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microscope-prototype's Introduction

Microscope-Prototype

Prototype Tests for Extraction of trajectories and calculation of avg. speed histograms: here.

Introduction

This repository contains instructions and basic prototype scripts for controlling our in-house low cost microscope, and the analysis of data acquired from it.

Creating Trajectories

flowchart TD
	CC("Create & Init Camera 📷") --> CV(Capture Video)
	CV --> EX("Extract Frames <br> to Array")
	EX --> Frames[("Frames (list of RGB arrays)")]
	Frames --For-each--> LF(Locate-Features)
	LF --> LST[(List of Features per frame)]
	LST --"<b>Link Features</b>"--> TRJ[(Trajectories)]

From Trajectories to Statistics

Average Speed Histogram

flowchart TD
	T(Time Estimate) --frame-rate--> V
	TRJ[(Trajectories)] --distance-travelled--> V(Average Speed in x & y)
	
	V --classify--> Hist[[2D-Histogram]]

Mean Squared Displacement (MSD)

Mean Squared Displacement for an ensamble of $N$ particles (swimmers):

$$ MSD(t) = \frac {1}{N} \sum_{i=1}^{N} | x_i(t) - x_i(0) |^2 $$

For n-dimesnions, we have:

$$ MSD = 2nDt $$

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