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Unbalanced Clustering In Spike Sorting

Vision (Small Project)

Authors: Alexander.STANCIU(alexander.stanciu96@gmail.com)
Richard.ARDELEAN(ardeleaneugenrichard@gmail.com)

Document Number: <reference #>


Version: 0.1

Publish Date: 2019-04-11


<Project Name> Version: <1.0>
Vision (Small Project) Date: <yyyy-mm-dd>
<document identifier>

Record of Processing
No. Version Date Status Who Description
1 21.03.2019 In progress? OP Document first draft

Record of Approval
No. Version Date Who Description

1 … …

Recipients of Document
No. Version Date of Distribution Recipients
1 …

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Table of Contents
1. Introduction 4
1.1 References 4

2. Positioning 4
2.1 Problem Statement 4
2.2 Product Position Statement 4

3. Stakeholder and User Descriptions 5


3.1 Stakeholder Summary 5
3.2 User Summary 5
3.3 User Environment 6
3.3.1 Users 6
3.3.2 Time limits 6
3.3.3 Infrastructure 6
3.4 Summary of Key Stakeholder or User Needs 6
3.5 Alternatives and Competition 6

4. Product Overview 6
4.1 Product Perspective 6
4.2 Assumptions and Dependencies 6

5. Product Features 7
5.1 FEAT 01: Cluster spikes to correctly identify neurons 7
5.2 FEAT 02: Spikes are sorted in reasonable amount of time 7
5.3 FEAT 03: Visualize the results 7

6. Other Product Requirements 7


6.1 Performance and accuracy 7
6.2 Open 7
6.3 User interface 7

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Vision (Small Project)


1. Introduction
The purpose of this document is to collect, analyze, and define high-level needs and features of
the Spike Sorter. It focuses on the capabilities needed by the stakeholders and the target users,
and why these needs exist. The details of how the Spike Sorter fulfills these needs are detailed in
the use-case and supplementary specifications.

1.1 References
This document references:
 Requirements Glossary
 Use Case Model

2. Positioning
2.1 Problem Statement
Because of the fact that it is very hard to put electrodes directly into the neuron, we have to put it
between them and this makes it difficult to distinguish between which spikes correspond to which
neurons.
The problem of Spikes not being assigned to neurons
affects Neuroscience researchers
the impact of which is Difficulty in finding out what each neuron does
a successful solution would Advancements in finding out how the brain functions
be
Finding a way to cluster unbalanced data in other fields
as well

2.2 Product Position Statement


The project intends to find an efficient way to cluster unbalanced data.
Researches are encountering difficulties in finding out which spike corresponds to which neuron
in a reasonable amount of time

For Neuroscience institutes


Who Needs to figure out the activity of each individual neuron in
a region of the brain
The Undersampling Spike is an algorithm used for spike sorting
Sorter
That undersamples the data and clusters the result in relevant
clusters
Unlike Other clustering algorithms
Our product Will identify overlapping clusters and clusters of small
density

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3. Stakeholder and User Descriptions


3.1 Stakeholder Summary

Name Description Responsibilities


Raul MURESAN President of the board of Project initiator and coordinator.
directors at the
Monitors the project progress and guides
Transylvanian Institute of
the development path
Neuroscience Cluj-Napoca
(Romania).
Students Computer Science student Ensures development of the project
at Technical University of
Cluj-Napoca
Project Associate Professor, Dr., Monitors the project progress
coordinator Eng. Computer Science
Department of the
Technical University of
Cluj-Napoca
Neuroscience Institutes that research Ensures that there will be a market
institutes how the brain works demand for the product’s features

3.2 User Summary


Name Description Responsibilities Stakeholder

Researcher User who wants Input the dataset of spikes Neuroscience Institutes
to sort spikes to
find the neurons
they belong to
Alexander Computer Ensures development of the Students
STANCIU Science student project
at Technical
University of
Cluj-Napoca
Richard Computer Ensures development of the Students
ARDELEA Science student project
N at Technical
University of
Cluj-Napoca
Mihaela Associate Monitors the project progress Project coordinator
DINSOREA Professor, Dr.,
NU Eng. Computer
Science
Department of
the Technical
University of
Cluj-Napoca

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Camelia Associate Monitors the project progress Project coordinator


LEMNARU Professor, Dr.,
Eng. Computer
Science
Department of
the Technical
University of
Cluj-Napoca
Rodica Associate Monitors the project progress Project coordinator
POTOLEA Professor, Dr.,
Eng. Computer
Science
Department of
the Technical
University of
Cluj-Napoca

3.3 User Environment

3.3.1 Users
The program will be operated by one person at a time.
3.3.2 Time limits
There is no predictable time limit, as the time depends on the size of the data.
3.3.3 Infrastructure
The product will run on any machine that is able to run python code.
3.4 Summary of Key Stakeholder or User Needs

Need Priority Concerns Current Solution Proposed Solutions


Cluster spikes to correctly 0 Researchers DECODE, Undersampling the
identify neurons HDBSCAN data so that the final
clusters have the same
density
Spikes are sorted in 1 Researchers DBSCAN, OPTICS, Use DBSCAN, which
reasonable amount of time DECODE, works fast on data
HDBSCAN, etc. meeting its
prerequisites, after
undersampling, which
will also have the
required execution
time
Visualize the results 0 Researchers DBSCAN, Python plot
DECODE,
HDBSCAN, etc.

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3.5 Alternatives and Competition


Competition is represented by all existing clustering algorithms.

4. Product Overview
The program should provide a fast sorting of the spikes in relevant clusters.

4.1 Product Perspective


Currently the program is self-contained, but could be part of a larger product in the future as the
neuroscience field evolves.

4.2 Assumptions and Dependencies


The spikes in the data set are correctly detected and the relevant features are condensed in at
most 3 dimensions.
Python 3.6.0 or later is installed.

5. Product Features
5.1 FEAT 01: Cluster spikes to correctly identify neurons
The product shall cluster the dataset in such a way that an expert human would agree on the
clustering.
5.2 FEAT 02: Spikes are sorted in reasonable amount of time
The maximum time complexity of the algorithm should be O(n*log(n)).
5.3 FEAT 03: Visualize the results
The application should show the resulting clusters in a way that makes it easy to distinguish
them.

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6. Other Product Requirements


6.1 Performance and accuracy
Will be measured using F1 score on generated labeled datasets
6.2 Open
The product should have the ability to be integrated in other projects.
6.3 User interface
The program should have an easy to understand user interface which requires no training to use.

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