Added p103a

LICENSE

@@ -1,39 +1,39 @@
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+Creative Commons CC0 1.0 Universal
+CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+Statement of Purpose
+
+The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work").
+
+Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. These owners may contribute to the Commons to promote the ideal of a free culture and the further production of creative, cultural and scientific works, or to gain reputation or greater distribution for their Work in part through the use and efforts of others.
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+For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights.
+
+1. Copyright and Related Rights. A Work made available under CC0 may be protected by copyright and related or neighboring rights ("Copyright and Related Rights"). Copyright and Related Rights include, but are not limited to, the following:
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+i. the right to reproduce, adapt, distribute, perform, display, communicate, and translate a Work;
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+ii. moral rights retained by the original author(s) and/or performer(s);
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+iii. publicity and privacy rights pertaining to a person's image or likeness depicted in a Work;
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+iv. rights protecting against unfair competition in regards to a Work, subject to the limitations in paragraph 4(a), below;
+
+v. rights protecting the extraction, dissemination, use and reuse of data in a Work;
+
+vi. database rights (such as those arising under Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, and under any national implementation thereof, including any amended or successor version of such directive); and
+
+vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof.
+
+2. Waiver. To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
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+3. Public License Fallback. Should any part of the Waiver for any reason be judged legally invalid or ineffective under applicable law, then the Waiver shall be preserved to the maximum extent permitted taking into account Affirmer's express Statement of Purpose. In addition, to the extent the Waiver is so judged Affirmer hereby grants to each affected person a royalty-free, non transferable, non sublicensable, non exclusive, irrevocable and unconditional license to exercise Affirmer's Copyright and Related Rights in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "License"). The License shall be deemed effective as of the date CC0 was applied by Affirmer to the Work. Should any part of the License for any reason be judged legally invalid or ineffective under applicable law, such partial invalidity or ineffectiveness shall not invalidate the remainder of the License, and in such case Affirmer hereby affirms that he or she will not (i) exercise any of his or her remaining Copyright and Related Rights in the Work or (ii) assert any associated claims and causes of action with respect to the Work, in either case contrary to Affirmer's express Statement of Purpose.
+
+4. Limitations and Disclaimers.
+
+a. No trademark or patent rights held by Affirmer are waived, abandoned, surrendered, licensed or otherwise affected by this document.
+
+b. Affirmer offers the Work as-is and makes no representations or warranties of any kind concerning the Work, express, implied, statutory or otherwise, including without limitation warranties of title, merchantability, fitness for a particular purpose, non infringement, or the absence of latent or other defects, accuracy, or the present or absence of errors, whether or not discoverable, all to the greatest extent permissible under applicable law.
+
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+
+d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work.

README.md

@@ -1,3 +1,58 @@
-# minis-benchmarking-data
-
-Benchmarking study data for minis software. Repository contains intracellular membrane potential noise recordings in cortical pyramidal cells.
+# minis-benchmarking-data
+Intracellular noise recordings and simulations of miniature excitatory postsynaptic potentials in cortical pyramidal cells. The data in this repository was used to produce the [manuscript](insert the link here) of the [minis](insert the link here) software benchamarking study.
+
+## Repository content
+### recs
+```recs``` folder holds data for all individual recordings in separate folders. Folders are named according to recording IDs: ```p103a```, ```p106b```, ```p108a```, ```p108b```, ```p108c```, ```p120b```, ```p122a```, ```p124b```, ```p125a```, ```p127c```, ```p128c```, ```p129a```, ```p131a```, ```p131c```. Each recording ID folder has the following structure:
+|**Folder name**          |**Description**   |
+|-------------------------|------------------|
+|abf 	                    | *This folder contains Axon Binary Format files produced by simulating excitatory postsynaptic potentials (EPSPs) and superimposing them on top of the filtered and smoothed intracellular membrane potential noise recordings. These files are produced by ```minis``` software running in the ```Simulate``` mode. ```minis``` in turn calls ```simulateDetectEvaluate``` function which performs the simulation, runs the ```minis``` detection algorithm on the noise + simulated EPSP time series data, and evaluates detection performance using signal detection measures. There are 4 simulated files per each test condition as described in the manuscript. File name parts identifying different conditions are listed below the table.*|
+|abf_raw 	                | *This folder contains ABF files that correspond to files in ```abf`` folder prior to being smoothed. These files are used to detect simulated EPSPs by Clampfit. Smoothed recordings are not suitable for Clampfit detection.*|
+|csv_MiniAnalysis 	      | *This folder contains ```Mini Analysis``` simulated EPSP detection output tables saved in the CSV format. The CSV files correspond each ABF file in the ```abf``` folder.*|
+|csv_pClamp_raw 	        | *This folder contains Clampfit simulated EPSP detection output tables saved in the CSV format. The CSV files correspond each ABF file in the ```abf_raw``` folder.*|
+|mat_MiniAnalysis 	      | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` and ```csv_MiniAnalysis``` folders. ```Mini Analysis``` part of the manuscript Figures 4 and 6-8 are based on the data stored in this folder. The output is saved in the MAT format and contains variables that are explained below this table. The output files are produced by the ```evaluateMiniAnalysisPostprocessing``` function.*|
+|mat_MiniAnalysis_select  | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` and ```csv_MiniAnalysis``` folders. ```Mini Analysis``` part of the manuscript Figures 9-11 are based on the data stored in this folder.* |
+|mat_MiniAnalysis2	      | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` and ```csv_MiniAnalysis``` folders. ```Mini Analysis``` part of the manuscript Figures 12-15 are based on the data stored in this folder.*  |
+|mat_minis	              | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` folder. ```minis``` part of the manuscript Figures 4 and 6-8 are based on the data stored in this folder. The output is saved in the MAT format and contains variables that are explained below this table. The output files are produced either by ```simulateDetectEvaluate``` or by ```evaluateMinisPostprocessing``` functions.* |
+|mat_minis_select         | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` folder. ```minis``` part of the manuscript Figures 9-11 are based on the data stored in this folder.* |
+|mat_minis2 	            | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf``` folder. ```minis``` part of the manuscript Figures 12-15 are based on the data stored in this folder.* |
+|mat_pClamp_raw           | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf_raw``` and ```csv_pClamp_raw``` folders. ```Clampfit``` part of the manuscript Figures 4 and 6-8 are based on the data stored in this folder. The output is saved in the MAT format and contains variables that are explained below this table. The output files are produced by the ```evaluatepClampPostprocessing``` function.* |
+|mat_pClamp_raw_select    | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf_raw``` and ```csv_pClamp_raw``` folders. ```Clampfit``` part of the manuscript Figures 9-11 are based on the data stored in this folder.* |
+|mat_pClamp_raw2	        | *Simulated EPSP detection performance evaluation analysis output files corresponding to individual files in the ```abf_raw``` and ```csv_pClamp_raw``` folders. ```Clampfit``` part of the manuscript Figures 12-15 are based on the data stored in this folder.* |
+|```<filename>.abf```		  | *Recording of intracellular membrane potential noise stored in the ABF file.* |
+
+#### Test Condition File Naming
+Files stored in folders ```abf```, ```abf_raw```, ```csv_MiniAnalysis```, ```csv_pClamp_raw```, ```mat_MiniAnalysis```, ```mat_MiniAnalysis_select```, ```mat_MiniAnalysis2```, ```mat_minis```, ```mat_minis_select```, ```mat_minis2```, ```mat_pClamp_raw```, ```mat_pClamp_raw_select```, and ```mat_pClamp_raw2``` correspond to individual testing conditions when part of their name contain the following characters:
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor4p2```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 4.2.
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor2p6```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 2.6.
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor1p8```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 1.8.
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor1p4```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 1.4.
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor1p2```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 1.2.
+- ```amp0p3_sAmp0p05_n500_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 2.5 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n1000_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 5 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n2000_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 10 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n4000_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 20 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n8000_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 40 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n1600_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 80 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n3200_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 160 events/second with the noise scaling factor of.
+- ```amp0p3_sAmp0p05_n6400_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 320 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp0p05_n12800_<...>_noiseScaleFactor1```: 0.3 mV simulated EPSPs at 640 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp1e_09_n500_<...>_noiseScaleFactor1```: Varying amplitude simulated EPSPs at 13 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp1e_09_n625_<...>_noiseScaleFactor1``` or ```amp0p3_sAmp1e_09_n1250_<...>_noiseScaleFactor1```: Varying amplitude simulated EPSPs at 33 events/second with the noise scaling factor of 1.
+- ```amp0p3_sAmp1e_09_n1000_<...>_noiseScaleFactor1``` or ```amp0p3_sAmp1e_09_n2000_<...>_noiseScaleFactor1```: Varying amplitude simulated EPSPs at 53 events/second with the noise scaling factor of 1.
+
+#### Detection Performance Evaluation Analysis Output
+Detection performance evaluation analysis output is produced separately for each testing condition and is saved in Matlab data files (MAT format) containing the following variables:
+|**Variable name**  |**Description**   |
+|-------------------|------------------|
+|dPrime 	          | *d' sensitivity index for each simulation file.*|
+|FPR 	              | *False positive rate for each simulation file.*|
+|sensitivity 	      | *sensitivity (or true positive rate) for each simulation file.*|
+|specificity 	      | *specificity (or true negative rate) for each simulation file.*|
+|performance 	      | *performance indicators for each simulation file. There are 7 indicators (rows) with the same sampling rate as the original data (columns). Row 1: Simulated EPSP positions. Row 2: Positions of hits (where detected rather than simulated) and misses. Row 3: Positions of hits and false alarms. Row 4: Hit positions. Row 5: Missed event positions. Row 6: False alarm positions. Row 7: Positions of correctly rejected noise events.*|
+|falseI 	          | *Indices of noise events. Also could be reprhrased as sample points corresponding to the peaks of designated noise events.*|
+|falseT 	          | *Times of noise events (peaks of designated noise events).*|
+|filename 	        | *Noise recording file name.*|
+
+### temps
+Clampfit EPSP templates (Axon Text File format) used to detect simulated EPSPs and described in the benchamarking manuscript.

recs/p103a/abf/algorithm_performance_data__amp0p3_sAmp0p05_n1000_RT0p5_sRT2p8_rho0_thr0p1_noiseScaleFactor1_smoothWindow1p5__04_Jan_2021_18_48_00_0001.abf

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