The in vitro neurite outgrowth assay is an established method for evaluating neuron structure and function across a broad range of neuroscientific studies, including neurotoxicity and neurodegeneration.
Recent advances in neuronal culture models using induced pluripotent stem cell (iPSC)-derived neurons provide unprecedented opportunities for developing relevant and scalable in vitro human neuronal models. For example, using label-free methods allows for the evaluation of neuronal outgrowth in live cells with minimal sample manipulation.
This application note showcases the use of label-free imaging techniques for live-cell analysis of neuron culture outgrowth in an iPSC-derived glutamatergic cell model.
Download this application note to explore:
- An advanced live-cell imaging system for analyzing neurite outgrowth
- The benefits of label-free approaches compared to fluorescent models
- Automated imaging and analysis for sensitive, high-throughput evaluation
Application Note
Neuroscience Research
Authors
Rebecca Mongeon, PhD
Joe Clayton, PhD
Agilent Technologies, Inc.
Abstract
Label-free cellular analysis provides a means to monitor and evaluate live cells over
time with minimal intervention. Analysis of live neurons using label-free methods
represents an important technique for high-throughput, image-based neurite
outgrowth assays. Agilent BioTek automated imaging systems feature integrated
environmental controls and multiplate capacities to enable a diverse range of longterm live-cell applications. This combination of automated live-cell microscopy
and image analysis enabled by the Agilent BioTek Gen5 neurite outgrowth module
presents a flexible, automated platform for label-free, kinetic neurite outgrowth
studies. Neurite outgrowth analysis capabilities are demonstrated for multiple
label-free imaging techniques through proof-of-principal investigations using an
iPSC-derived neuron culture model. Automated image collection and analysis were
performed in a high-density microplate format that enabled analysis of both timeand concentration-dependent changes to neuron culture outgrowth across multiple
phenotypic parameters.
Automated, Label-Free, Kinetic
Neurite Outgrowth Analysis
Kinetic, label-free neurite outgrowth evaluation
of live iPSC-derived neuronal cultures, enabled
by a fully automated, multimodal imaging and
analysis platform
2
Introduction
The in vitro neurite outgrowth assay is an established method
for evaluating neuron structure and function across a broad
range of neuroscientific studies, including neurotoxicity and
neurodegeneration.1-3 Recent advances in the development of
neuronal culture models using induced pluripotent stem cell
(iPSC)-derived neurons provide unprecedented opportunities
for relevant and scalable in vitro human neuronal models
for neurobiology research.4
Cultured iPSC-derived neurons
exhibit key cellular events involved in neurite outgrowth,
providing an essential cell model for incorporation into the
standardized battery of benchmarked in vitro assays for
evaluating developmental neurotoxicity.5
Furthermore, iPSCderived models support personalized medicine approaches
that require in vitro screening applications to predict adverse
drug reactions.6
Label-free methods present an opportunity to evaluate
neuronal outgrowth in live cells with minimal sample
manipulation. Compared to label-free approaches, fluorescent
models for live-cell analysis require significant investments
in both model development and validation, given the need to
demonstrate that the fluorescent markers do not interfere
with the biology under investigation. In contrast, label-free
methods are immediately accessible across sample types,
including samples for which fluorescent modifications may be
impractical. Furthermore, the cytotoxic and phototoxic effects
commonly associated with fluorescent protein expression
or dyes are avoided with label-free approaches.7
Label-free
methods, however, do not afford specificity in analysis, and
so are only appropriate for investigations of relatively pure
cell populations and have limited use for neurite outgrowth
analysis in the context of more complex models, such as
cocultures.
In this application note, we investigate neuron culture
outgrowth of an iPSC-derived glutamatergic cell model using
label-free imaging techniques for live-cell analysis. We detail
how automation of both the image collection and analysis
processes facilitates sensitive, high-throughput evaluation
of neurite outgrowth while minimizing user intervention and
effort. The automated kinetic imaging approach provides
detailed insights into time-dependent differences between
treatments that are difficult or impossible to capture through
end-point evaluations. Furthermore, insights gained from
kinetic live-cell studies can guide decisions around key time
frames for follow-up investigations with end-point analyses.
Small-molecule modulators of neurite outgrowth were
applied to iPSC-derived neuron cultures across a
concentration series to investigate both time- and
concentration-dependent effects on outgrowth. Multiple
cellular phenotypic measurements relevant to neuron culture
outgrowth, including length and branching parameters, were
evaluated to demonstrate the performance of this platform
for high-throughput, label-free approaches in neurite
outgrowth studies.
Experimental
Materials
Chemicals
All chemicals were purchased from Sigma unless otherwise
noted, including the outgrowth effectors blebbistatin (part
number B0560), 6BIO (part number B1686), and triptolide
(part number T3652). Staurosporine was purchased from
Tocris Bioscience (part number 1285).
Cell culture
iCell GlutaNeurons (FUJIFILM Cellular Dynamics, Inc.; part
number R1061) were cultured in BrainPhys Neuronal Medium
(StemCell Technologies; part number 05790) supplemented
with iCell Neural Supplement B (iCell kit component), iCell
Nervous System Supplement (iCell kit component), N-2
Supplement (Gibco; part number 17502048), and laminin
(Sigma; part number L2020). iCell GlutaNeuron cultures
were plated on Greiner glass-bottom, 96-well microplates
(Greiner; part number 655892). Microplates prepared for iCell
GlutaNeuron cultures were first coated with poly-L-ornithine
solution (Sigma; part number A-004-M), followed by complete
media supplemented with laminin.
Instrumentation
The Agilent BioTek BioSpa live cell analysis system,
comprised of the BioSpa 8 automated incubator and the
Agilent BioTek Cytation 5 cell imaging multimode reader (in
this case), was used to automate the live-cell workflows. The
Cytation 5 was outfitted with a 20x phase contrast objective
(part number 1320517) and the BioSpa 8 software managed
the environmental conditions and imaging sessions.
3
Methods
Cell culture
Culture procedures followed manufacturer recommendations
for iCell GlutaNeurons. Microplates were prepared for culture
the day before plating. Plates were first coated overnight
at room temperature with poly-L-ornithine solution. The
following day, coated plates were rinsed five times with
sterile phosphate-buffered saline (PBS) and incubated in a
humidified tissue culture incubator (at 37 °C and 5% CO2
) for
at least one hour before plating cells with complete media.
iCell GlutaNeurons were thawed and plated following
manufacturer protocol recommendations. Live cell
estimations were performed with the trypan blue exclusion
method. Cells were plated at a density of ~ 10,000 live cells
per well. To minimize evaporative effects across the plate,
regions between wells were partially filled with sterile water.
To promote even cell dispersal across the well, plates were
allowed to rest at room temperature for ~ 30 minutes to
permit cell adhesion before transferring to the BioSpa 8
automated incubator with humidity and environmental
controls set at 5% CO2
and 37 °C. Imaging was started after
approximately 45 minutes of equilibration within the BioSpa 8
automated incubator.
After 24 hours of initial outgrowth, the microplate was
removed from the BioSpa 8 incubator, and a dilution series
of outgrowth effectors were applied to cultures during a
50% media exchange. An additional 50% media exchange
was performed 48 hours later (72 hours postplating) with
maintenance of final drug concentrations.
Image capture and processing
Default settings of the Gen5 neurite outgrowth module
provided a starting point for soma and neurite detection, and
were further optimized as shown in Table 1. Optimal values
for the parameters indicated in Table 1 will vary based on
experimental conditions, and users are expected to evaluate
and adjust these parameters as needed.
Data analysis and fitting
Agilent BioTek Gen5 software was used for all data plotting
and fitting, unless otherwise noted. Evaluations of average
outgrowth rates were evaluated using the MeanV calculation.
The maximal rate of change in outgrowth was evaluated
using the MaxV calculation. Dose–response relationships
were fit with four-parameter logistic curves, and Z-scores
were calculated using the difference between the treatment
mean and control mean expressed in multiples of the
standard deviation of control. In the Gen5 software syntax,
the following formula was applied in a transformation step to
calculate the Z-score for outgrowth metrics:
(X-MEAN(CTL1))/SD(CTL1).
Neurite Outgrowth Analysis Settings
Soma Detection Phase Contrast Brightfield
Threshold Slider Level Neutral Neutral
Minimum/Maximum Size 10/100 10/100
Soma Closing Size 2 1
Rolling Ball Diameter 5 10
Image Smoothing Strength 15 10
Neurites
Detection Mode Intensity Intensity
Threshold Slider Level 70 80
Neurite Mask Closing Size 0 0
Rolling Ball Diameter 3 5
Image Smoothing Strength 3 3
Discard Short Neurites 10 10
Discard Short Fragments 10 10
Discard Short-Ending Branches 10 10
Table 1. Agilent BioTek Gen5 neurite outgrowth module detection settings.
4
Results and discussion
Live-cell neurite outgrowth with the Agilent BioTek
live cell analysis system
A generalized label-free kinetic neurite outgrowth assay
schematic is shown in Figure 1. Cultures were plated on highdensity microplates and imaged for evaluation across five
days of outgrowth. The BioSpa 8 automated incubator was
used to automatically deliver microplates to the Cytation 5
cell imaging multimode reader across multiday imaging
sessions. Label-free images of neurons collected in phase
contrast or brightfield imaging modes were automatically
captured on the Cytation 5 across the plate and analyzed
with the neurite outgrowth module in Gen5 software. Neuron
cultures were assessed across multiple metrics of outgrowth,
including total and average neurite outgrowth length. Both
kinetic and dose–response analyses were performed in Gen5
software to evaluate treatment effects on outgrowth.
The BioSpa 8 automated incubator supports long-term
outgrowth evaluations for up to eight microplates and is
compatible across the Cytation instrument line, including
the Agilent BioTek Cytation C10 confocal imaging reader.
For lower-throughput (e.g., single microplate), kinetic neurite
outgrowth assays, the Agilent BioTek Lionheart FX automated
microscope is also compatible with the Gen5 neurite
outgrowth module in both label-free and fluorescent
imaging modes.
Label-free neurite outgrowth analysis comparing phase
contrast and brightfield methods
Agilent BioTek imagers support multiple modes for label-free
imaging, including phase contrast and brightfield methods.
Phase contrast imaging is a commonly used method to
enhance the signal-to-noise (contrast) of neurons and neurite
processes for label-free imaging.
Although phase contrast is typically the preferred method
for label-free imaging of neurons, brightfield imaging was
explored as an alternative label-free imaging method that
does not require specialized objectives. iPSC-derived
neuron culture outgrowth was assessed by imaging at 20x
magnification in both phase contrast and brightfield imaging
modes (Figure 2).
Example phase contrast images of iCell GlutaNeuron cultures
at three time points are displayed in Figure 2A. Minimal
outgrowth is detected in the first image taken directly
following plating (Figure 2A, left panel). Neurons rapidly
extend processes and a substantial increase in outgrowth
is observed by 24 hours (Figure 2A, middle panel). Neurons
continue to gradually increase neurite outgrowth through the
five-day time course (Figure 2A, right panel). Gen5 neurite
outgrowth module analysis performed on iCell GlutaNeuron
cultures detected both soma and neurites in phase contrast
images at each time point as depicted in the bottom panels
of Figure 2A.
Example brightfield images of iCell GlutaNeurons throughout
the experiment are depicted in Figure 2B, corresponding to
the same field of view and time points indicated in Figure
2A. Gen5 neurite outgrowth analysis on brightfield images
identified soma and neurites at each time point as depicted in
the bottom panels of Figure 2B.
Neurite outgrowth was quantified over time using the Gen5
neurite outgrowth module and is presented as total neurite
length over time for both phase contrast and brightfield. The
mean total neurite outgrowth length for all untreated wells
(n = 12) is presented in Figure 2C for both imaging methods.
Phase contrast imaging generally provided increased contrast
for neurite detection, however, similar outgrowth results
were quantified using both imaging methods, suggesting
that brightfield imaging strategies may also be suitable for
neurite outgrowth analysis with this platform. For simplicity,
throughout the remainder of this application note, neurite
outgrowth analysis is limited to phase contrast imaging.
Figure 1. Generalized workflow for automated, label-free neurite outgrowth assays with the Agilent BioTek BioSpa 8 live cell analysis system. The system supports
label-free Image collection for multiday outgrowth assays for up to eight microplates. Agilent BioTek Gen5 software performs image analysis to quantify neurite
outgrowth, as well as the downstream data analysis needed to evaluate kinetic responses and concentration-dependent treatment effects.
5
Figure 2. Automated image capture and kinetic outgrowth analysis. (A) Top: Phase contrast images of iPSC-derived neurons at three time points after plating as
indicated. Bottom: Phase contrast images from the top row after neurite outgrowth analysis with soma (yellow) and neurite skeleton (cyan) overlay. Scale bars
correspond to 200 µm. (B) Top: Brightfield images from the same field of view as shown in panel A. Bottom: Brightfield images from the top row after neurite
outgrowth analysis with soma (yellow) and neurite skeleton (cyan) overlay. Scale bars correspond to 200 µm. (C) Total neurite length plotted over five days of
outgrowth evaluated for phase contrast (red) and brightfield (green) images for all iCell GlutaNeuron control wells (including representative images shown). Data
points correspond to mean of technical replicate wells (n = 12) and standard deviation. (D) Average per-cell neurite length for all control well images. Data points
(red) correspond to mean of technical replicates (n = 12) and linear fit to mean (black line overlay) was used to determine average neurite outgrowth rate between
24 and 120 hours. (E) Total neurite outgrowth evaluated over the first 6 hours after plating by kinetic imaging every 10 minutes. Data points correspond to mean
of technical replicate wells (n = 3) and standard deviation. (F) Average per-cell neurite length evaluated over the first 3 hours in culture. Data points indicate mean
of technical replicate wells (n = 3) and linear fit to mean data (black line overlay) was used to determine average neurite outgrowth rate over the first three hours
of culture.
Kinetic evaluation of label-free outgrowth
To evaluate the rate of outgrowth, the per-cell average
neurite length was calculated (Figure 2D) and fit using linear
regression over the period of 24 to 120 hours (Figure 2D,
black lines fit overlay). The average per-cell outgrowth rate
over this time corresponded to ~ 15 µm/day. The outgrowth
assay shown in Figure 2, panels A to D, was intended to
capture changes in outgrowth over several days, so the
imaging interval was set to collect images every three hours.
However, iCell GlutaNeurons demonstrated an apparent jump
in outgrowth between the initial image and the next imaging
time point taken three hours later (Figure 2C and D).
To explore this initial increase, a separate experimental kinetic
evaluation (Figure 2E) was performed at a higher imaging
frequency to capture the time course of this early outgrowth.
Images captured at 10-minute intervals confirmed that iCell
GlutaNeurons exhibited a rapid and continuous increase in
outgrowth over the first three hours in culture. Gen5 analysis
of the average neurite outgrowth length over the first three
hours in culture yielded per-cell outgrowth rates of
~ 500 µm/day (Figure 2F). After the initial early outgrowth
period, neurons transitioned to a gradual outgrowth phase
(15 µm/day, Figure 2D) over the next days in culture.
6
Figure 3. Plate layout and overview. Drugs were applied in increasing
concentrations, and plots of total neurite outgrowth length over time
(red) are displayed in the Agilent BioTek Gen5 software plate view for
all wells.
Kinetic evaluation of neurite outgrowth in response to
drug treatment
Kinetic analysis of outgrowth for both enhancers and
inhibitors of neurite outgrowth was conducted over a five-day
time course. The plate view display in Figure 3 provides a
high-level graphical representation of the outgrowth kinetics
for each of the 96 wells throughout the experiment.
Quantification of the total neurite length over time was
plotted for the highest two drug concentrations and untreated
controls (Figure 4), with representative phase contrast image
and Gen5 neurite outgrowth analysis overlaid for each drug at
the final time point tested.
Staurosporine is a broad-spectrum kinase inhibitor associated
with multiple cellular effects including apoptosis and neurite
outgrowth across multiple neuronal models.8-9 A complex
effect of staurosporine on iPSC-derived neuron culture can
be observed in Figure 4A. The highest concentration of
staurosporine tested (1 µM) initially promoted increased
neurite outgrowth over the first hours of application
(Figure 4A, green trace). Initial outgrowth, however, was
followed by a dramatic reduction in total neurite length, owing
to generalized cell death. A rapid transition from outgrowth
enhancement to cell death has previously been reported for
high concentrations of staurosporine.8
Application of 0.3 µM
staurosporine, however, demonstrated a rapid and sustained
enhancement of neurite outgrowth without overt neurotoxicity
(Figure 4A, blue trace).
Blebbistatin is a myosin II inhibitor that is thought to promote
outgrowth through inhibition of retrograde actin flow.10
Treatment with 10 µM blebbistatin in this assay showed a
small increase in outgrowth but was not significantly
different from the control outgrowth, as evaluated by Z-score
(Z-score < 2).
6BIO is an inhibitor of the glycogen synthase kinase 3β
protein thought to be involved in multiple signaling events
of neuron outgrowth.11 Treatment of iCell GlutaNeurons at
the highest concentration of 6BIO (10 µM) resulted in an
immediate reduction in outgrowth followed by a plateau in
growth across the time frame tested (Figure 4B, green trace).
Lower concentrations of 6BIO (3 µM) resulted in similar
outgrowth suppression (Figure 4B, blue trace).
Triptolide is a diterpene compound identified from a
traditional Chinese medicinal herb that is under investigation
for multiple anticancer effects.12 Treatment with triptolide
in iCell GlutaNeurons, resulted in dramatic inhibition
of outgrowth over time as shown for the two highest
concentrations tested (Figure 4D). It was noted, however, that
the onset of outgrowth inhibition appeared to be relatively
delayed compared to the other effectors of outgrowth tested
here (staurosporine and 6BIO), and so comparisons of
treatment onset timing were further evaluated.
Neurite outgrowth drug-response timing
Average neurite length over time was compared for different
drug responses and untreated control wells, as shown in
Figure 5A. The effect of staurosporine and 6BIO on average
neurite length were observed even at the first time point
after drug addition. The rapid effect onset is consistent with
the mechanism of action for each drug: both drugs target
the signaling pathways directly involved in regulating the
cytoskeletal structures required for neurite stability and
extension.8,9,11 By comparison, the inhibitory effect of triptolide
on neurite outgrowth was relatively delayed: total neurite
length remained similar to control values up to ~ 24 hours
after triptolide addition. After ~ 24 hours, neurite length
gradually decreased through the rest of the experimental time
frame. After 72 hours of exposure (corresponding to the 96-
hour image time point) triptolide had inhibited average neurite
length to a greater extent than treatment with 6BIO.
7
Figure 4. Kinetic responses of iPSC-derived neurons to outgrowth enhancers and inhibitors. (A to D) Example phase contrast image with soma (yellow) and
neurite (cyan) detection overlays for neurons treated with small-molecule drugs as indicated. Image corresponds to the final kinetic time point (120 hours). The
Agilent BioTek Gen5 software plot for total neurite length over time for highest (green) and second highest (blue) drug test concentration and control (red). Data
points indicate mean and standard deviation of technical well replicates.
To quantify response onset, Gen5 software was used to
evaluate the time point corresponding to the maximum rate
of change in neurite length for each condition. The maximum
rate of change was calculated over a 9-hour time window
(three imaging data points). The maximum rate evaluation
yielded an average posttreatment response timing that
corresponded to 3 hours for staurosporine, 2 hours for 6BIO,
and 46 hours for triptolide.
Figure 5. Treatment response timing comparison. (A) Average neurite length per cell over time for treatments as indicated (Prism GraphPad visualization). Data
points represent mean and standard error of technical replicates (n = 3) for each condition. Grey arrow indicates drug addition time. (B) Average neurite branches
over time for the same treatments in panel A (Prism GraphPad visualization). Data points represent mean and standard error of technical replicates (n = 3) for
each condition. Grey arrow indicates drug addition time.
In addition to neurite length, the average branch counts
were visualized over time for the same treatment conditions
(Figure 5B). A similar response profile for average neurite
branches was observed across each drug treatment when
compared to average neurite length. The covariation of these
two distinct morphological parameters is consistent with
previous observations that treatments altering neurite length
often produce a similar effect on branching-related metrics.8
8
Figure 6. Dose–response evaluation from label-free neurite outgrowth
analysis over the final 12 hours of kinetic imaging. (A) Dose–response
curves for total neurite length. Data points correspond to mean and standard
deviation for technical replicates (n = 3) and corresponding four-parameter
fits (dashed lines). (B) Dose–response curves for average neurite branches
per cell. Data points correspond to mean and standard deviation for
technical replicates (n = 3) corresponding four-parameter fits (dashed lines).
(C) Dose–response curves for average neurite branches per cell. Data points
correspond to mean and standard deviation for technical replicates (n = 3)
and corresponding four-parameter fits (dashed lines).
Neurite outgrowth effector dose–response analysis
Drug effects on neurite outgrowth were also evaluated for
concentration-dependent effects through dose–response
analysis across multiple outgrowth metrics (Figure 6). For
each metric, the average value over the final 12 hours of the
kinetic imaging session was calculated in Gen5 software and
used to generate the dose–response curves. This timeframe
was chosen to represent the final treatment effect for
analysis purposes. However, the region of the kinetic dataset
chosen for analysis is highly customizable in Gen5 software,
and supports both mean and integral (area-under-the-curve)
evaluations.
Figure 6A displays the Gen5 dose–response analysis for
total neurite length. Fitting provided EC50/IC50 estimates for
staurosporine (0.034 µM), 6BIO (0.86 µM), and triptolide
(0.0078 µM). As previously noted for staurosporine8
and
indicated in Figure 4A, the total neurite length increased
with treatment concentration until the highest concentration
tested, where outgrowth was suddenly reduced, owing
to cell death. Accordingly, the highest concentration was
not included for fitting purposes in order to evaluate the
remaining data (open circles, Figure 6A). As shown in
Figure 4B, blebbistatin did not demonstrate a significant
response up to the 10 µM concentration tested here.
Dose–response analysis was also performed for branchingrelated neurite outgrowth metrics, as shown in Figure 6,
panels B and C. Overall, treatments that decreased total
neurite length were also associated with decreases in both
the average number of branches per cell (Figure 6B) as well
as the average neurite count per cell (Figure 6C). Fits of the
average neurite branches curves in Figure 6B provided
EC50/IC50 estimates for 6BIO (0.359 µM) and triptolide
(0.0039 µM), but not for staurosporine, as the response did
not saturate and conform to a four-parameter fit. Significant
changes in neurite counts per cell were observed only for the
inhibitors in Figure 6C and corresponded to IC50 estimations
for 6BIO (3.1 µM) and triptolide (0.004 µM).
9
Conclusion
Label-free imaging enables kinetic investigations in neuron
culture while also avoiding the phototoxic and cytotoxic
effects of fluorescence-based approaches. The Agilent
BioTek BioSpa live cell imaging system for label-free neurite
outgrowth assays enables high-throughput investigations
with benchtop accessibility. The approach presented in this
application note demonstrates quantitative kinetic neurite
outgrowth analysis using multiple modes of label-free imaging
techniques. Both phase contrast and brightfield transmitted
light images captured on the Agilent BioTek Cytation 5 cell
imaging multimode reader enabled sensitive, kinetic analysis
of culture outgrowth over time. Other Cytation models, as well
as the Agilent BioTek Lionheart FX automated microscope,
are expected to generate comparable results. iPSC-derived
neuron cultures were maintained throughout the five-day
growth period by the Agilent BioTek BioSpa 8 automated
incubator which maintained environmental conditions and
delivered samples to the integrated imaging system. This
automated robotic incubator system can maintain up to eight
microplates simultaneously, increasing throughput for longterm image-based studies.
Agilent BioTek Gen5 software automated both image
acquisition and analysis through a single interface. Imageprocessing steps, such as kinetic image alignment, were
automatically handled before analysis. The Agilent BioTek
Gen5 neurite outgrowth module automatically detected
and analyzed both neuron soma (cell bodies) and neurite
processes to provide multiple phenotypic parameters relevant
for culture outgrowth analysis. Kinetic analysis of neurite
outgrowth metrics, such as outgrowth length, was evaluated
to determine average outgrowth rates, as well as maximum
rate of change to quantify drug-response timing. In addition
to time-dependent analysis, dose–response analysis
capabilities provided EC50/IC50 quantification of neurite
outgrowth parameters to evaluate concentration-dependent
treatment effects.
Label-free imaging and analysis capabilities on the Agilent
BioTek live cell analysis system complement the imager’s
multimodal, fluorescence-based approaches to provide a
flexible solution for a spectrum of image-based analyses
methods. The combination of automated live-cell and endpoint analysis provides a single-instrument solution
enabling high-throughput studies across time scales and
imaging modes.
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Published in the USA, June 18, 2024
5994-7556EN