Real-Time Metabolic Analysis in 3D Brain Models
App Note / Case Study
Published: October 16, 2025
Credit: Agilent
Understanding cellular metabolism in complex 3D brain models is crucial for revealing insights into aging, disease and neurodegeneration. Traditional methods using 2D cultures or isolated mitochondria often miss the physiological nuances of brain tissue.
This app note highlights an optimized system for assessing mitochondrial respiration and glycolysis in brain tissue slices. It introduces a workflow that enables real-time, high-sensitivity metabolic profiling with consistent, reproducible results.
Download this app note to explore:
- How to capture robust oxygen consumption and acidification data in 3D brain models
- Tissue preparation and assay optimization strategies that enhance data quality
- A proven system for improving accuracy in mitochondrial studies using ex vivo tissue
Application Note
Cell Analysis
Authors
Pamela Swain,
Suzanne Armitstead, and
Veronica Silva
Agilent Technologies, Inc.
Abstract
Neuronal development and function are among the most energy demanding
biological processes in the body. The brain requires a constant, ready source of
energy to function properly, relying on both mitochondrial respiration and glycolysis
to continually supply ATP to meet this demand. Disruption of oxygen metabolism
and mitochondrial function are consistent pathological features of various aging
and neurodegenerative diseases associated with cognitive decline. Different brain
regions and structures have differing functions and energy demands. To study
mitochondrial metabolism in the brain, researchers often use cultured neurons or
isolated mitochondria from brain tissue. These techniques require large amounts of
tissue and do not capture the complex tissue microenvironment, or the interplay of
the multiple cell types present in brain tissue.
In this application note, we introduce the Agilent Seahorse XF Flex analyzer together
with a streamlined workflow that allows for detection and quantitative assessment
of energy metabolism in small biopsy punches of distinct brain regions. We provide
examples of metabolic data from brain tissue samples using the Agilent Seahorse
XF Flex 3D Capture Microplate-L and the Agilent Seahorse XF 3D Mito Stress Test
kit. In addition, techniques for preparing and optimizing brain tissue used in the
Seahorse XF assays and analyzing data are discussed.
The Agilent Seahorse XF platform is an integrated label-free solution that seamlessly
combines the Seahorse XF analyzer, sensor cartridges, assay kits, and software to
deliver real-time functional metabolic data. This platform provides key parameters,
such as oxygen consumption rate (OCR) and extracellular acidification rate (ECAR),
which are vital indicators of mitochondrial health, toxicity, glycolysis, and overall
cellular (dys)function.
A Superior System for Real-Time
Metabolic Analysis with Brain Tissue
and Other 3D Models2
Introduction
The demand for tools and reagents for the analysis of 3D
cellular models is growing rapidly. Precision tissue slices,
organ-on-a-chip, bioprinting, and organoids are key examples
of these 3D models. Precision tissue slices are noteworthy
because they are accessible, inexpensive, and include
supportive cell types, preserving the natural environment of
the tissue. Tissue samples are used extensively in research
and drug screening due to their ability to mimic the in vivo
environment and their ability to provide a more accurate
representation of physiology compared to traditional 2D cell
cultures.1,2,3,4
The Agilent Seahorse XF analyzer is the gold standard
method for assessing metabolic function. It measures oxygen
consumption rate (OCR) and extracellular acidification rate
(ECAR), which reflect mitochondrial respiration and glycolysis,
respectively. While this technology has been fundamental for
understanding how metabolism affects cellular functions and
drives disease progression, the data obtained mostly used
two-dimensional cultured cells or isolated mitochondria, and
may not fully capture the complex environment of tissue.
To address this, researchers have developed ex vivo methods
to measure mitochondrial respiration using tissue slices
including brain. These approaches provide a physiological
representation of the cellular environment, including
intercellular coordination and metabolic coupling among
different cell types. Understanding brain bioenergetics
has evolved from a simplistic view to a dynamic model of
metabolic reprogramming and adaptation. This involves
mitochondria utilizing various energy substrates and
allocating ATP production between glycolysis and oxidative
phosphorylation. Studies have shown metabolic shifts in glial
cells upon inflammatory activation in aging and pathological
conditions.5,6,7,8 These studies provide insights into brain
tissue workflows, but they employ a variety of Seahorse
XF instrumentation and consumables that have not been
optimized for tissue.
In this application note, we introduce a new Seahorse XF
system for the interrogation of energy metabolism in 3D
models using brain tissue slices as an example. This system
incorporates the Seahorse XF Flex 3D Capture Microplate-L,
the Seahorse XF 3D Mito Stress Test kit, a vibratome tissue
slicer, and the Seahorse XF Flex analyzer (Figure 1).
Figure 1. The Agilent Seahorse XF Flex 3D tissue workflow illustration, highlighting the key steps in the assay.3
Component Concentration (mM)
NaCl 120
KCl 3.5
CaCl
2 1.3
Mg2Cl2 1.0
KH
2PO4 0.4
HEPES 5
D-glucose 10
Table 1. Artificial cerebral spinal fluid composition. Adjust the buffer pH to
7.4 and store at 4 ºC. Oxygenate for 1 hour before use.
The Seahorse XF Flex analyzer features improved sensitivity
and precision with advanced experimental design and data
analysis elements. The 3D capture plate-L is a 24-well plate
and has a sample chamber at the bottom of each well that
is 250 µm deep and 3.15 mm in diameter. These dimensions
allow for the analysis of tissue slices of the same or smaller
sizes. The plate is also provided with a capture ring for
each well, which is designed to hold tissue material in place
and can form a transient microchamber of 8.5 µL when
measurements are taken. The mesh on the capture ring has
a large pore size, allowing for sufficient reperfusion of gases
and chemicals, as well as recovery of medium conditions
during Seahorse XF assays. The Seahorse XF 3D Mito Stress
Test kit contains modulators of the electron transport chain
and supports study models that require high doses, such as
tissue samples and small organisms. The system provides
enhanced sensitivity, reproducibility and improved usability.
Experimental
Tissue preparation and set up of the Seahorse XF Flex
3D Capture Microplate-L
Nine-week old female Sprague Dawley rats were obtained
from Taconic Biosciences (SD-F, MPF health status) and
acclimated several days at Hooke Laboratories where the
rat brain was dissected on the morning of the Seahorse XF
assays. After dissection, rat brains were immediately placed
in chilled and oxygenated artificial cerebral spinal fluid (aCSF)
buffer (Table 1) and delivered to the Agilent laboratory, in
Lexington, MA, where the tissue was prepared for Seahorse
XF assays.
Before processing the tissue, 100 mL aCSF supplemented
with 0.6 mM pyruvate, 100 mL Seahorse XF aCSF
supplemented with 0.6 mM pyruvate and 0.4% fatty acid free
BSA, and 20 mL aCSF supplemented with 7.5 mM pyruvate,
pH 7.4 (see Table 2A, 2B, and 2C, respectively), were warmed
up. The pH was adjusted to 7.4 at 37 ºC and filter sterilized
before use. 100 µL of the buffer in Table 2A was added to
each well in the 3D capture plate-L and set aside until tissue
punches were ready.
Component Final (mM) Stock Solution (mL)
aCSF Buffer 198.8
100 mM Pyruvate 0.6 1.2
pH 7.4
Table 2A. Agilent Seahorse XF aCSF assay media with 0.6 mM pyruvate
(no BSA).
Component Final (mM) Stock Solution (mL)
aCSF Buffer 99.4
100 mM Pyruvate 0.6 mM 0.6
200 mg/mL BSA 4 mg/mL 2.0
pH 7.4
Table 2B. Agilent Seahorse XF aCSF assay media with 0.6 mM pyruvate and
0.4% BSA.
Upon arrival, the brain tissue was sliced using a
Compresstome VF-510-0Z Vibrating Microtome (Precisionary
Instruments, LLC) in chilled and oxygenated aCSF buffer,
following the manufacturer's recommendations (also see
Figure 2 for key steps). The Compresstome settings used
to prepare the brain slices were Speed 2 and Oscillation 4.
Tissue slices were transferred to a 6-well plate or petri dish
containing oxygenated aCSF buffer and with a punch pad
(TedPella; catalog number 15087-1) placed at the bottom of
each well or petri dish. Tissue punches were then produced
using a biopsy punch tool of desired size (TedPella; catalog
number 15110-10, 15110-15, or 15110-20), and delivered to
the 3D capture plate-L containing 100 µL buffer per well.
Component Final (mM) Stock Solution (mL)
aCSF Buffer 18.5
100 mM Pyruvate 7.5 1.5
pH 7.4
Table 2C. Agilent Seahorse XF aCSF assay media with 7.5 mM pyruvate
(no BSA).4
Figure 2. Illustration of key steps involved in the preparation of rat brain tissue slices, using the Compresstome from Precisionary Instruments, LLC.
No tissue was placed in wells A1 and D6 as they were used as
background wells. Tissue punches were centered in each well.
Then, one 3D capture ring was placed in each well, including
background wells, with mesh side down and pushed firmly
down to the well bottom. Each well was then topped up with
the buffer in Table 2B (with BSA) to a total volume of
600 µL. It was ensured that no bubbles were trapped in the
wells. Then the 3D capture plate-L with tissue samples was
placed in a 37 ºC non-CO2 incubator for 45–60 minutes
before the assay.
Perform the Seahorse XF 3D Mito Stress Test
Seahorse XF assays were performed following the
instructions described in the Agilent Seahorse XF 3D
Mito Stress Test kit User Guide, including preparation of
compounds, reagents, and sensor cartridges. The Seahorse
XF buffer in Table 2A was used to prepare oligomycin A and
rotenone/antimycin A injection solutions and the Seahorse
XF buffer in Table 2C was used to prepare FCCP injection
solution. The Seahorse XF 3D Mito Stress Test template
provided in the Agilent Seahorse Wave Controller software
was used and adjusted when needed. This template is
optimized for tissue samples with default setting of a
3-minute mix, 0-minute wait, and 3-minute measure for
each cycle. The number of cycles is set to 3 for basal, 15 for
oligomycin A, 3 for FCCP, and 8 for rotenone/antimycin A
(Figure 3).
Figure 3. Agilent Seahorse XF 3D Mito Stress Test template in the Agilent
Seahorse XF Flex Controller software.
Protein quantification
At the conclusion of the Seahorse XF assay, medium was
removed from each well of the 3D capture plate-L, followed
by three washes with PBS to remove the BSA present in the
aCSF buffer. The background wells were also washed and
used as background controls for the protein assay. After the
third wash, 100 µL of RIPA lysis buffer (Thermo Scientific)
containing protease inhibitor (Thermo Scientific) was added
directly to the bottom of each well. The plate was then
wrapped in parafilm and frozen at –80 ºC overnight. The plate
was thawed and tissue slices were homogenized by pipetting
the RIPA buffer through the mesh several times until tissue
was lysed. Next, the plate was centrifuged at 250 g for 10
minutes and 25 µL of lysate was transferred in duplicate to a
96-well assay plate. This was done carefully with an electronic
pipet so that residual volume remained in pipet and no air
or bubbles were introduced to 96-well assay plate. A BSA
standard curve was prepared and 25 µL of each standard was
added to assay plate along with background controls.5
Materials Vendor Part Number
Seahorse XF Flex 3D Capture
Microplate-L
Agilent Technologies
103864-100
Seahorse XF 3D Capture
Screen Insert tool 101135-100
Seahorse XF 3D Mito Stress
Test kit 103016-100
Seahorse XF 1.0 M glucose
solution 103577-100
Seahorse XF 100 mM
pyruvate solution 103578-100
Seahorse XF Flex analyzer S7851A or S7851AN
Cytation 1 imaging system
Artificial Cerebral Spinal Fluid
(aCSF)
Made fresh within 48 h of assay day, pH 7.4, sterile filtered
and stored at 4 ºC. Oxygenate for 1 hour before use.
Compresstome VF-510-0Z
Vibrating Microtome
Precisionary Instruments
VF-510-0Z
Crazy glue VF-VM-GLUE-CANAL
2% Agarose tablets VF-AGT-VM
1, 1.5, and 2 μm Tissue
punches with plungers TedPella
15110-10, 15110-15, 15110-20
Cutting mat 15087-1
RIPA lysis buffer
Thermo Scientific
89900
Protease inhibitor 87786
Pierce BCA Assay 23225
Figure 4. Representative well images
with the methods of area determination.
The inner black area indicates the
location of tissue sample. (A.) Example
using the measurement tool within
the Agilent BioTek Gen5 software to
determine the diameter of the tissue
sample in both X and Y axis. (B.)
Example of Gen5 area measurement
in red which automatically determines
diameter and area of sample but only if
the tissue samples are in center of well
and not impacted by the edge of the
sample chamber (visible black ring).
A.
B.
Total protein content was determined using the Pierce
BCA Assay (Thermo Scientific) following manufacturer’s
instructions. Briefly, 200 µL of prepared assay reagent was
added to each well and plate was covered with a plate seal,
and mixed on a plate shaker for 0.5–1 minute. The plate
was incubated at 37 ºC for 30 minutes and absorbance
at 562 nm was read using an Agilent BioTek Synergy H1
multimode reader. The standard curve was used to determine
the total protein content of each unknown sample, which was
used to normalize Seahorse XF assay data.
Determination of tissue surface area
The Agilent BioTek Cytation 1 cell imaging multimode reader
was used to acquire high-contrast brightfield images of the
tissues in the 3D capture plate-L prior to the installation of
the capture ring. Gen5 software was used to determine the
average diameter or area for each tissue disc (see illustration
in Figure 4).
XF 3D Mito Stress Test data analysis
Analysis and data transformation of the Seahorse XF 3D
Mito Stress Test result files were performed using Seahorse
Analytics, a web-based software platform. Using kinetic OCR
measurements, dedicated features (widgets) in Seahorse
Analytics automatically calculated key 3D Mito Stress Test
assay parameters.
Materials and equipment
Results and discussion
Assay optimization requisition
To effectively examine metabolic and bioenergetic function
effectively using Agilent Seahorse XF analyzers, it is essential
to first determine the appropriate amount of tissue material
required to perform Seahorse XF assays and the optimal
concentrations for all modulators.
The 3D capture plate-L has a sample chamber of 250 µm
deep by 3.15 mm in diameter at the bottom of each well.
Therefore, tissue sizes should not exceed 250 µm in thickness and 3 mm in diameter. It is recommended to leave some
space in the sample chamber to allow sufficient gas and
nutrient exchange between the tissue and medium.
During assay optimization, 1, 1.5, and 2 mm diameter brain
tissue discs with 200 µm thickness were tested using the
Seahorse XF 3D Mito Stress Test kit. As shown in Figure 5,
the punch sizes showed linear relationship to OCR values,
indicating the sizes in this range can be appropriate or
acceptable to move forward.6
To determine the optimal size, the O2 and proton level data
must be examined using a full Mito Stress Test (MST),
essentially to include the full range of the signals in an assay.
In general, the starting basal O2 level should be around
152 mmHg, and not below 100 mmHg. Also, at the start of
each measurement, the O2 level must be fully recovered, and
at the end of each measurement, the O2 level should not fall
below 40 mmHg. This is because extended period of exposure to extremely low O2 levels (hypoxia) can have adverse
impact on tissue health. In addition, the pH level should be
within the linear range for the sensors between pH 7.5
(+/- 0.1) to 6.5 (+/- 0.1). Outside this range, measurement
accuracy can be compromised.
Figure 5. OCR signal correlates to tissue punch sizes. The images below the
chart were taken using an Agilent BioTek Cytation 1 cell imaging multimode
reader, showing the tissue discs under the capture ring in the well.
For the Seahorse XF Flex analyzer, the instrument protocol
for mixing height and speed is optimized for the 3D capture
plate-L, allowing medium condition to fully recover to the
original state at the beginning of each measurement. Figure 6
is an example of acceptable data, showing O2 levels of around
130 mmHg at the start of the assay and full O2 level recovery
at the beginning of each measurement (Figure 6A). The pH
level data also falls withing the range of 7.5 (+/- 0.1) to
6.5 (+/- 0.1) (Figure 6B).
A.
B.
Figure 6. Examples of appropriate levels of oxygen consumption (A) and pH
level data (B).
The optimal modulator concentration for obtaining robust
results is tissue dependent and a titration experiment for each
modulator must be performed for each tissue type during
assay optimization. This titration is especially important
for FCCP as too low or too high concentrations can lead to
diminished response and underestimation of the maximal
respiratory capacity. Buffer conditions can also affect optimal
modulator concentration, such as inclusion of BSA or serum
in assay medium. Therefore, an optimization experiment is
also needed when medium conditions are changed. For high
respiring tissue types, higher concentrations of substrate,
such as pyruvate and glucose, may be added in the FCCP
injection buffer to minimize substrate depletion during assay.7
Figure 7 is an example of an FCCP concentration optimization
experiment using the Seahorse XF 3D Mito Stress Test kit and
rat cortex tissue discs, 200 µM thick and 2 mm in diameter.
In this test, all samples were injected with oligomycin A
at a final concentration of 30 µM following three baseline
measurements. FCCP at varying concentrations was injected
after twenty measurements post oligomycin A injection. The
assay buffer contains approximately 0.32% BSA. The data
shows that all FCCP concentrations increased respiration, and
the highest OCR is observed at 20 µM. Therefore, the optimal
concentration for FCCP is determined to be 20 µM.
A.
B.
Figure 7. FCCP optimization. All experimental groups were injected with
oligomycin A at 30 µM final concentration after three basal measurements
as indicated in the kinetic graph. A. OCR at measurement 24, the first
measurement after FCCP injection. Concentration indicated in the graphs
are final concentrations in the well. B. OCR Kinetic graph. n=5-6.
Optimization experiments for oligomycin A and rotenone/
antimycin A were also performed (data not shown). Based on
the results, it was determined that the optimal concentrations
for oligomycin A and rotenone/antimycin A were 30 µM and
10 µM, respectively.
System performance evaluation
The results of a Mito Stress Test for rat brain tissue, using
the new system incorporating the 3D capture plate-L, the
3D MST kit, and Seahorse XF Flex analyzer and following
the optimized conditions described in the previous section
is presented in Figure 8. As shown, a robust basal OCR and
decent responses kinetics to all modulators were observed
(Figure 8A). All key parameters indicating mitochondrial
function were also obtained (Figure 8B).
A.
B.
Figure 8. Agilent Seahorse XF Mito Stress Test with rat brain tissue discs
(200 µm × 2 mm) performed using the 3D capture plate on XF Flex analyzer.
A. OCR Kinetic graph. B. Key parameters of mitochondrial function. n=12
MST wells. n=3 tissue control wells.8
In contrast, the same assay performed with the Seahorse
XF islet capture microplate on the Seahorse XFe24 analyzer
showed very small or no responses to modulators (Figure 9).
This side-by-side comparison clearly demonstrates the
improved sensitivity and data robustness provided by the new
system that incorporates the 3D capture plate-L and Seahorse
XF Flex analyzer. The data also shows that the response
to oligomycin A is much slower than the typical response
observed in cultured 2D cells, therefore, it is recommended to
incorporate a minimum of 10 measurements post oligomycin
A injection. It is also recommended that a tissue control
(without adding modulators) is added for each assay to
monitor the stability of respiration signals throughout the
assay during assay optimization.
Figure 9. OCR kinetic graph of the Agilent Seahorse XF Mito Stress Test
with rat brain tissue discs (200 µm × 2 mm), performed using the Agilent
Seahorse XF islet plate on the Agilent Seahorse XFe24 analyzer. n=12 MST
wells. n=3 tissue control wells.
Tissue preparation considerations
To perform a successful Seahorse XF real-time metabolic
assay, is it crucial to use tissue materials that remain healthy
and viable for hours to ensure functionality throughout the
assay. Although, conditions suitable for sample preparation
may vary depending on tissue types, cold temperatures are
often used. For instance, brain and liver tissues are usually
handled in ice-cold aCSF or Krebs-Henseleit Buffer (KHB),
respectively, which is oxygenated with either 100% O2 or
95% O
2:5% CO2. These conditions can potentially reduce the
impact of injury from slicing. Adipose tissue, on the other
hand, can be prepared at room temperature. Regardless,
the tissue materials should be prepared as soon as possible
after dissection. It is advisable to consult with experts who
are experienced in handling the specific tissue type for other
assay types.
It is also important to obtain uniform tissue sizes to achieve
consistent assay results. Although the literature has reported
several methods to generate small tissue pieces, such as
using surgical scissors, biopsy punch tools, and various types
of tissue cutters, we recommend the use of a vibratome
tissue slicer, such as the Compresstome VF-510-0Z from
Precisionary Instruments LLC, together with a biopsy punch
tool. This method can quickly produce precise tissue samples
in large quantities while minimizing cellular damage. The
Compresstome VF-510-0Z is easy to use and can generate
viable tissue slices with consistent thickness in the 150 to
200 µm range, which is the thickness range recommended for
performing Seahorse XF assays. It is found that for some
tissue type, such as brain tissue, allowing tissue slices to rest
or acclimate at room temperature in oxygenated buffer before
punching the tissue into discs can help with data consistency.
Following tissue slicing, a biopsy punch tool is employed to
generate consistent tissue samples or discs. Tissue discs
from desired tissue regions can be selected for studying
spatial differences in metabolism. Biopsy punch tools with
built-in plungers are preferred as they allow easy delivery
the samples to the center of the sample chambers in the 3D
capture plate-L. A soft pad under the tissue slices is also
recommend when punching the slices, as this allows for a
clean cut while forcing the tissue disc into the plunger, so the
tissue disc can be easily transferred and delivered to the
sample chambers in the 3D capture plate-L. In addition,
general-use paintbrushes can assist in the handling of
delicate tissue slices and discs. Soft bristles help prevent
damage to tissue slices during transfer.
The working volume for the 3D capture plate-L ranges from
600 to 1000 µL per well. However, we recommend starting
with an initial volume of 50 to 100 µL of medium in each well
before placing tissue samples. This small volume helps to
keep the tissue sample in the well center and facilitates the
installation of the 3D capture ring. After the installation of the
capture ring, it is recommended to capture images of the
tissue samples in the wells using a brightfield imaging
system (4×), to check for bubbles. Bubbles trapped under the
mesh may lead to abnormal O2 and pH signals, resulting in
highly variable rate data. Bubbles should be eliminated before
performing a Seahorse XF assay. The images also help to
evaluate tissue placement, ensuring all wells have tissue
samples as intended. Figure 10 is a brightfield image of a 3D
capture plate-L loaded with tissue and capture rings,
showing that in most wells, tissue disc placement was
appropriate, except for well A3.9
Figure 10. Brightfield Images of Agilent Seahorse XF Flex 3D Capture
Microplate-L. 4× BFHC montage images of 2 mm discs of rat brain cortex
tissue from 200 µm slice, after 3D capture ring installation.
Half of the tissue disc in this well is pinched under the ring.
Examination of the OCR signal shows that the OCR value
from this well is less than 50% of the average value for
the plate.
Data analysis and normalization options
Analysis of Seahorse XF metabolic assay data can be performed using the Agilent cloud-based software application,
the Seahorse Analytics. It provides desktop-like interactivity with an intuitive interface and is available at any time
and from anywhere in the world. A 3D Mito Stress Test
kit companion view is available with widgets specifically
designed for assays with 3D models. This companion view
provides the option of data analysis without oligomycin
injection.
Normalization of Seahorse XF metabolic assay data is
important in interpretation of assay results. There are
several options that can be considered for 3D samples,
including total protein, sample size or weight, and
percentage of baseline signal (baselining). The optimal
method, however, depends on the 3D models being
studied, study objectives, as well as assay conditions
(such as medium composition).
Quantification of total protein can be a convenient method
as tissue samples in the assay plate can be stored in lysis
buffer at –80 ºC for days after the Seahorse XF metabolic
assay. It is important that tissue material is properly lysed.
If assay medium contains BSA or serum, a washing step
is required. Figure 11 compares the data normalized with
total protein and the not normalized data. As shown, two
samples in the blue experimental group exhibited reduced
OCR values throughout the assay.
A.
B.
Figure 11. OCR kinetic graph of an Agilent Seahorse XF Mito Stress Test
with rat brain tissue discs (200 µm × 2 mm), performed using the 3D capture
plate-L on the Agilent Seahorse XF Flex analyzer. Each line represents an
individual well. A. Not normalized data. B. Normalized data based on total
protein per well.
After normalizing to total protein, the OCR values were
adjusted to similar levels as other samples in the same
group. Keep in mind that this method not only measure
intracellular protein content but also is affected by the
amount of extracellular matrix protein present in
tissue materials.
Normalization by sample size/area or weight can also be
readily achieved by automated imaging systems. It is commonly used when methods of generating consistent tissue
samples are not available. Figure 12 is an example of data
normalized to tissue surface area. This is the exact same
data from Figure 5 where it shows that the OCR values
range from 190 to 730 pmol/min among sizes of 1, 1.5,
and 2 mm. The normalized data shows that OCR values
per unit of area among these tissue sizes are within 30%.10
Figure 12. OCR signals normalized to sample area, using the un-normalized
raw data from Figure 5.
In some cases, Seahorse XF assay data can be normalized by baseline signal or any measurement in the kinetic
traces. So, all other measurements are expressed as a percentage of the baseline signal. This method is applicable
when a comparison of responses to an acute treatment to
modulators is needed. It is especially useful when tissue
materials vary among replicates within the same
experimental group.
Figure 13 is an example of the baselined result of OCR
kinetic graph using the same raw data from Figure 8A.
As shown, the error bars for all the data points are smaller
compared to Figure 8A, and the data is much cleaner
than the original not baseline data. This method can be
easily performed using the “Baseline“ button in the
Seahorse Analytics or in the Wave software.
Figure 13. Baselined OCR kinetic graph of Figure 8A.
Conclusion
Agilent Seahorse XF technology revolutionized bioenergetic measurements in live cells by enabling metabolic
analysis in real time. This enabling technology has been
fundamental for gaining the understanding of how metabolism drives disease progression and helping advance
therapeutic development.
The Seahorse XF Flex analyzer along with purposedesigned 3D capture plate-L expands this revolutionary
system beyond traditional two-dimensional cell cultures,
empowering physiologically relevant discoveries with
three-dimensional models, such as tissues materials. It is
demonstrated with brain tissues that this system provides
the necessary sensitivity to gain robust tissue respiration
signal and clear responses to mitochondrial modulators,
making it a superior tool for real-time metabolic analysis
in tissues. With the guidance discussed in this application note, metabolic interrogation of brain tissue can be
achieved with greater success and minimized effort.
This system and streamlined workflow can also be easily
adapted for other tissue types and organisms in a wide
range of biomedical research applications.
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Function Ex Vivo With Acute Mouse Slice Punches.
STAR Protoc. 2021, May 23; 2(2):100559. DOI:
10.1016/j.xpro.2021.100559www.agilent.com/lifesciences/xf-analyzers
For Research Use Only. Not for use in diagnostic procedures.
RA250418.240
This information is subject to change without notice.
© Agilent Technologies, Inc. 2025
Published in the USA, April 28 2025
5994-8309EN
Products used in this application
Agilent products
Agilent Seahorse XF Flex Analyzer
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