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From YouTube: DevoWorm (2020, Meeting 40): Elastography/Gigapixels, DevoL Paper/Torch Dreams, Interactions/Agency
Description
Papers on Optical Elastography and Gigapxiels, finishing up DevoLean software paper and demo of Torch Dreams, plus papers on Cell-cell Interactions and Biological Agency. Attendees: Susan Crawford-Young, Richard Gordon, Mayukh Deb, Krishna Katyal, Shruti Rajvanshsingh, Assaf Wodeslavsky, Jesse Parent, and Bradly Alicea.
A
When
did
you
send
them
a
week
ago,
or
so.
C
D
A
They
live
near
steinbach
or
they
work
with
people
from
steinbach
and
steinbeck
has
they
said,
40
infection
rate
yeah,
that's
a
hot
spot.
C
A
E
So
welcome
to
the
meeting.
I
guess
we
have
a
couple
things
today.
I
think
mayak
wanted
to
get
back
in
touch
about
the
joss
paper.
Then
krishna,
I
think,
did
you
have
something
to
share.
E
E
A
All
right,
so
I
have
to
share
the
screen.
How
do
you
do
that.
A
I'll
turn
off
my
video
okay,
maybe
that's
it
so.
A
But
all
right
there,
I'll
just
turn
it
off
like
this.
There
we
go
I'll,
try
again.
A
Okay,
it
doesn't
want
to
share
sorry.
I
have
I
have
it's
only
eight
slides
so.
E
Okay,
well
rather,.
E
Yeah
yeah:
well,
can
you
send
them
to
well
sure,
can
you
share
a
link?
Are
they
on
gmail
or
are
they
on
like
something
where
you
can?
I
can
share
them
or.
E
E
Why
don't
you
just?
Why?
Don't
you
just
is
something
you
talk
about,
or
is
it
something
that,
like
you
need
to
present.
A
It's
just
that
I'm
working
kind
of
working
in
this
area,
you
get
optical
clearance
tomography
and
you
can
either
take
a
whole
bunch
of
pictures
all
at
once
with
like
a
white
light,
a
very
bright
white
light
and
get
all
of
the
different
frequencies,
including
infrared,
and
then
combine
the
pictures
to
get
a
good
look
at,
say
skin
or
you
can
use
a
swept
source
which
sweeps
through
the
frequencies
and
get
a
combined
image.
A
That
way
and
then
we're
trying
to
add
optical
coherence,
elastography
by
moving
the
tissue
and
watching
how
it
responds
like
and
that's
sort
of,
like
doctors
used
to
massage
tissue
to
see
what
was
up
with
it,
because
if
you've
got
a
cancerous
tissue,
it's
a
different
as
it
has
different
mechanical
properties
than
the
other
tissues
and
anyways.
H
B
Susan,
I
have
a
question
yeah.
The
elasticity
of
a
of
a
volume
of
tissue
can,
of
course,
be
anisotropic
and
represented.
H
A
B
Okay,
can
you
do
me
a
favor
send?
Does
he
have
some
papers
on
how
to
use
tensors
for
optical
elastography?
I
guess.
A
We're
just
getting
into
that.
I
have
some,
I
I'll,
send
you
with
synga
his
phd
thesis.
A
E
A
Anyway,
there
are
only
eight
slides,
it's
just
some
sample
images
showing
that
what's
possible,
and
the
idea
is
that
you
don't
need
dye
and
you
don't
need
to
cut
the
tissue
you
can
do
it
live
and
they're
developing
a
device
that
will
do
margin
cancer
margins,
while
in
the
operating
room
with
this.
That's
the
kennedy,
wasinga
group.
B
A
B
You
mean
the
market:
okay,
yeah.
Okay,
a
margin
is
based
on
the
following
assumption:
let's
take
a
skin
cancer.
Okay,
the
skin
cancer
cells
are
assumed
to
be
able
to
move,
and
the
margin
is
a
guess
as
to
how
far
they
can
move.
So
you
cutter
you
not
only
cut
out
the
tumor,
you
cut
out
the
surrounding
tissue
and
that's
called
the
margin.
H
B
Okay
and
then
they
send
the
margin
to
a
pathologist
to
see.
If
there
are
any
cells
near
the
edge
of
the
margin,
if
there
are,
then
they
got
to
cut
more.
The
margin
becomes
bigger,
oh
yeah,
okay,
okay,
so
be
very
nice
to
have
a
direct
measurement
of
what
the
margin
actually
is
right
right
up
till
now,
it's
been
totally
guess.
Work.
H
E
A
Okay,
well,
just
I
had
just
chose
a
couple
of
images
out
of
the
papers
just
to
show
that
it
works
like
they
were
nice,
nice
images.
So
you
can
share
the
slides
if
you
want,
or
just
just
read
the
papers
that
they're
the
one
on
optical
coherence.
Elastography
is
a
little
bit
more
involved,
but
that's
okay,
yeah
hi
yeah.
E
Yeah,
so
here
are
the
the
papers
here,
so
this
is
optical
coherence,
elastography
for
tissue
characterization.
So
this
is
a
review
paper,
and
this
is
let's
see.
This
is
the
first
figure
here
which
is.
I
guess
this
is
the
position
of
oc
among
other
elastography
techniques.
E
So
if
I
zoom
into
this,
you
can
see
that
I
like
these
kind
of
graphs,
because
they
show
kind
of
like
the
space
of
of
I've,
seen
these
for
neuro
imaging
too,
where
they
have
like
the
spatial
resolution,
which
is
on
the
order
of
you,
know
one
millimeter
and
10
to
the
negative
one
millimeter
10
to
the
second
millimeter,
which
is
you
know,
they're
different
distance
scales,
centered
on
a
millimeter
so
and
then
you.
E
A
E
Okay,
so
oc
is
optical,
let's
see
oh
actually,
those
are
the
different
methods.
Yeah
different
methods,
afl.
G
E
Atomic
force
microscopy
oc
is
the
optical
elastography.
I
don't
know
what
some
of
these
others
are.
They
don't
really
have
it.
A
I
thought
they
were
just
below
it,
but
anyway
ultrasound
mri,
oh
atomic
force
microscopy.
E
Yeah,
so
this
is
the
field
of
view
spatial
resolution,
so
this
is
like
how
you
know
when
you
like,
it's
like
microscopy
where,
if
you
have
a
higher
resolution,
you
can
get
to
a
smaller
spatial
resolution
and
then
that's
connected
to
the
field
of
view,
which
is,
if
you
have
a
single
image.
What
what
distance
does
it
cover
across
the
image?
So
you
see
atomic
fork
force
microscopy
is
way
down
here
and
then
oc
is
up.
E
C
B
You
just
need
to
have
your
your
your
camera,
whatever
it
is,
have
a
look,
much
larger
traverse.
B
But
it's
widely
used,
I
I
just
saw
a
webinar
on
where
somebody
took
a
whole
microscope
slide,
one
by
three
inches
and
they
scanned
it
at
very
high
resolution.
The
whole
the
whole
slide
at
60
deaths,
so
they
got
depth
of
focus
also
out
of
it,
and
then
they
montage
the
whole
thing.
B
E
B
E
So
this
is
the
paper
here,
the
first
paper
they
go
into
a
lot
of
these
oh
go
good.
B
B
H
H
E
Go
ahead
I'll
blow
up
all
right,
yeah
yeah!
So
this
is
let's
see
if
we
can
find
another
image
here,
because
they
just
kind
of
go
through
the
technical
details
of
oce
and
then
some
of
the
math
and
displacement
amplitude
or
strain.
So
they
go
through
sort
of
young's
modulus
and
how
they
calculate
that.
E
Let
me
go
through
some
more
math
and
this
is
on
the
viscoelastic
models,
so
they
talk
about
like
the
mathematically
modeled,
the
tissue,
what
else
I'm
trying
to
find
another
image
here,
but
I
don't,
I
think
this
is,
I
think
that's
the
only
image
they
have
in
this
paper.
A
E
A
Yeah-
and
you
can
see
that
the
oct
and
the
elastogram
combined
will
give
you
as
much
information
as
as
the
histology
image.
So
that
means
you
can
do
it
without
dying
in
living
tissue.
That's
what
you're
looking
at.
C
E
And
then
this
figure
nine
is
this
one
is
this
is
another
one
you
wanted
to
show
her.
A
Oops
at
the
top,
this
is
just
the
signal
you
get
back
down
below
and
the
top
whoops
there
it
is.
You
can
see
the
difference
between
the
adipose
tissue
and
the
tumor,
and
then
this
the
histology
image
is
in
pink,
so.
A
G
A
A
Or
yeah
it's
just
wherever
you've
got
tumor-like
image,
so
the
tumor
is
there
and
I
can't
show
you
but
yeah.
You
can
see
the
difference
between
the
tumor
and
the
adipose
tissue,
so
you
would
know
where
to
cut
basically.
A
No,
that
that's
okay,
this
whole
the
end
of
the
paper
here,
you
can
see
how
much.
E
This
is
a
quantitative
elastogram,
so
this
is
kind
of
like
where
they
actually
quantify
the
they
get
at
the
pixel
level.
I
guess.
E
Yeah,
so
that's
that's
that
paper,
then
the
other
paper
is
multi-spectral
near-infrared
absorption
imaging
for
histology
of
skin
cancer.
So
this
is
a
similar
thing
where
they,
your
infrared
images.
So
this
is.
A
A
If
you
keep
on
going,
there's
see,
there's
multi,
spectral
images,
there's
the
setup
and
you
have
a
lamp
that
produces
multiple
wavelengths
and
then
you
have
a
camera
that
takes
the
image
at
multiple
wavelengths
and
then
you
can
combine
the
images
to
well
to
get
a
good
histology
image
of
the
tissue.
E
A
A
Okay,
I
have
several
interesting
things
happening
with
me,
including
a
dog
barking
and
stuff
anyways.
Then
there
was
then
there's
some
images
that
of
this
skin,
that
there
there
they
go,
there's
all
of
the
different
frequencies
and
you
can
see
at
1100
and
1200
that
you've
got
pretty
clear
images
1300
as
well,
and
they
say
that
it's
not
they
didn't
have
set
it
up
correctly.
For
the
900.
H
A
It's
not
optimized
for
900
nanometers,
but
you
probably
do
better.
Yes,
and
if
you
keep
on
going
down-
and
you
can
see
the
there,
these
three
histology
images
compared
to
optical
clearance,
tomography
and
optical
currency
elastography,
I
believe
anyway,
you
can
see
detail
yeah,
quite
decent
detail
using
using
that
method.
A
B
A
I
suppose,
if
you
were
a
doctor,
you'd
want
to
see
the
the
real
thing
and
and
then
mess
with
it
yourself
to
see.
If
you
can
see
more
detail.
Okay,.
A
Best
with
them,
yeah
matlab
has
a
lot
of
imaging
tools
in
it.
Okay,
including
wavelet
tools.
E
A
Yeah
anyways
yeah
image
js
is
good
too,
and
it's
free
that
lab
is
not.
Although
the
university
here
decided,
they
were
going
to
buy
it
for
their
students.
Hooray.
Finally,.
E
A
E
An
idea
a
lot,
you
know
there's
some
of
you
here,
probably
don't
you
know,
maybe
a
little
bit
above
your
head
in
terms
of
the
technique
and
all
that,
but
so
we're
you
know
we're
looking
at
different
ways
to
image
tissue
here
we
have.
You
know
we
have
the
regular
microscopy
that
we
usually
feature
in
the
meetings,
but
that's
usually
on
something.
That's
fixed
or
you
know
a
culture
of
cells
or
of
something
else,
maybe
worms
so
we're
taking.
E
You
know
we
can
take
images
like
that,
but
then
we
can
also
do
histology,
which
is
where
we
take
images
of
tissues.
Sometimes
they
fix
the
tissue
with
a
chemical
solution
and
they
slice
it
up
and
they
put
it
on
a
slide
or
they'll.
Do
it
live,
and
this
is
kind
of
what
we're
talking
about
is
doing
this
sort
of
imaging
live.
E
Where
you
put
it,
you
know
an
imaging
device
on
like
someone's
skin
and
you're,
actually
looking
at
the
skin
live,
and
you
want
to
see
detail
underneath
so
like
they're
looking
for
cancer,
tumors
or
they're
looking
for
other
things
in
the
skin,
you
can
see
them
and
dick
has
done
a
lot
of
work
on
that.
So
susan
is
actually
looking
into
some
of
these
methods.
E
So
this
is
this.
Is
you
know
this
is
all
really
interesting.
I
mean
you
know
if
we
want
to,
I
sent
out
these
two
papers
last
week
there
are
other
papers.
Of
course
you
know,
there's
a.
I
think
that
probably
has
bibliographies
on
this.
If
he's
you
know
willing
to
share
them,
if
you're
interested
you
can
get
in
touch
with
him
sure
yeah.
E
So
next,
I
guess
the
next
thing
we'll
move
to
is
mayuk.
He
got
back
in
touch
about
the
jaws,
the
journal
of
open
source
software
paper.
E
Okay,
there's
dick
gordon's
email
here.
If
you
want
to
contact
him,
so
let's
see
the
paper
is
here.
Let's
see,
let
me
share
my
screen
because
we've
got,
I
think
I
was
presenting.
Okay
looks
like
we
have
a
soft
here,
so
he's
been
around
open
worm
a
bit
and
he
you
know
he's.
I've
talked
to
him
before.
How
are
you.
J
Yeah,
okay,
nothing
new
by
me.
I'm
listening
in
interesting.
H
J
E
Yeah,
thank
you.
Let's
see,
let
me
I'm
gonna
share
my
screening
in
here.
So
we'll
talk
about
this.
This
is
the
paper
that
kind
of
came
out
of
last
year's
google
summer
of
code,
so
we,
but
we
created
this
divo,
learn
framework,
but
we
also
created
the
diva,
learn
software
package
and
that
was
mayulk's
project.
E
So
this
is
the
repository
it's
on
divo,
learn
on
on
github,
so
github
we
have
a
diva
learn
organization,
as
we
know
for
some
of
the
new
people.
Maybe
you've
not
seen
this,
but
we
have
different
things
going
on
here,
so
we
have
education,
theory
building.
You
know
some
data
science
demos.
E
We
then
we
have
diva
learn
which
is
the
standalone
software
and
then
c
elegans
diva
learn
which
is
actually
odual's
project
from
last
year,
which
is
taking
a
lot
of
the
resources
that
we've
had
up
to
this
point
and
putting
them
into
a
library
of
machine
learning
tools.
So
we
do.
We
have
machine
learning,
resources,
deep
learning,
resources
here,
but
we
also
have
some
other.
E
You
know
resources
in
terms
of
education
in
terms
of
just
general
data
science
like
how
do
I
analyze
data
once
I
get
it
and
you
know
get
it
processed
by
these
algorithms
and
then
this,
like
I'm
thinking
here,
of
putting
together
a
guide
for
model
organisms,
which
is
what
we
originally
had
in
devo
zoo,
but
like
more
like,
so
newcomers
could
come
in
and
learn
about
an
organism
like
zebrafish,
just
basic
information,
because
you
know
you
have
people
who
might
be
coming
here.
E
Who
are
computer
scientists,
or
you
know,
they've
not
heard
of
some
of
these
organisms
and
so
be
nice
to
give
them
some
information
background
on
some
of
them.
Nothing,
like
you,
know
nothing
too,
comprehensive,
but
just
enough
so
that
they
know,
like
you
know
what
they're
looking
at
if
they
have
a
data
set
that
they're
using.
E
So
this
is
the
joss
paper,
so
this
is
all
sort
of
organized.
Actually,
this
repository
has
some
images
and
some
video
yeah.
So
this
is
where
the
paper
resides.
This
is
the
manuscript
here
and
I
don't
know
if
I
got
to
have
this
or
I
think
I
made
a
mistake
on
the
formatting
here,
but
this
is
the
title
so
pre-trained
deep
learning
models
that
enable
computational
developmental
biology,
research
and
education.
E
It
might
be
a
little
long
but
we'll
I'll
I'll.
Think
about
that
more.
So
it's
my
oak
myself
and
usual-
and
this
is
our
affiliations
this.
So
this
is
the
format
that
they
want.
So
the
journal
of
open
source
software,
they
it's
it's
a
sort
of.
It's
run
on
github,
it's
a
peer
review
journal,
but
they
run
everything
on
github,
so
you're
supposed
to
submit
a
markdown
file
in
a
certain
format,
and
we
need
to
like
finalize
that
format.
I
think
this
is
not
quite
right,
but
I
don't
know
what
it
is.
E
I
think
my
oak,
maybe.
I
E
I
E
Yeah
yeah,
so
sorry,
so
this
is
the
yeah.
So
the
summary
we
have
some
just
it's
a
summary
of
what
you
know
what
was
done.
This
is
for
the
the
software
package
and
then
the
technical
details.
So
I
I'm
sure
that,
like
you
know,
I
put
this
together
this
weekend.
E
Just
kind
of
walking
through
this
was
taken
kind
of
from
the
summer
of
code
report,
so
my
hook
might
be,
you
know,
might
find
some
problems
with
it.
I
mean
you
know
if
you
want
to
add
to
it
and
add
detail
or
make
it
clear.
I
E
E
Yeah,
I
mean
just
just
the
point
on
this.
You
know
we
want
to
be.
We
want
it's
important
to
be
able
to
cite
where,
where
we
got
the
data
from
some
of
these
open
source
tools
that
we
cite
or
some
of
these
open
source
repositories,
you
know
they.
If
they
want
to
get
funding,
they
have
to
have
citations
of
them
by
other
people.
So
if
you
know
we
can
cite
them
and
then
they
have
those
in
support
of
like
their
further
development.
E
That's
that's
what
that's
that's
a
positive
thing,
so
we
want
to
make
sure
to
cite
them
as
much
as
possible.
So
that's
that's
in
this
part,
so
we
mentioned
like
the
epic
data,
set
the
worm
image
database
and
then
we've
given
a
citation
and
then
that
will
help
them
out.
Then
I
redrew
some
of
these
figures.
So
this
is
the
this.
Is
the
figure
sort
of
like
a
schematic
for
this
software?
E
So
this
is
where
you
have
the
github
source.
What's
on
github,
and
this
is
the
user
environment,
this
is
for
devo
diva
learn.
I
should
probably
change
it
to
the
version
number
two
and
then
this
kind
of
describes
how
it
works.
E
It's
very
data
science
friendly
compatible
with
numpy
and
pandas,
and
then
this
is
the
an
image
of
the
umbrella.
So
then
we
could
start
talking
about
go
transitioning
from
the
divo
learn
program
to
the
divor
divo
learn
framework,
which
is
this
framework
where
you
have
devolver
in
the
program
here
and
then
this
larger
framework
of
things
and
then
that's
where
like
gojoler's
project
is
here
and
then
this
is
some
of
the
existing
infrastructure.
E
And
then
I
kind
of
mentioned
that,
because
you
know
it's
like
people
will
be
able
to
go
to
the
github
organization
and
contribute
and
it'll
drive
everything
forward,
and
then
they
have
some
acknowledgements
here
and
then
the
references
so
the
references,
I
think
that's
good,
but
it
was
well
or
my
yoke
or
as
well.
If
you
want
to
add
in
any
references,
you
can
just
keep
being
mindful
of
this
numbering
scheme,
because
you
know,
if
you
put
in
a
strange
number,
it
throws
everything
off.
E
So
if
you
put
in
something
try
to
find
that
where
it
belongs
in
the
numbering
scheme
and
then
change
it
and
then
a
word
on
the
references,
I
think
this
is
the
way
they
want.
The
paper
is
submitted,
so
they
want
it
with
the
references
in
like
this.
E
We
also
have
the
references
in
this
bib
text
format,
so
I
have
everything
in
the
bib
text
format.
So,
if
we
add
in
references
we
can
add
them
in
like
this,
and
this
actually
makes
it
compatible
with
latex.
So
we
can,
you
know,
add
in
we
have.
I
E
The
idea
is
that
we'll
submit
this
soon
to
the
journal
of
open
source
software,
they'll
review
it
and
then
it'll
become
like
a
published
thing.
They'll
give
it,
I
think
they
assign
it
to
doi,
and
then
you
know,
that's
it's
a
small
publication.
It
shouldn't
be
any
longer,
I
think,
than
two
or
three
pages,
and
then
you
know
then
we'll
have
this
yeah.
I
think
it's
pretty
prestigious,
but
it's
it's.
The
idea,
I
think,
is
it'll
get
exposure
to
a
larger
audience
of
people.
So
there'll
be
a
lot
of
open
source
software.
B
Well,
for
instance,
web
of
science
has
a
number
of
databases
that
they
recognize
okay
and
they
then
index
those
okay.
E
I'm
not
sure
how
they
deal
with
them.
We
know
that,
like
github
a
lot
of
people
when
they
want
to
publish
something
that
they've
done
on
github
like
a
release,
they'll
often
use
like
a
third
party
like
zenoto,
and
it
generates
what
they
call
a
doi,
and
some
of
the
databases
will
pick
up
like
the
those
sorts
of
things,
but
I'm
not
sure
that
the
web
of
science
picks
up
like
those
sorts
of
citations.
I'm
not
now
the
journal
of
open
source
science.
E
E
So,
oh,
my
oak,
you
had
you
wanted
to
present
on
something
called
torch
dreams.
Are
you
still
going
to
do
that
or.
I
I
Okay,
so
is
my
screen
visible,
yeah,
yeah,
yeah,
okay,
well
quickly,
go
to
the
repository
so
basically
like
what
happens
in
developmental
biology.
Is
that,
like
we
see
patterns
which
emerge
from
basically
like
seemingly
random
things
right,
so
we
can
see
like
similar
things
which
happen
inside
like
which
can
be
of
which
can
be
done
using
neural
networks
so
basically
like,
for
example,
I'll
just
show
an
image
quick
quickly.
I
For
example,
we
have
this
noise
that
this
is
basically
random
noise
right.
But
if
we
feed
this
image
to
a
neural
network,
it
starts
hallucinating.
Certain
kinds
of
patterns
like
different
layers
within
the
model,
hallucinate
different
kinds
of
patterns,
and
if
we
optimize
this
noise
to
further
like
to
further
optimize
for
those
pattern
hallucinations,
we
basically
get
a
lot
of
very
like
fascinating
patterns
within
deep
learning
models
and
they
vary
from
like
model
to
movie.
E
Wow,
so
that's
pretty
good,
so
that's
generated
all
from
like
noise
or
like.
I
I
That
is
when
you
are
basically
helping
eating
quote
unquote,
so
even
neural
networks,
when
we
feed
them
those
kinds
of
random
images,
they
have
certain
activations
of
animals
or
even
like
castles
or
even
palaces,
and
things
like
that.
So
even
like
we
can.
We
can
optimize
that
input
image
such
that
those
such
that
those
hallucinations
are
they
get
enhanced
further.
So
we
can
see
what
the
neural
network
was
hallucinating
or
seeing
in
that
random
noise.
I
I
I
I
And
then
again
I
optimize
another
layer
and
we
can
see
something
like
grass
or
like
I
don't
know
what
this
is,
but
this
is
some
kind
of
a
pattern
that
seems
that's
emerging
after,
like
like
500
600
iterations
of
optimization,
like
I
am
back
propagating
on
the
image
instead
of
the
deep
learning
model.
That
is
what
is
happening
inside
okay,
so
like
the.
I
If
I
want
to
summarize
it
in
one
statement,
it's
like
if
it
looks
like
a
cat,
make
the
image
look
more
like
a
cat
that
is
basically
a
one-line
summary
of
what's
happening
inside
so
then
I'll
just
and
then
what
I
did
was
that
I
like,
instead
of
optimizing
these
two
channels
individually,
I
optimize
them
together
simultaneously
and
after
doing
that,
I
got
something
like
this,
which
is
a
mix
of
both
and
we
can
even
see
eyes
things
like
eyes
and
stuff.
So
it's
kind
of
fascinating.
E
I
B
Okay,
basically,
they
can
acknowledge
anything.
We
fancy.
E
Well,
there
there's
actually
yeah,
there
are
people
doing
research
too,
on
like
visual
illusions
and
like
neural
nets,
and
there
I
think,
there's
a
guy
in
japan
who
does
a
lot
of
work
on
this.
Where
they're
looking
at,
I
think
a
long
time
ago
we
did.
I
did
a
presentation
on
on
like
what
is
the
name
of
that
thing.
It's
it's
where
you
perceive
faces
and
things,
and
you
know
that
doesn't
don't
have
faces,
and
so
those
are
things
that
you
know
we
can.
E
I
E
Yeah
yeah,
that's
good,
so
does
anyone
else
have
any
news
they
wanted
to
talk
about
or
like
any
any
updates.
Krishna
jesse
shreddy.
F
E
F
Yeah,
what
is.
D
F
A
I
think
I
understand
what
you
do.
Is
you
take
an
image
of
the
object,
you're
testing
with
optical
clearance
tomography,
which
is
infrared
light,
and
then
you
perturb
it
like
you,
push
on
it
or
squeeze
it
or
poke
it
or
send
an
air
puff
at
it.
A
And
then
you
take
some
more
images
and
you
compare
images.
So
you
can
watch
the
mechanical
response
of
the
object
to
determine
both
the
well
both
the
actual
change
in
the
image
and
the
phase
portions
of
the
image
to
to
see
what
the
elasticity
of
the
object
is.
The
viscoelasticity.
F
Yeah,
do
we
have
some,
you
can
say
predefined
general
disasters
is
the
yeah.
Do
we
have
some
normal
threshold
range,
something
like
that.
F
Okay,
okay,
do
we
have
a
general
baseline
for
all
the
human
beings
or
we,
you
know,
make
that
threshold
value
specific
to
a
single
person
or
others
we
have
like,
for
example,
if
we
are
exploring
the
same
skin
cells,
then
we
have
a
certain
value
for
that
or
do
we
calculate
the
skin
values
of
a
particular
person,
because
everyone,
though
you
can
say
the
elasticity
of
skin
or
any
you
can
say,
tissue
can
vary
from
person
to
person
regarding
age
or
you
can
say.
A
Usually
it's
a
comparison
like
they
haven't,
there's
they're
still
being
researched
and
they're
trying
to
get
what
they
call
qualitative
images
where,
where
you
can
compare
this
image
from
this
person
to
that
image
of
that
person,
but,
like
I
said
you
need
to
put
in,
you
need
some
sort
of
known
substance
and
usually
it's
a
gel
that
has
been
made
similar
to
the
tissue,
and
you
can
test
that
with
other
systems
to
know
exactly
what
its
stress
strain
rate
is,
and
then
you
can
use
that
to
compare
to
the
tissue
that
you're
measuring,
but
often
what
they're
doing
right
now
is
just
comparing
this
tissue
in
this
person
over
here
with
the
tissue
next
to
it.
A
B
Let
me
make
a
general
comment:
the
there
is
a
general
problem
which
has
hardly
been
addressed,
and
that
is
the
detection
of
melanoma,
which
is
a
dark
pigmented
tumor.
It
can
be
started
very
small
in
the
skin
in
dark
skinned
people
when
the
visual
contrast
is
low-
and
maybe
these
optical
coherence
techniques
might
solve
that.
But
it's
still
an
unsolved
problem.
B
And
can
it
see
melanin
on
a
dark-skinned
person.
A
F
I
have
one
more
query:
can
we
do
instead
of
using
that?
Can
you
know
find
a
normal
range
for
human
for
specific
tissue
like
taking?
You
can
say
that
instead
statistical
mean
of
100
000
people,
and
then
you
can
say
I
find
some
general
tendency
of
what
would
be
the
range
and
if
that
range
is
exceeded,
or
you
can
say
intercede,
so
we
can
say
that
there
are
some
abnormality.
E
Well,
yeah,
it
sounds
good,
so
I
was
gonna
if
you
have
to
go
now.
It's
fine,
but
I
was
gonna
finish
up
today
with
a
few
papers,
just
kind
of
go
over
them
briefly.
E
E
E
All
right,
so
I'm
gonna
as
our
obligatory
paper
cue
here.
I
know
we
presented
susan's
optical
tomography
papers,
but
I
have
a
couple
other
things
to
look
at
here.
So
okay,
here
we
are
so
two
papers
that
I
found
this
week.
One
of
them
is
really
interesting.
I
think,
if
you're
interested
in,
like
cell
cell
signaling
and
morphogenesis,
it's
called
inferring
the
spatial
code
of
cell
cell
interactions
and
communication
across
the
whole
animal
body,
and
so
this
is
actually
something
from
c
elegans.
E
E
They
don't
have
the
you
know
the
usual
external
part
of
the
worm
that
we
see,
but
then
you
have
these
cells
and
you're
looking
at
intercellular
distances
and
then
they're
looking
at
those
things
in
terms
of
transfer,
transcriptomics
within
cells
and
then
they're
trying
to
infer
cell
cell
interactions,
so
the
abstract
is
cell
cell
interactions
are
crucial
for
multicellular
organisms
as
they
shape
cellular
function
and
ultimately,
organismal
phenotype.
E
However,
the
spatial
code
embedded
in
the
molecular
interactions
that
drive
a
sustained
spatial
organization
and
then
the
organization
that
in
turn
drives
the
intracellular
interactions
across
the
living
animal
remained.
It
remains
to
be
elucidated,
so
here
they're,
looking
at
the
expression
of
ligands
receptor
pairs
obtained
from
a
whole
body,
single
cell
transcriptome
of
c
elegans,
and
this
is
in
the
larvae.
E
So
they
use
a
3d
atlas
of
c
elegans
cells.
They
implement
a
genetic
algorithm
to
select
ligand
receptor
pairs,
most
informative
of
the
spatial
organization
of
cells.
So
from
the
transcriptome
data,
which
we
don't
talk
about
a
lot
in
this
group,
they
have
a
bunch
of
transcription
factors
that
they
measure
and
those
trans.
E
Some
of
those
transcription
factors
represent
these
ligand
receptor
pairs,
and
so
then
you
can
actually
take
the
data
set
and
run
this
algorithm
on
it
to
select
the
ones
that
are
maybe
most
enriched
in
certain
cells,
and
that
tells
you
something
about
like
the
interactions
between
the
cells
validating
the
strategy.
The
selected
ligand
receptor
pairs
are
involved
in
known
cell
migration,
morphogenesis
processes
and
we
confirm
a
negative
correlation
between
cell
cell
distances
and
interactions.
E
So
this
means
that
you
have
this:
the
relationship
between
cell
cell
distance
and
interactions,
so
the
farther
away
the
cells
are
the
the
fewer
interactions
there
are
so
they're
identifying
these
interactions
and
their
relationship
with
intracellular
distances,
and
they
can
look
at
this
at
a
molecular
scale
instead
of,
like
a
phenotypic
scale,
so
they're
trying
to
link
these
two
levels
of
explanation.
E
Let
me
see
if
there
are
any
images
in
this
paper
that
are
really
interesting,
because
I
mean
going
through
the
methods
might
be
a
bit
much
it's.
You
know,
pretty
intense
and
I'll,
give
you
a
link
to
this
folder
when
we're
done,
but
so
they're
looking
at
this.
So
the
methods
they
have
single
cell
rna,
seq
data,
so
there's
a
method
called
single
cell
rna-seq,
which
is
where
they
take
this.
The
cells
in
the
extract,
rna
and
they're.
E
Looking
at
all
the
rna,
that's
expressed
across
the
genome,
so
there's
a
sequencing
tool
that
they
use
to
align.
What
they
do
is
they
extract
rna
sequences
which
are
like
dna
sequences,
but
a
little
bit
different,
and
then
they
align
them
with
the
genome.
So
you
have
all
these
little
fragments
of
sequence
that
represent
what
they
call
transcripts
and
they
align
them
with
the
genome.
So
they
can
tell
where
these
what
genes
are
being
expressed-
and
they
can
do
this
at
the
single
cell
level,
which
means
each
cell.
E
You
can
extract
its
own
rna-seq
profile,
and
so
they
have
this
data
set
containing
27
cell
types
at
the
larval
l2
stage,
which
is
you
know,
pretty
early.
You
know
moderately
early
in
the
larval
development,
and
so
they
were
able
to
use
that
as
a
transcriptome
and
then
they
were
able
to
align
this
with
a
3d
digital
atlas
of
the
larval
l1
stage.
E
You
know
related
to
different
things
that
are
being
expressed
or
not,
and
so
this
is
how
they
get
the
correlation
between
molecular
activity
and
cells
being
either
closer
or
farther
away,
and
so
then
they
also
did
some
bioinformatics
here,
where
they
looked
at
different
ligand
receptor
pairs
and
looked
for
like
c
elegans,
specific
receptor
pairs
and
there's
a
lot
of
detail
in
here,
but
basically
they're,
sort
of
validating
the
you
know
the
rna
sequences
that
they
get
to
say
that
indeed
they
are
related
to
these
ligand
receptor
pairs
and
that
they're
strongly
predictive
of
that
activity,
and
then
they
do
this.
E
They
use
this
break
curtis
score,
which
was
representing
the
potential
of
interaction.
So
it
repre
considers
a
number
of
active
lr
pairs,
which
are
these
ligand
receptor
pairs,
that
a
pair
of
cells
has,
while
also
incorporating
the
potential
that
each
cell
has
to
communicate
independently.
E
E
Let's
see,
I'm
still
looking
for
some
figures
here.
They
don't
really
have
any
in
here
that
I
can
oh
wait
a
minute:
okay,
they're
putting
them
at
the
end
again,
okay.
So
this
is
a
good
example
here
of
what
I'm
talking
about.
So
you
have
the
cci
score
here.
You
have
these
cell
types.
E
So
now
you
have
the
cell
types
and
you
have
the
score,
and
this
basically
tells
you
sort
of
the
cell
cell
interactions
between
different
pairs
of
cells,
so
you
might
have
like
germline
cells,
which
are
segregated
out
from
the
rest
of
the
cell
types,
which
you
should
expect
touch
receptor
neurons.
E
So
you
have
touch
receptor
neurons
across
here
other
interneurons,
and
you
get
this
degree
of
of
the
cci
score,
which
is
a
degree
of
interaction
body,
wall
muscle
versus
germline.
You
can
see
or
versus
touch
receptor
neurons.
You
can
see
it's
about
the
same
value
and
you
have
this
heat
map,
where
you're,
showing
maybe
a
little
bit
higher
cci
score
for
cholinergic
and
pharyngeal
neurons,
for
example,
or
pharyngeal,
neurons
and
ciliated.
Sensory
neurons,
so
neurons
are
interacting
together
more
strongly.
E
That's
maybe
what
we
should
expect
and
then
so
they
have
that
they
have
sender
and
receiver
cells.
We
talked
about
umap
a
couple
weeks
ago,
this
method
of
doing
a
multi-dimensional
analysis
and
so
they're,
using
that
in
this
paper
to
look
at
sender
and
receiver
cells.
E
And
then
they're
looking
at
these
pairs
selected
in
each
one
of
their
genetic
algorithm,
so
they're
looking
they're
looking
now
at
the
transcripts
and
they're
looking
at
the
abundance
of
these
transcripts,
so
transcripts
occur
at
a
certain
copy
number
in
each
cell,
so
the
more
copy,
the
higher
copy
number,
the
more
the
more
abundant
it
is,
and
that
tells
you
something
about
its
activity
that
it's
higher.
You
know
it's
more
active
in
those
cells,
which
means
that
if
you
have
two
cells
that
have
a
ligand
receptor,
that's
highly
active.
E
That
means
that
they're,
probably
interacting
somewhat
so
that's
that's
the
sort
of
the
logic
there,
but
they're
using
this
genetic
algorithm
to,
I
guess
some
simulate
or
resample
the
data,
and
then
they
analyze
in
this
graph
and
they
look
at
the
change
here
of
signaling
function
for
different
things,
receptor
types!
E
So
that's
that's
kind
of
an
interesting
graph
because
they're
using
these
colored
arrows
yeah.
So
I
think
that's
I
mean
this
is
a
pretty
intense
paper.
I
think
if
you
want
to
read
more
I'll
I'll,
give
you
the
link-
and
you
can
read
it,
but
this
is
a
nice
graph
here
of
c
elegans,
as
sort
of
the
phenotype
laid
out
and
showing
like
all
these
different
cell
types,
their
location
and
then
their
degree
of
interaction
here.
E
Okay,
my
oak
had
to
leave,
and
so
did
dick,
but
I'll
go
through
one
more
paper
and
that's
his
biological
research,
and
this
is
something
I
think
jesse
would
be
interested
in.
Specifically,
this
is
life
with
purpose.
This
is
an
aon
article,
it's
a
popular
article
here
and
we
talked
a
couple
weeks
ago
as
well
about
this
new
paper
on
sort
of
non-neuronal,
cognition,
michael
levin,
and,
and
you
know
they
wrote
this
paper
on
non-neuronal
cognition.
That
was
called
cognition
all
the
way
down.
E
The
idea
here
is
that
biologists
bach
at
any
talk
of
goals
or
intentions,
but
a
bold
new
research
agenda
has
put
agency
back
on
the
table,
and
so
this
article
goes
through.
You
know
the
role
of
maybe
like
purpose
or
goals
or
intentions
in
biology,
and
so
some
people
have
suggested
that
you
can
use
a
model
of
cognition
to
represent
goals
and
and
intentions
in
biological
systems
that
don't
have
a
brain,
and
so
this
is
a
little
bit
more
on
this
in
this
direction.
E
So
they
talk
about
animal
immune
systems,
for
example,
which
don't
have
a
brain,
but
they
have
a
sort
of
a
gold
goal-oriented
behavior.
So
they
try
to
knock
down
invading
viruses
and
invading.
E
Other
things
in
the
body
and
they
try
to
minimize
the
damage
to
the
organism,
and
so
there's
this
thing
called
adaptive:
immunity
which
allows
the
immune
system
to
to
do
its
thing
and
and
but
you
know,
then
you
say
well.
How
can
this
be?
If
it
doesn't
have
a
brain?
How
can
you
have
this
kind
of
intentional
system?
E
So
you
know
this
description
of
the
immune
system.
They
ask:
isn't
this
an
absurdly
anthropomorphic
way
of
describing
a
biological
process?
Single
cells?
Don't
have
minds
of
their
own,
so
surely
they
don't
have
goals,
determination,
gusto
when
we
attribute
aims
and
purposes
to
these
primitive
organisms.
E
Are
we
just
succumbing
to
an
illusion,
and
so
they
asked
they
bring
up
this
classic
psychology
experiment
which
reveals
the
human
impulse
to
attribute
goals
and
narratives
to
what
we
see-
and
this
is
a
an
example
of
this
hydra
and
symbol-
experiment
where
okay,
so
in
this
experiment,
they
show
people
crudely
animated
movie,
featuring
a
circle
and
two
triangles,
and
then
they
ask
viewers
what's
going
on
in
this
image.
E
So
it's
kind
of
a
minimal
image
of
some
sort
of
action
and
ask
people
what's
going
on
and
they
attribute
some
sort
of
thing.
That's
you
know,
there's
a
some
narrative
to
it.
So
these
triangles
and
circle
in
this
box
they're
escaping
the
space,
and
you
know,
whereas
this
could
just
simply
be
a
phage
or
a
macrophage
in
biology
so
where
they
could
just
be
abstract,
geometric
shapes,
but
we
assign
some
sort
of
meaning
to
this.
E
And
so
that's
the
idea,
and
so
the
question
is,
is
like:
if
we're
observing
something
at
the
biological
scale
you
know
is
there's,
are
we
just
assigning
narratives
to
it
when
we
come
up
with,
say
a
theory
of
how
something
works
or
even
describing
it
or
you
know,
are
we
justified?
Because
maybe
there
is
something
going
on
in
terms
of
like
you
know,
agency
or
action,
and
so
that's
a
good.
I
think
that's
a
good
way
to
kind
of
think
about
this.
Is
you
know
it
to
be?
E
Mindful
of
you
know,
are
we
just
kind
of
like
adding
in
our
own
story
that
you
know
is
sort
of
anthropomorphic
and
maybe
something
we
would
do
if
these
were
human
agents
instead
of
just
shapes
or
cells
or
whatever
they
are
and
so
yeah?
So
this
paper
said
you
know
they
point
out.
The
author
here
points
out.
One
of
biology's,
most
enduring
dilemmas,
is
how
it
dances
around
the
issue
at
the
core
of
such
a
description
agency,
the
ability
of
living
entities
to
alter
their
environment
with
purpose
to
student
agenda.
E
People
criticize
you
very
much
if
you
talk
about
like
agency
or
sometimes
if
you
talk
about
teleology,
but
you
know
it's,
the
question
is:
is
that
really
justified,
or
maybe
there
is
something
there?
So
you
know,
cells
and
bacteria
aren't
really
trying
to
do
anything
just
as
organisms
don't
evolve
in
order
to
achieve
anything,
that's
the
idea,
and
so
we
want
to
be
careful,
but
we
don't
also
want
to
throw
the
baby
out
with
the
bathwater.
E
So
so
they
they
suggest
that
a
bottom-up
theory
of
agency
could
help
us
interpret
what
we
see
in
life
from
cells
to
societies,
as
well
as
in
some
of
our
smart
machines
and
technologies,
we're
starting
to
wonder
whether
artificial
intelligence
systems
might
themselves
develop
agency.
But
how
would
we
know
if
we
can't
say
what
agency
entails?
E
Only
if
we
derive
complex
behaviors
from
simple
first
principles
says
the
physicist
suzanne
still
the
university
of
hawaii.
Can
we
claim
to
understand
what
it
takes
to
be
an
agent,
and
so
this
is
the
then
they
go
kind
of
go
through
what
an
agent
is,
and
so
you
know
it's
a
pretty
good
article
if
you're
interested
in
that
area,
I
think
but
yeah
there's
a
lot
of
discussion
to
be
had
about
that.
I'm
not
sure
what
the
you
know
I
mean
we
can
apply
to.
E
I
think
a
lot
of
problems
in
this
group,
but
you
know
it's
it's
available
for
people
to
read.
Maybe.
E
Meetings,
we
can
talk
a
little
bit
more
about
this,
but
I
know
that
jesse
and
I
and
some
other
people
been
having
conversations
about
this,
which
is
why
I
bring
it
up
and
dick
also,
I
think,
has
talked
about
expressed
interest
in
talking
about
the
biology
of
purpose
in
the
past.
I
think
he's
written
some
things
on
this,
so
I'm
not
really
sure
you
know
I
kind
of
brought
this
up
after
he
left,
but
we
will
talk
about
in
future
meetings.
So.
L
L
Just
that
I
didn't
thank
you
for
going
over
that
I
didn't
get
to
that's
on
my
reading
list
for
sure,
but
I
really
I
look
forward
to
going
over
that
more
in
depth
and
maybe
incorporated
into
some
things
here
but
yeah.
Thank
you.
E
A
M
J
Yeah,
I
I
love
the
analogy
to
the
antibody
system
of
the
immune
system:
it's
brilliant
and,
and
then
the
squares
and
the
shape
apes,
brilliant.
But
you
know
it
makes
you
think
so.
Do
we
really
think.
J
E
E
So,
okay!
Well,
thanks
for
attending.
If
you
again,
if
you
have
any
papers
to
recommend
or
if
you
want
to
present
anything
in
a
meeting,
please
let
me
know
in
advance
and
and
we
meet
at
the
same
time
every
week
so
next
week
we
have,
I
think,
an
open
schedule.
So
if
you
want
to
do
something,
we
can
do
it,
otherwise
I
will
send
out
some
maybe
some
follow-up
to
this
meeting
and
hope
to
see
everyone
next
week
have
a
good
week
thanks,
bye,
bye,
thank.