follow the slides live at

https://slides.com/delestro/phd-defense/live

A multiple cell tracking method dedicated to the  analysis of memory  formation in vivo

Felipe Delestro

25th October 2018

PhD defense

under the supervision of Auguste Genovesio

MELANIE PEDRAZZANI

LISA SCHEUNEMANN

Gènes et Dynamique des Systèmes de Mémoire

ESPCI

THOMAS

PREAT

Bio-Imagerie Computationnelle et Bioinformatique

IBENS

AUGUSTE

GENOVESIO

FELIPE

DELESTRO

If the brain were so simple we could understand it, we would be so simple we couldn't. Lyall Watson

Homo sapiens

5cm

Bandettini PA,

Twenty years of functional MRI: The science and the stories.

Neuroimage. 62(2):575–588. (2012)

Mus musculus

Homo sapiens

5cm

Moser M-B, Rowland DC, Moser EI.

Place Cells, Grid Cells, and Memory. 

Cold Spring Harbor Perspectives in Biology. (2015)

Drosophila

melanogaster

1 mm

ODOR

Octan-3-ol (OCT)

ODOR

A. Pascual, & T. Préat,

Localization of long-term memory within the Drosophila mushroom body.

Science 294, 1115–1117 (2001).

Octan-3-ol (OCT)

Dolan DNA Learning Center

Cold Spring Harbor Laboratory

www.dnalc.org

Yu, D., Keene, A. C., Srivatsan, A., Waddell, S. & Davis, R. L.
Drosophila DPM neurons form a delayed and branch-specific memory trace after olfactory classical conditioning.
Cell 123, 945–957 (2005).

In quantitative terms, what are the changes in the brain after learning, at the single cell level ?

Honegger, K. S., Campbell, R. a a & Turner, G. C.
Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body.
J. Neurosci. 31, 11772–85 (2011)

state of the art

  • Analysis only for 2D slices
    (incomplete view of the brain)
     
  • Manual or assisted detection
    (biased and low throughput)

Tugba, G.-O., Davis, R. L., Guven-ozkan, T. & Davis, R. L. Functional neuroanatomy of Drosophila olfactory memory formation. Learn. Mem. 21, 519–526 (2014)

Campbell, R. a a et al. Imaging a population code for odor identity in the Drosophila mushroom body. J. Neurosci. 33, 10568–81 (2013)

Lin, A. C., Bygrave, A. M., de Calignon, A., Lee, T. & Miesenböck, G. Sparse, decorrelated odor coding in the mushroom body enhances learned odor discrimination. Nat. Neurosci. 17, 559–68 (2014)

Aso, Y. et al. The neuronal architecture of the mushroom body provides a logic for associative learning. Elife 3, e04577 (2014)

Strategy

  • Record the full extent of the Mushroom body in 3D
    By using of a confocal spinning disk we'll be able to perform fast and complete acquisitions
     
  • Automatically detect the neurons in 3D
    An automated procedure guarantees an unbiased analysis
     
  • Analyse the difference between groups
    A quantitative approach will allow us to infer how the memory trace is represented in the brain

mCherry & GCaMP
with a VT30559-GAL4 promoter

Expression is restricted to the kenyon cells (mushroom body neurons)

mCherry & GCaMP
with a VT30559-GAL4 promoter

Expression is restricted to the kenyon cells (mushroom body neurons)

MELANIE PEDRAZZANI

LISA SCHEUNEMANN

Dimensions

X: 256 pixels (41.28µm)

Y: 512 pixels (82.56µm)

Z: 45 slices   (67.50µm)

 

Acquisition time

20ms per slice

0.9 s per stack

135 s per acquisition

mCherry

GCaMP

Dimensions

X: 256 pixels (41.28µm)

Y: 512 pixels (82.56µm)

Z: 45 slices   (67.50µm)

 

Acquisition time

20ms per slice

0.9 s per stack

135 s per acquisition

mCherry

GCaMP

About 200 recordings of unique flies where made for the standardisation of the protocol

Aditional 122 flies were used for the final analysis

(more than any other work)

This corresponds to about 4.6 hours of recorded signal, stored in more than 800 thousands of image slices

Data challenges

XY

YZ

Nuclei (mCherry)  |  Max projections

x

y

z

mCherry (nuclei)

Volumetric reconstruction

normal

artifact

normal

artifact

Max projection through time

Slices of problematic stack

Nuclei (mCherry)

Signal (GCaMP)

Natural brain movement

x

y

z

y

Data analysis

DETECTION

TRACKING

SIGNAL

DETECTION

TRACKING

SIGNAL

Find the position of the nuclei of neurons from the Mushroom body

Follow each one of the detected neurons through time

Measure the correspondent signal for the individual neurons

DETECTION

TRACKING

SIGNAL

Neuron detection

The goal is to find the positions of nuclei from the Mushroom body, so that the individual neurons can be identified

normal

artifact

normal

artifact

Toyoshima, Y. et al.

Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.

PLoS Comput. Biol. 12, 1–20 (2016)

Štěpka, K. et al.

Performance and sensitivity evaluation of 3d spot detection methods in confocal microscopy.

Cytom. Part A  (2015)

Estimating nuclei size

Using the Full Width at Half maximum, we can estimate the nuclei diameter

time frames

0

250

Detection validation

Synthetic images

A computer generate image, with similar characteristics to the original image, and known ground truth

Detection validation

synthetic

real

Synthetic images

A computer generate image, with similar characteristics to the original image, and known ground truth

Detection validation

Manual annotation

Using the CellCounter ImageJ plugin to manually mark the nuclei position in 3D

Detection validation

Real image

Synthetic image

time frames

0

250

DETECTION

TRACKING

SIGNAL

Neuron tracking

Once having the positions of every neuron, we need to link the detections trough time.

Chenouard, N. et al.
Objective comparison of particle tracking methods.
Nat. Methods 11, 281–289 (2014)

Non-rigid deformation

Natural movements of the brain cause deformations during the acquisition

top view

side view

Frame 1

Frame 2

Frame 1

Frame 2

Myronenko, A. & Song, X.

Point set registration: coherent point drift.

IEEE Trans. Pattern Anal. Mach. Intell. 32, 2262–75 (2010).

Ester, M., et al. 
A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise.
Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining,  pp. 226-231. (1996)

DBSCAN

Original detections

Registered detections

time frames

clusters

Clusters in original coordinates

time frames

0

400

Every detection projected into a single 3D space

Tracks for one of the detected clusters

cluster fix

using time information to fix merged clusters

cluster fix

using time information to fix merged clusters

cluster fix

using time information to fix merged clusters

cluster fix

using time information to fix merged clusters

cluster fix

using time information to fix merged clusters

original detections

tracked nuclei

DETECTION

TRACKING

SIGNAL

Measuring signal

The last step is to actual measure the activity signal from the neurons, while the fly receives a stimulus

intensity 2d histogram

Nuclei & Signal
Axial max projection

before stim

during stim

Memory traces

What are the quantitative changes in the brain to represent the memory trace ?

unpaired control

paired conditioning

Unpaired (no long-term memory)

Paired (long-term memory formed)

Neuron recruitment

Response intensity

Mann-Whitney two-sided test

p-value: 0.0014

 

t-test

p-value: 0.248

Contributions

Data acquisition

Detection & Tracking

Memory traces

Fine-tuning of a system capable of acquiring 3D+Time images of the Mushroom body, while the fly experiences an odor

Development of an open-source and fully automated detection and tracking algorithm, capable of handling the high density of neurons and movements of the brain 

This unique set-up allowed us to quantify, for the first time, the recruitment of new neurons during long-term memory formation

Perspectives

Graph features

More subtle characteristics of the neuronal activation pattern could be revealed by the use of graphs 

Training during acquisition

An update on the fly chamber could allow the electric stimulation during the imaging, showing live how the brain is reacting 

Genetic modifications

The system here developed would allow us to verify how different levels of expression of specific genes change the neuron recruitment

Song, L. L., Liang, R., Li, D. D. & Al., E. A
Systematic Analysis of Human Disease-Associated Gene Sequences In Drosophila melanogaster.
Genome Res. 59, 1114–1125 (2001)

2015

2016

Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct 

2014

AUGUSTE GENOVESIO

FELIPE DELESTRO

MINHUI WU

THOMAS PREAT

PAUL TCHENIO

MELANIE PEDRAZZANI

YANN DROMARD

LISA SCHEUNEMANN

2017

2018

Computational Bioimaging and Bioinformatics

Auguste Genovesio

Elise Laruelle

France Rose

Nikita Menezes

Tiphaine Champetier

Toni Paternina

Solène Weill

Mathieu Bahin

Amira Kramdi

Ouardia Ait Mohamed

Maxime Corbé

Guillaume Delevoye

Fatemeh Habibolahi

Benoit Noël

Delase Amesefe

Alice Othmani

Ayfer-Marie Montibus

Asm Shivuddin

Perrine Lacour

Sreetama Basu

Charles Bernard

Jennifer Salazar

Alexis Renault

Leila Bastianelli

Minhui Wu

Elton Rexhepaj

Quentin Viautour

Charles Wang

Yingbo Li

 

Supplementary slides

Projections, detections & signal

SMAX comparison

standardization with naïve flies

Detection on naive flies

Volumes from
groups

Automated fly filter

Naïve

Paired

Unpaired

AIR

OCT

AIR

AIR

OCT

AIR

MCH

AIR

MCH

AIR

Paired
control

Unpaired
control

OCT

OCT

OCT

OCT

OCT

MCH groups

3D detections paper

MB details

Frame 1

Frame 2

Frame 3

Frame 1

Frame 2

Frame 3

DBSCAN

DBSCAN parameter scan

Detection removal without split

ICY Multiple hypothesis tracking

Variables

  • Expected track length
  • Minimum probability of existence for confirmation
  • Probability of existence threshold
  • Expected XY displacement
  • Expected Z displacement
  • Expected new objects per frame
  • Expected number of objects in first frame
  • Depth of track trees
  • Gate factor for association

real

synthetic

Synthetic movie

Detection tracks with duplicates

Starting cluster stage...

Estimation of eps for DBSCAN:
Calculating distances between pairs: [65 & 178] [44 & 57] [254 & 2] [52 & 13] [88 & 110] [221 & 104] [163 & 138] [239 & 166] [234 & 133] [382 & 393] [381 & 247] [1 & 301] [335 & 102] [88 & 273] [83 & 11] [68 & 313] [321 & 58] [214 & 186] [351 & 350] [207 & 127] [232 & 394] 
Done after 21 iterations, normal distribution with pvalue of 0.0341911133526

Global mean distance:	7.80852894987
Estimated eps value:	3.90426447493

Estimation of min_samples for DBSCAN:
Target: 726.615 clusters

6873 clusters for min_samples of 1	Difference from target: 6146.385
1946 clusters for min_samples of 2	Difference from target: 1219.385
892 clusters for min_samples of 3	Difference from target: 165.385
540 clusters for min_samples of 4	Difference from target: 186.615
419 clusters for min_samples of 5	Difference from target: 307.615
353 clusters for min_samples of 6	Difference from target: 373.615
278 clusters for min_samples of 7	Difference from target: 448.615
256 clusters for min_samples of 8	Difference from target: 470.615
227 clusters for min_samples of 9	Difference from target: 499.615
219 clusters for min_samples of 10	Difference from target: 507.615
215 clusters for min_samples of 11	Difference from target: 511.615
209 clusters for min_samples of 12	Difference from target: 517.615
216 clusters for min_samples of 13	Difference from target: 510.615

Best value for min_samples: 3

Initializing final DBSCAN...
eps: 3.90426447493
min_samples: 3
Number of clusters: 892

DBSCAN parameter estimation

Checking and fixing clusters...
Number of labels with duplicates: 70 (7%)
Resolving duplicates . . . . . . 
62 cases with mode 0 (88%)
7 cases with mode 1 (10%)
0 cases with mode 2 (0%)
0 cases with mode 3 (0%)
0 cases with mode 4 (0%)
.
.
.
0 cases with mode 705 (0%)
0 cases with mode 706 (0%)
0 cases with mode 707 (0%)
1 cases with mode 708 (1%)

Remaining duplicates: 699
Number of labels with duplicates: 699 (43%)
Resolving duplicates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
197 cases with mode 0 (28%)
433 cases with mode 1 (61%)
69 cases with mode 2 (9%)

Remaining duplicates: 126
Number of labels with duplicates: 126 (7%)
Resolving duplicates . . . . . . . . . . . 
49 cases with mode 0 (38%)
77 cases with mode 1 (61%)

Remaining duplicates: 0

Iterative cluster fix

CPD parameters

Chained registration

Axial drift through time

Axial drift

Rigid Vs Non-rigid registration

Only affine

Affine + CPD

Signal filtering

Responsive neuron

Baseline neuron

3D + Time

Center crop

Voronoi maximum size

(relative to nuclei diameter)

x1

x2

x5

x10

no limit

Similarity matrix

Similarity matrix

Axial precision & Interpolation

        sigma  detections
0    0.000000       61006
1    7.507692          25
2   12.061538          24
3   14.400000          24
4   15.261538          24
5   15.384615          24
6   15.507692          24
7   16.369231          26
8   18.707692          23
9   23.261538          28
10  30.769231          11
11  41.969231           1

Sigma and object size

nuclei

signal

detection

z

intensity 2d histogram

nuclei

signal

Signal colocalization

Signal quality

Signal (GCaMP)

Signal quality

Signal quality

Signal quality

Signal quality

Data managment

Raster image registration

Raster image registration

PSF distortion

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Synthetic images

Voxel dimensions

Copy of PhD defense

By Felipe Delestro

Copy of PhD defense

  • 515