

[3.1.5] - 2017-02-12

Added

  • Second pipeline mode for directly managing projects.
  • Experiment pipeline is for functions that run on experiments individually.
  • Project pipeline is for functions that run on all the checked experiments at once.

[3.1.4] - 2017-02-12

Added

  • Several functions to the pipeline

[3.1.3] - 2017-02-12

Added

  • Automatic sorting of the function list based on their dependencies

[3.1.2] - 2017-02-11

Fixed

  • Bug with the update preventing creation of new folders

[3.1.1] - 2017-02-11

Added

  • Color coding for progress in pipeline mode

Added

[3.1.0] - 2017-02-11

Added

  • Pipeline mode fully working. But most functions still need to be passed to the new format
  • Several standalone functions for the new pipeline mode

Fixed

  • Typo on refineROI mode

[3.0.31] - 2017-02-08

Added

  • Option on PCA analysis to import an old PCA basis

[3.0.30] - 2017-02-07

Added

  • Option on PCA analysis to import an old PCA file

[3.0.29] - 2017-02-07

Fixed

  • ROI with wrong colors on the ppt reports
  • Improved the speed of grid-like ROI detection
  • Added warnings on spike feature extraction

[3.0.29] - 2017-02-07

Fixed

  • Several trace features were not working as intended

[3.0.28] - 2017-02-07

Added

  • Unsupervised trace classifier based on fuzzy clustering
  • Several new features for trace classification
  • More detailed error messages

Fixed

  • Error when a population was not defined in the aggregated statistics

[3.0.27] - 2017-02-06

Added

  • SaraReport now allows statistics on glia events
  • Much more detailed error repot messages

Fixed

  • Very specific bugs on spike selection

[3.0.26] - 2017-02-06

Added

  • Spike/event features based on schmitt trigger inference
  • Export options for both spikes and spikea features in the view spikes menu
  • Option to remove the average (or percentile) trace from the recording

Fixed

  • Bugs on the ppt report
  • Bug on trace classifier when using other experiments
  • Bug when importing multiple experiments with wrong extension capitalization

[3.0.25] - 2017-02-05

Fixed

  • Bugs on the trace selection in the spikes window

[3.0.24] - 2017-02-05

Fixed

  • Bugs on the new options window
  • Bugs on the trace selection

[3.0.23] - 2017-02-05

Added

  • Enabled pipeline mode. Menus and function selection working. Still a lot to go.

Fixed

  • Several bug fixes in trace and group selection
  • Several bug fixed in ppt report

[3.0.22] - 2017-02-04

Fixed

  • PPT report should be working again

[3.0.21] - 2017-02-01

Added

  • Automatic fluorescence processing now works for both single and batch experiment modes
  • Basis for the new pipeline mode

Fixed

  • Bug when loading smoothed traces that were already in numeric mode
  • Several bugs on the trace selection and ordering process. Simplified the functions

[3.0.20] - 2017-01-27

Added

  • Real time spike detection on camControl (via foopsi)
  • Standalone version of viewRecording can be called via the plugins menu

Modified

  • Improvements on camControl

[3.0.18] - 2017-01-26

Modified

  • Improvements on camControl

[3.0.16] - 2017-01-25

Modified

  • Improvements on camControl

[3.0.15] - 2017-01-25

Modified

  • auto levels now works much better. It is iterative and persistent

Fixed

  • Several bugs on view traces menu for subpopulations
  • Spike features menu was not working
  • Consistency check on windows systems was not working properly

[3.0.14] - 2017-01-25

Added

  • camControl plugin to control Hamamatsu cameras

[3.0.13] - 2017-01-24

Added

  • viewRecording as a standalone function

[3.0.12] - 2017-01-24

Fixed

  • Issue with the udpater in windows

[3.0.11] - 2017-01-24

Added

  • Foopsi model for spike inference fully working
  • Automatic ROI detection as a new analysis menu (working towards pipeline model)

Modified

  • Swapped around the way the options for spike inference training work

[3.0.10] - 2017-01-20

Fixed

  • Bug with the output of spike inference training
  • Burst detection was not working with ill-defined groups
  • The recording image was not displaying correctly after changing the file handle path

[3.0.9] - 2017-01-19

Fixed

  • Bug when the update required changes in the progressbar

[3.0.8] - 2017-01-19

Added

  • Menu to check consistency of the files and to force updates

[3.0.7] - 2017-01-18

Fixed

  • Issues with the file by file updater

[3.0.5] - 2017-01-17

Added

  • Completed view groups options by adding the group list on the left.
  • Ability to delete, rename and sort groups from the view groups menu.

[3.0.4] - 2017-01-17

Fixed

  • Bug when loading ROI

[3.0.3] - 2017-01-17

Fixed

  • Bug when the Tree structure was not being loaded correctly from uiExtras package
  • Bug when the updater was not creating the appropiate directories

[3.0.2] - 2017-01-16

Fixed

  • Bug when the ROI list was an empty cell
  • Bug when trying to execute PCA analysis with old groups in the experiments

[3.0.1] - 2017-01-15

Added

  • Complete redesign of the way experiments are managed. Now there are two main working modes. Single experiment or batch mode. On single experiment you can proceed as usual, view and analyzing stuff one by one. On batch mode you just check the list of experiments that you want to analyze and each function will be performed on the checked list. Also the averaged statistics will only appear on the batch mode and apply to the checked experiments in the current order. The experiment order and labels can now be changed by right clicking on the experiment list.
  • Complete redesign of the update function, now it updates file by file instead of downloading a single big zip every time.
  • There is no concept of active experiment anymore. Experiments are loaded and saved on demand. Now if you have more than one view window open at any given time, experiments will not be saved on exit unless forced. Now there is an option to force save on each of the viewing windows.
  • New view groups window to simply view the defined groups (populations) and do some statistics on them.
  • Ability to export the groups generated by PCA and k-means analysis back to the original experiments.
  • List of analysis, viewing and statistics functions are now created programatically with the loadModules() function, now it should be much faster to create new menus via plugins.
  • Added beeswarm-like option to view distributions
  • Several minor undocumented changes

Modified

  • Several old functions are now incomplete. Namely the automatic processing of multiple functions at the same time.
  • notBoxPlot now shows each point with a beeswarm-like structure

[2.4.2] - 2016-12-16

Added

  • Splash screen
  • Logo

Fixed

  • Bug on the progressbar for smoothing traces

[2.4.1] - 2016-12-14

Added

  • Option to select export file format on preprocessing
  • Option to export pca contributions
  • Early check for GUI Layout toolbox

[2.4.0] - 2016-12-13

Added

  • Improvmeents on glia analysis
  • New window for spike inference training
  • Option to display the spikes features distributions
  • Redesigned progressbar - iterative, sequential and circular
  • Nonmodal options window
  • Options window help automatically generated
  • Spikes are now visible on view recording and view glia windows

Modified

  • Better handling on the positioning of new figures and the first time they become visible
  • Rework on automatic processing

Fixed

  • PCA contributions were being incorrectly displayed
  • Missing java library declaration for xlsx exports

[2.3.4] - 2016-12-1

Added

  • Improvements on glia analysis
  • Option to compress (or not) export movies

Fixed

  • Bug when selecting populations for the peeling
  • Bug when resetting training traces
  • Bug with new preprocessing options

[2.3.3] - 2016-11-29

Added

  • Statistics and plots for the glia events

[2.3.2] - 2016-11-29

Added

  • Option to view the populations on the view recordings gui

[2.3.1] - 2016-11-28

Fixed

  • Update error if netcal.json was not present

[2.3.0] - 2016-11-27

Added

  • Log panel on all GUI windows
  • New projects are also added to the recent projects list
  • Preparing menus for spike inference
  • Option to train populations with learning traces from other experiments

Modified

  • Complete rework on the log messaging system
  • Complete rework on how the gui handles are passed through windows
  • Removed the tabbed structure from the main window, since I haven't found any use for it since the beginning.
  • Name of main windows - for better understanding
  • Positioning of new figures, so there is less overlap
  • Recent projects menu now display as multiple lines if the path is too large

Fixed

  • Aggregated PCA windows
  • Possible infinite loop when updating menus
  • Recent project order is updated so the latest load always become the last one in the list
  • Recent project list is read backwards, so the last one is the top one on the list

[2.2.7] - 2016-11-26

Added

  • Option for loading recent experiments
  • Option for batch burst analysis
  • Option to plot tangent transitions in the experiment comparisons plots

Modified

  • Completed burst viewing on view recording

Fixed

  • Several

[2.2.6] - 2016-11-25

Added

  • Several new avg trace options in the preprocess menu

Modified

  • Complete rework on the import/export groups menu - now based on trees

[2.2.5] - 2016-11-24

Added

  • Major work on glia analysis
  • Key bindings for view recording

[2.2.4] - 2016-11-24

Fixed

  • Bug when plotting experiment comparisons

[2.2.3] - 2016-11-24

Fixed

  • Bug when comparing experiments

[2.2.2] - 2016-11-23

Fixed

  • Bug when preprocessing new experiment

[2.2.1] - 2016-11-23

Modified

  • Fixed group imports and exports

[2.2.0] - 2016-11-23

Added

  • Check for invalid zip files
  • Additional external functions
  • Added plots to compare population flows between experiments
  • Option to extract traces with a median filter
  • Added fft trace baseline correction
  • Options for real size and image reset on viewROI menu
  • Added help menu on the options window

Modified

  • Complete rework on all GUIs to allow arbitrary groups.
  • Complete rework on the experiment comparison
  • Complete rework on the multi-experiment statistics
  • Complete rework on the experiment and populations selection procedures

Fixed

  • Lots

[2.1.9] - 2016-11-17

Modified

  • Merged ROI preferences options into a class
  • Merged automatic ROI procedures into one

[2.1.8] - 2016-11-16

Added

  • New popup window for experiment selection when there are too many experiments (>25)
  • Options class for peeling
  • Batch peeling procedure

Modified

  • Redesigned the experiment lists menus
  • Redesigned the peeling functions
  • Option to show spikes and burst length in view traces menu, now each burst in its own color
  • Several spike features

Fixed

  • Burst length based on fluorescence analysis now is a lot more accurate
  • New spike features were not being saved properly

[2.1.7] - 2016-11-16

  • Skipped

[2.1.6] - 2016-11-15

Added

  • FCA menu
  • View traces: menu to show the baseline (if saved)
  • Option to sort traces by FCA order

Modified

  • View traces: for the smooth traces, the dashed line now shows where the 0 fluorescence level should be
  • View traces: redesigned the alignTraces option
  • Added several new options for trace smoothing

[2.1.5] - 2016-11-14

Added

  • Option to see the new fluorescence-based spike burst size on the traces menu

Modified

  • The spike features are now obtained from the spike inference menu (not inside view spikes)

[2.1.4] - 2016-11-11

Fixed

  • Automatic updater was not working

[2.1.3] - 2016-11-11

Fixed

  • Bug while importing quick_dev mat files from dcimg recordings
  • Gui display on glia functions

[2.1.2] - 2016-11-9

Added

  • Button in the options window to revert any changes to the default values

[2.1.1] - 2016-11-9

Fixed

  • Several bugs with handling the new options classes
  • Bugs in the preprocessing window

Modified

  • Completeley redesigned the smoothing menu

[2.1.0] - 2016-11-7

Added

  • Compliance with semantic versioning - had to update to directly to 2.1.0 for compatibility issues

Fixed

  • Bug when importing HIS files with unstandard datatypes
  • Bug when comparing experiments

[2.0] - 2016-11-7

Added

  • Help section, including acknowledgments and the changelog.
  • Started the coding guidelines (see GUIIDELINES.md)
  • Enabled the use of Markdown. This should speed up creating help sections and posterior documentation
  • Several undocumented changes (check commits)

Modified

  • Completey redesigned the options class and the optionsWindow menu. Not it has a lot more functionality
  • Reestructured several menus
  • Base netcal options are stored in an external json file, not a matlab object

Fixed

  • Progressbar can safely be closed (even if was already closed)

Deleted

  • Bunch of unused external dependencies

[1.109] - 2016-11-3

Fixed

  • Bug selecting points in the PCA plot.

Modified

  • Work around to export features on the PCA analysis as separate bugs. There is a memory bug when creating too large xls files in there

[1.108] - 2016-11-3

Fixed

  • Bug when exporting aggreted experiments from the PCA analysis - due to the new trace structure

[1.107] - 2016-11-2

Added

  • Traces of individual cells can be selected on the View Recording menu by right clicking on top of the cell
  • Spikes and bursts from the HCG can be seen on the View Recording menu from its menu
  • Option to export a movie (and figure) with the current View Recording options

Modified

  • Export option on the glia menu to match those on the view recording

Fixed

  • Bugs on some progress bars when the number of total iterations was below 100

[1.106] - 2016-11-2

Added

  • Option to do K-Means analysis of spike data with NaN values

Fixed

  • The znorm option in K-Means was not really doing a z-norm (only rescaling)

[1.105] - 2016-11-2

Added

  • New options to select specific features from the spikes
  • New feature using the fluorescence trace to define burst length

Modified

  • Generalized the feature list on several plots

Fixed

  • Current experiment was not being saved before doing batch PCA analysis

[1.104] - 2016-11-2

Added

  • Option to reset all training on the view traces menu

Fixed

  • Bug when selecting traces to train (caused by the new colormap)s

[1.103] - 2016-10-31

Added

  • Colormap selection on all menus now also show the colorbar

Changed

  • Program now shows release notes of the latest 3 versions

[1.102] - 2016-10-31

Added

  • Spike features options are now passed like any other options
  • Added temporal range to the spike features extraction

[1.101] - 2016-10-31

Changed

  • Current experiment is no longer stored inside the current project
  • Consistency check on finish ROI selection to delete old traces
  • Cleanup of project files

Fixed

  • Fixed a bug when cloning current experiment
  • Fixed a bug in the aggregated density menu

[1.100] - 2016-10-31

Added

  • Options are now saved both inside the experiment and the project files (not only for the project)
  • Created base class for options windows
  • Batch smoothing options
  • Added K-means options on view PCA
  • Added PCA export by features

Changed

  • Progressbar support for multiple bars and color changes with completion, not randomly
  • Changed all options classes to adhere to the new base class
  • Merged analysis menus together
  • Redesigned the batch process system

Removed

  • Classifier class is no longer stored in the experiment

Fixed

  • Bug when cancelling export to xls
  • No need to Add Gui handles when loading options classes

[1.99] - 2016-10-29

Undocumented. Check commits

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