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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content=
"width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>reveal.js</title>
<link rel="stylesheet" href="dist/reset.css">
<link rel="stylesheet" href="dist/reveal.css">
<link rel="stylesheet" href="dist/theme/custom.css" id="theme">
<!-- Theme used for syntax highlighted code -->
<link rel="stylesheet" href="plugin/highlight/monokai.css" id=
"highlight-theme">
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<p>Before you start:</p>
<ul>
<li>Allow <b>video autoplay</b> of the browser</li>
</ul>
</section>
<section data-background-video="assets/100_zebra.mp4"
data-background-video-loop="loop">
<img src="assets/su.png" width="25%" style=
"float: left; background: rgba(255,255,255,0.5)"><img src="assets/ljp.png"
width="25%" style=
"float: right; background: rgba(255,255,255,0.5)"><br>
<br>
<br>
<br>
<h2 style=
" color:black;-webkit-text-stroke:2px white;">
Assessing chemical preference of young
zebrafish</h2>
<h3 style=
"color:black;-webkit-text-stroke:2px white;">
Benjamin Gallois</h3>
</section>
<section data-background-video="assets/dataset.m4v"
data-background-video-loop="loop">
<h2 style=
"color:black;-webkit-text-stroke:2px white;">I.
FastTrack: a general purpose tracking
software</h2><br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</section>
<section>
<h3>Image-based tracking</h3>
<p>Locating objects over time from a video
recording.</p><video data-autoplay="true" loop=
"true" controls="true" class=
"r-stretch"><source src="assets/intro.webm" type=
"video/webm"></video>
</section>
<section>
<h3>Challenges</h3>
<ul>
<li>Object detection</li>
<li>Complex object interactions</li>
<li>Trade-off accuracy / specialization</li>
<li>Trade-off accuracy / speed</li>
</ul>
</section>
<section>
<h3>Tracking in the lab</h3>
<div style="width:45%; float:left">
<u>Simplifications:</u>
<ul>
<li>Controlled lighting</li>
<li>Uniform background</li>
<li>Good image quality</li>
<li>Often quasi 2D</li>
</ul>
</div>
<div style=" width:45%; float:right">
<u>Requirements:</u>
<ul>
<li>Low fault tolerance</li>
<li>Minimal human interventions</li>
<li>Versatile</li>
</ul>
</div>
</section>
<section>
<h3>Existing software</h3>
<div style="width:45%; float:left">
<h4><u>Properties-based</u></h4>
<p>Use dynamic properties to keep the
identities <span class="citation">(Rodriguez,
Alvaro, et al. 2018)</span></p>
<ul>
<li style="color:green">Fast</li>
<li style="color:red">Error
propagation</li>
</ul>
</div>
<div style="width:45%; float:right">
<h4><u>Individuals-based</u></h4>
<p>Extract a fingerprint for each individual
<span class="citation">(Romero-Ferrero,
Francisco, et al. 2019)</span></p>
<ul>
<li style="color:red">Computationally
intensive</li>
<li style="color:green">Close to perfect
accuracy</li>
</ul>
</div>
</section><!--<section>
<h3>What is missing?</h3>A software that is:
<ul>
<li>Fast and accurate</li>
<li>Reliable</li>
<li>Easy to install and to use</li>
<li>Flexible and adaptable to existing
workflow</li>
</ul>
</section>-->
<section>
<h3>
Two-Dimensional tracking Dataset</h3>
<ul style="font-size: smaller;">
<li>41 movies under CC BY-NC-SA 4.0
license</li>
<li>7 animal species (from cells to
mice)</li>
<li>Active particles</li>
<li>Microfluidic droplets</li>
<li>Macrocopic objects</li>
<li> <a href=
"http://chat.ljp.upmc.fr/datasets/TD2/">
http://chat.ljp.upmc.fr/datasets/TD2/</a>
</li>
</ul>
<video data-autoplay="true" loop=
"true" controls="true" class=
"r-stretch"><source src="assets/dataset.m4v" type=
"video/webm"></video>
</section>
<section>
<h3>FastTrack: a general tracking software</h3>
<ul>
<li>Fast and automatic tracking algorithm</li>
<li>Ergonomic correction tool</li>
</ul><img src="assets/readme.png" class=
"r-stretch">
</section>
<section>
<h3>Detection</h3><img src=
"assets/Figure_ellipse.svg" width="100%">
<video data-autoplay="true" loop="true" controls=
"true" class="r-stretch"><source src=
"assets/detection.mp4" type="video/mp4"></video>
</section>
<section data-transition="slide-in fade-out">
<h3>Matching</h3><img src="assets/matching_0.svg"
class="r-stretch">
<p>Keep the identity of the objects from one
image...</p>
</section>
<section data-transition="fade-in fade-out">
<h3>Matching</h3><img src="assets/matching_1.svg"
class="r-stretch">
<p>To the next.</p>
</section>
<section data-transition="fade-in fade-out">
<h3>Matching</h3><img src="assets/matching_2.svg"
class="r-stretch"> $$c_{11}=\frac{d_{11}}{s_d} +
\frac{a_{11}}{s_a}$$
</section>
<section data-transition="fade-in fade-out">
<h3>Matching</h3><img src="assets/matching_3.svg"
class="r-stretch"> $$c_{12}=\frac{d_{12}}{s_d} +
\frac{a_{12}}{s_a}$$
</section>
<section data-transition="fade-in fade-out">
<h3>Matching</h3><img src="assets/matching_4.svg"
class="r-stretch"> $$c_{13}=\frac{d_{13}}{s_d} +
\frac{a_{13}}{s_a}$$
</section>
<section data-transition="fade-in fade-out">
<h3>Matching</h3><img src="assets/matching_5.svg"
class="r-stretch"> $$C = \begin{bmatrix} c_{11} &
c_{12} & c_{13}\\ & & \\ & & \end{bmatrix}$$
</section>
<section>
<h3>Matching</h3>
<p><u>Soft cost</u></p>$$c_{ij} = \frac{\delta
d_{ij}}{s_d} + \frac{\delta a _{ij}}{s_{a}} +
\frac{...}{...}$$
<p><u>Hard cost</u></p>
<ul>
<li>Distance: if $d_{ij}>h_d$, then $c_{ij}
= \infty$</li>
<li>Memory: if object $i$ lost more than $h_t$
time, then remove the $i^{th}$ line</li>
</ul>
<p><u>Global optimization</u></p>
<p>Best assignment possible using Hungarian
algorithm <span class="citation">(J. Munkres,
1957)</span></p>
</section>
<section>
<h3>Post processing</h3>
<ul>
<li>Keyboard and mouse shortcuts</li>
<li>Swap, delete ids</li>
<li>Annotation frame by frame <span class=
"citation">(Sturman, Oliver, et al.,
2020)</span></li>
</ul><video data-autoplay="true" loop="true"
controls="true" class="r-stretch"><source src=
"assets/replay.webm" type="video/webm"></video>
</section>
<section>
<h3>Performance</h3><img src=
"assets/Figure_benchmark.svg" class="r-stretch">
</section>
<section>
<h3>Dataset classification</h3>
<ul>
<li>Metric to classify tracking difficulty</li>
<li>Does not necessitate groundtruth
trajectories</li>
<li>Robust to tracking errors</li>
</ul>
</section>
<section>
<h3>Incursion</h3>
<p>Incursion: object exits its Voronoï cell defined
at a time $t$, after a travel time
$\tau$.</p><img src="assets/incursion.svg" class=
"r-stretch">
</section><!--<section>
<h3>Incursion</h3>
<p>Number of incursions depends on:</p>
<ul>
<li>Timescale $\tau$</li>
<li>Density $d$</li>
<li>Distribution of displacements</li>
<li>Geometric properties of Voronoï cells</li>
<li>Degree of motion alignment</li>
</ul>
</section>-->
<section>
<h3>Reduced displacement</h3>
<div style="width:45%; float:left; margin-top:5%">
<img src="assets/Figure_pinc.svg" class=
"r-stretch"></div>
<div style="width:45%; float:right; margin-top:5%">
<p>Reduced displacement $\rho=r\sqrt{d}$</p>
<ul>
<li>Typical distance to neighbors
$\rho=1$</li>
<li>Typical distance to Voronoï cell edges
$\rho=\frac{1}{2}$</li>
</ul>
</div>
</section>
<section>
<h3>Geometric probability of incursion</h3>
<div style="width:45%; float:left;"><img src=
"assets/pinc.svg" class="r-stretch"></div>
<div style="width:45%; float:right;">
<p style="font-size:smaller">Geometric
probability of incursion: proportion of angles
for which incursions occur for a given
displacement $\rho$.</p><u>Per Voronoï cell</u>
<p style="font-size:smaller">
$$p(\rho)=\frac{\color{red}{\Sigma_{out}(\rho)}}{\color{red}{\Sigma_{out}(\rho)}
\color{black}{+}\color{blue}{\Sigma_{in}(\rho)}}
$$
$$p(\rho)=\frac{\color{red}{\Sigma_{out}(\rho)}}{2\pi}$$</p>
</div>
</section>
<section>
<h3>Geometric probability of incursion</h3>
<div style="width:45%; float:left"><img src=
"assets/voronoi.svg" height="500px"></div>
<div style="width:45%; float:right">
<p style="font-size:smaller">To account for many
shapes and sizes:</p>$$p_{inc}(\rho)=\left<
p(\rho) \right>_{cells}$$ <img src=
"assets/sig.svg" height="250px"></div>
</section>
<section>
<h3>Probability of incursion</h3>
<p style="font-size:smaller">If the dynamics is
uncorrelated with the geometric properties of the
Voronoï cells: $$\color{green}{P_{inc}} =
\int_{0}^{\infty} \color{blue}{R(\rho)}
\color{red}{p_{inc}(\rho)} \,d \rho $$</p>
<ul style="font-size:0.6em">
<li style="color:green;">$P_{inc}$ probability
of incursion</li>
<li style="color:blue;">$R(\rho)$ distribution
of displacements at the timescale $\tau$</li>
<li style="color:red;">$p_{inc}(\rho)$
geometric probability of incursion</li>
</ul><img src="assets/Pinc.svg" class="r-stretch">
</section>
<section>
<h3>Probability of incursion</h3>
<p>At $\tau=1$, $P_{inc}$ highly sensitive to
tracking errors that shift $R(\rho)$ to the
right.</p><img src="assets/Pinc_err.svg" class=
"r-stretch">
</section>
<section>
<h3>Timescale analysis</h3><img src=
"assets/timescale.svg" class="r-stretch">
<p>$$P_{inc} = \frac{L}{1 + exp(-k
.log(\frac{\tau}{\tau_0}))}$$</p>
</section>
<section>
<h3>Timescale analysis</h3><img src=
"assets/timescale_deg.svg" class="r-stretch">
<p>$$\delta = \frac{N_{err}}{N_{obj}}$$</p>
<p>Insensitive up to 1 error every 1000
detections.</p>
</section>
<section>
<h3>Timescale analysis</h3><video src=
"assets/ZFJ_001.webm" controls="" data-autoplay=
"true" loop="true" class="r-stretch"></video>
<p>ZFJ_001 very difficult movie: $$\delta \approx
0.003$$ without post-processing.</p>
</section>
<section>
<h3>Optimal framerate</h3>
<ul style="font-size:smaller">
<li>Oversampled: lot of storage space, higher
processing time</li>
<li>Undersampled: lot of incursions, higher
post-processing time</li>
<p>Define $\tau_1$ the timescale at which the
incursion probability is equal to a single
incursion in the whole movie.</p>
<li>$\tau_1<1$: undersampled</li>
<li>$\tau_1>1$: oversampled</li>
</ul><img src="assets/sampled.svg" class=
"r-stretch">
</section>
<section>
<h3>Conclusion</h3>
<div style="width:45%; float:left">
<ul>
<li>Easy to install</li>
<li>Available on Linux, MacOS and
Windows</li>
<li>Versatile</li>
<li>Open-source & API documented</li>
</ul>
</div>
<div style="width:45%; float:right">
<ul>
<li>New measure of trackability with
$P_{inc}$</li>
<li>$\tau_1$ a criterion to find the
optimal experimental framerate</li>
</ul>
</div>
</section>
<section data-background-image=
"assets/dual_photo.jpeg">
<h2 style=
"color:white;-webkit-text-stroke:2px black;background: rgba(0,0,0,0.5)">
II. Assessing chemical preference of young
zebrafish</h2>
</section>
<section>
<h3 style="margin-bottom: 0">Chemical
perception</h3><span class="citation">(Hara,
Toshiaki J., 2012)</span> <span class=
"citation">(Yarmolinsky, David A., Charles S.
Zuker, and Nicholas JP Ryba, 2009)</span>
<ul>
<li>Most ancien sensory system dating back 500
millions years ago</li>
<li>Wide range of taxa: unicellular to
mamalian</li>
<li>Highly conservated features</li>
<li>Mediate feeding and reproduction</li>
</ul>
</section>
<section>
<h3 style="margin-bottom:0">
Olfaction</h3><span class="citation">(Laberge,
Frédéric, and Toshiaki J. Hara., 2001)</span>
<ul>
<li>Olfactory epithelium (snout) projecting
into the olfactory bulb (brain)</li>
<li>Mediate feeding, reproduction, fright
reaction</li>
</ul><img src="assets/olfactory_schematic.png"
class="r-stretch">
</section>
<section>
<div style="width:45%; float:left;">
<h3>Gustation</h3>
<ul>
<li>Taste buds located on the head, lips,
oropharyngeal cavity and barbels</li>
<li>Mediate feeding, reproduction</li>
</ul>
</div>
<div style="width:45%; float:right;">
<h3>Common chemical sense</h3>
<ul>
<li>Solitary chemosensory cells in the
epidermis</li>
</ul>
</div>
</section>
<section>
<h3>The zebrafish</h3>
<div style="width:45%; float:left">
<ul>
<li>Small and robust vertebrate</li>
<li>Well studied chemical senses: first
odor responses $\approx$ 3 dpf <span class=
"citation">(Li, Jun, et al.,
2005)</span></li>
<li>Various behaviors: phototaxis, OMR,
predation</li>
<li>Whole brain imaging using lightsheet
microscopy and transgenic larval
fish<span class="citation">(Panier, Thomas,
et al., 2013)</span></li>
</ul>
</div>
<div style="width:45%; float:right">
<img src="assets/larva.jpg" width=
"75%"><video data-autoplay="true" loop="true"
width="75%" style=
"position:relative; transform: translateY(-11%);"><source src="assets/omr.mp4"></video><video data-autoplay="true"
loop="true" width="75%" style=
"position:relative; transform: translateY(-11%);"><source src="https://files.trentesaux.fr/extra/blog/zf_brain.webm"></video>
</div>
</section>
<section>
<h3>Zebrafish phototaxis</h3>
<div style="width:45%; float:right">
<ul>
<li>Light-seeking navigation</li>
<li>Spatial & temporal phototaxis</li>
<li>Map behavior onto a neuronal model</li>
</ul>
</div>
<div style="width:45%; float:left">
<img src="assets/phtotaxis.jpg" width="100%">
<span class="citation">(Chen, Xiuye, and
Florian Engert, 2014)</span>
<img src="assets/karpenko.svg" width="100%">
<span class="citation">(Karpenko, Sophia,
et al., 2020)</span>
</div>
</section>
<section>
<h3>Chemical perception</h3>
<ul>
<li>Biological noise</li>
<li>Chemical noise: intermittency,
concentration variations</li><br>
</ul>
</section>
<section>
<h3>Assessing chemical preference</h3>
<ul>
<li>Find an attractive product</li>
<li>Study chemically-driven navigation</li>
<li>Neuro-imaging <span class=
"citation">(Candelier, Raphaël, et al.,
2015)</span></li>
</ul>
</section>
<section>
<h3>Assessing chemical preference</h3>
<p><b>Mandatory product screening</b></p>
<ul>
<li>What product?</li>
<li>What concentration?</li>
<li>What age?</li>
</ul>
<p>Time consuming experimental work.</p>
</section>
<section data-background-video=
"assets/compartment.webm" data-background-size=
"contain" data-background-video-loop="true" style=
"color: white;-webkit-text-stroke:0.7px black;">
<h3>Dual</h3>
<ul>
<li>High-throughput screening setup</li>
<li>Do It Yourself setup easy to replicate and
scalable</li>
<li>Open source, robust and versatile</li><br>
<li>Separate the tank in two
compartments</li>
<li>Precisely controlled concentration</li>
<li><b>Fish can choose its prefered
side</b></li>
</ul>
</section>
<section data-background-image="assets/dual.png">
</section>
<section data-background-video="assets/meca.mp4"
data-transition="fade-in fade-out"></section>
<section data-background-video="assets/box.mp4"
data-transition="fade-in fade-out"></section>
<section>
<img src="assets/chip.svg" class="r-stretch">
</section>
<section>
<h3>Dye</h3>
<ul>
<li>Infrared, biocompatible, chemically inert,
neutral</li>
<li>Silicone oil emulsion prepared by Léa-Laetitia
Pontani</li>
<li>$\approx 0.5 mL$ for $1 L$ of solution</li>
</ul><img src="assets/dye.png" class="r-stretch">
</section>
<section>
<h3 style="margin-bottom:0">Experimental
protocol</h3><img src="assets/protocol.svg" class=
"r-stretch">
</section>
<section>
<h3>Analysis</h3>
<ul>
<li>Complex image analysis problem</li>
<li>Complex behavior</li>
</ul><video data-autoplay="true" loop="true"
controls="true" class="r-stretch"><source src=
"assets/manual_sample.webm"></video>
</section>
<section>
<h3 >Markov model</h3><img src="assets/events.svg"
width="70%">
<div style="width:45%; float:left;margin-left:5%;">
<img src="assets/model.svg" width="100%"></div>
<div style=
"width:45%; float:right;font-size:smaller;margin-top:8%;margin-right:5%;">
$$p = \frac{n_{BP}}{n_{BP} + n_{BB}}$$ $$b =
\frac{n_{PB}}{n_{PB} + n_{PP}}$$
</div>
</section>
<section>
<h3>Markov-based analysis</h3>
<div style="width:45%; float:left; margin-top:5%">
<u>Exploration</u> $$\rho_{Markov} =
2Min(p,b)-1$$
<ul style="font-size:smaller">
<li>$\rho_{Markov} = 1$ exploration</li>
<li>$\rho_{Markov} = -1$ exploitation</li>
<li>$\rho_{Markov} = 0$ mixed behavior</li>
</ul>
</div>
<div style="width:45%; float:right; margin-top:5%">
<u>Preference</u> $$\Pi_{Markov} = p-b$$
<ul style="font-size:smaller">
<li>$\Pi_{Markov} = 1$ attraction</li>
<li>$\Pi_{Markov} = -1$ repulsion</li>
<li>$\Pi_{Markov} = 0$ neutral</li>
</ul>
</div>
</section>
<section data-transition="none-out">
<h3>Numerical simulation</h3><img src=
"assets/pi_pb_0.svg" class="r-stretch">
<ul>
<li>All $(p,b)$ are not accessible: sequence
length & p and b rational numbers</li>
<li>Strong preference $\implies$
exploitation</li>
</ul>
</section>
<section data-transition="none">
<h3>Numerical simulation</h3><img src=
"assets/pi_pb_1.svg" class="r-stretch">
<ul>
<li>All $(p,b)$ are not accessible: sequence
length & p and b rational numbers</li>
<li>Strong preference $\implies$
exploitation</li>
</ul>
</section>
<section data-transition="none">
<h3>Numerical simulation</h3><img src=
"assets/pi_pb_3.svg" class="r-stretch">
<ul>
<li>All $(p,b)$ are not accessible: sequence
length & p and b rational numbers</li>
<li>Strong preference $\implies$
exploitation</li>
</ul>
</section>
<section data-transition="none">
<h3>Numerical simulation</h3><img src=
"assets/pi_pb_4.svg" class="r-stretch">
<ul>
<li>All $(p,b)$ are not accessible: sequence
length & p and b rational numbers</li>
<li>Strong preference $\implies$
exploitation</li>
</ul>
</section>
<section>
<h3>Dye effect</h3><img src="assets/dye_bias.svg"
class="r-stretch">
</section>
<section>
<h3>Product screening</h3>
<ul>
<li>Citric acid: repulsive on adult zebrafish
<span class="citation">(Abreu, Murilo S., et
al. 2016)</span></li>
<li>ATP: attractive on adult zebrafish
<span class="citation">(Wakisaka, Noriko, et
al. 2017)</span><br></li>
<li>2 weeks zebrafish</li>
<li>ATP: 24h of starvation before
assessment</li>
</ul>
</section>
<section>
<h3>Citric acid</h3><img src=
"assets/citricacid_markov.svg" class="r-stretch">
</section>
<section>
<h3>ATP</h3><img src=
"assets/atp_markov.svg" class="r-stretch">
</section>
<section>
<h3>ATP: fish by fish</h3><img src=
"assets/3dATP.svg" class="r-stretch">
</section>
<section>
<h3>Conclusion and perspective</h3>
<p><u>Acquisition</u></p>
<ul>
<li>Forced bath experiment</li>
</ul><img class="r-stretch" src=
"assets/protocol_forced.svg">
</section>
<section>
<h3>Conclusion and perspective</h3>
<p><u>ATP persistence</u></p>
<ul>
<li>Add more cycles</li>
</ul><img class="r-stretch" src="assets/river.svg">
</section>
<section>
<h3>Conclusion and perspective</h3>
<p><u>ATP fish age</u></p>
<ul>
<li>Effect not present for larval zebrafish
$\approx$ 7 days</li>
<li>Check on <i>Danionella translucida</i><div class="citation">(Schulze, Lisanne, et al., 2018)</div></li>
</ul>
<video data-autoplay="true" loop=
"true" controls="true" class=
"r-stretch"><source src="assets/danionella.webm" type=
"video/webm"></video>
</section>
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