Fixed-Cell Imaging Reagents

Improved fixed-cell imaging results

Pre-packaged reagent kits with optimized workflows combined with easy-to-use and powerful microscopes enable you to get the most from your fixed-cell imaging experiments. Below you can find products for fixation and permeabilization, cellular labeling, and image capture.

Watch the webinarSee promotion offer

Free Guide - Five steps for publication-quality cell imaging

Download the guide

5 steps for effective fixed-cell imaging

Follow these 5 steps to capture the best possible fixed-cell images to help ensure that your cell images are publication-ready the first time:

Step 1. Cell and tissue preparation

To achieve optimal imaging quality, begin by setting up your study to spotlight proteins and cell structures of interest while keeping everything else out of the picture. Fixation and permeabilization prepare the cell samples for labeling—first by locking cellular structures, proteins, and nucleic acids in place, and then by making it possible for antibodies and fluorescent stains to permeate the interior of cells and label the targets of interest. Blocking prevents the fluorescent labels from nonspecifically binding to proteins that are not relevant to your research, thereby minimizing the signal-to-noise ratio.

Stained cell images, with and without optimized fixation

After fixation and permeabilization, U2OS cells were stained with NucBlue Live Cell Stain and ActinGreen 488 ReadyProbes Reagent. Treatment A used methanol-based solution for fixation, and Treatment B used the formaldehyde-based Image-iT Fixation/Permeabilization Kit. The methanol-based fixation in A results in fragmentation of the actin cytoskeleton and disruption of the cells. The Image-iT Fixation/Permeabilization Kit provides optimal fixation conditions for most cell types.

Product Description Cat. No.
Image-iT Fixation/Permeabilization Kit
  • Fixative: high-purity 4% formaldehyde in PBS, pH 7.3
  • Permeabilization solution: 0.5% Triton X-100
  • Blocking buffer: 3% BSA, fraction V, delipidated, New Zealand source, in DPBS
  • Wash solution: PBS, pH 7.4
R37602
BlockAid Blocking Solution 50 mL B10710
1.1 Culture conditions–Fixed cell imaging: 5 steps for publication-quality images
The first step in obtaining a good image is tissue preparation. For cultured cells, the cells must have good cell health and morphology, as well as good confluency. Healthy cells equal healthy data.

1.2 Fixation–Fixed cell imaging: 5 steps for publication-quality images
The next step of tissue preparation is fixation. Fixation refers to a chemical means of killing and preserving cells in a particular physiological state, and in many cases, to preserve morphology. Proper fixation equals preservation of target.

1.3 Permeabilization–Fixed cell imaging: 5 steps for publication-quality images
The next step is the permeabilization of the cells which is the key to opening intracellular compartments.

1.4 Blocking–Fixed cell imaging: 5 steps for publication-quality images
The next step after permeabilization is blocking, and there are a number of blocking techniques. Protein blocking equals specific antibody binding. Dye charge blocking means less non-specific binding.

1.5 Autofluorescence–Fixed cell imaging: 5 steps for publication-quality images
The last step in cell preparation is autofluorescence. Cells and tissue can have a certain degree of autofluorescence that can confuse the specific signal, and lower the signal-to-background. Overcoming autofluorescence means greater sensitivity.

Step 2. Labeling your sample

Labeling various targets with separate fluorescent colors allows you to visualize different structures or proteins within cells in the same sample. Ways to label your target fluorescently include fluorescent dyes, immunolabeling, and fluorescent fusion proteins—all of which provide a means to selectively mark structures and proteins within the cell and allow you to see them more easily when you image.Many fluorescence tools for cell biology are essentially fluorophores that have been modified in different ways or conjugated to various molecules to give them a certain function or allow them to bind to specific organelles or proteins.Through chemical modifications, a single fluorophore can be produced in a number of variant forms, each with a different specificity. For example, the green-fluorescent Invitrogen Alexa Fluor 488 dye molecule can be modified to target actin filaments, can be attached to an IgG for use in immunolabeling, or can act as a whole-cell stain.The Invitrogen portfolio offers more than 51,000 high-quality primary antibodies. Some of these antibodies are attached directly to a broad range of intensely fluorescent markers and labels, including Invitrogen Alexa Fluor dyes. Explore our extensive portfolio of antibodies at thermofisher.com/primaryantibodies.

ActinGreen488 mitoSecAbAF750

Cultured cells were prepared for staining using the Invitrogen Image-iT Fixation/Permeabilization Kit and were treated with Invitrogen BlockAid Blocking Solution. The sample was labeled with a primary antibody that recognizes mitochondria, followed by an Alexa Fluor 750 dye–conjugated secondary antibody (purple), Invitrogen NucBlue cell stain (blue), and Invitrogen ActinGreen 488 ReadyProbes Reagent (green). The image was captured on an Invitrogen EVOS FL Auto Imaging System.

2.1 Primary antibody choice–Fixed cell imaging: 5 steps for publication-quality images
After preparation, the second step to publishable images is to label the sample, usually involving primary antibodies to your specific targets of interest.

2.2 Primary antibody protocol optimization–Fixed cell imaging: 5 steps for publication-quality images
Every primary antibody must be optimized separately. There are many protocols available, and it is important to understand a “one size fits all” approach gives inferior results, as every antibody is slightly different.

Step 3. Detecting your samples

Detecting complex biological assemblies requires maximum clarity of fluorescence signals and separation of signals from background noise. Standard immunofluorescence labeling rarely provides the best signal-to-noise visibility. The difference between producing a good and a great publication-quality image requires fine-tuning your sample’s signal for peak specificity, definition, and amplification.

Quickly and easily choose the labeling solution you need

Lg superboost multiplex icc/ihc

Fixed and permeabilized HeLa cells, treated using the reagents in the Image-iT Fixation/Permeabilization Kit, were incubated with an anti-tubulin primary antibody and an Alexa Fluor 488 goat anti–mouse IgG (H+L) secondary antibody. Cells were then incubated with an anti–ATP synthase subunit IF1 antibody and labeled with the reagents in the Alexa Fluor 594 Tyramide SuperBoost Kit (goat anti–mouse IgG and Alexa Fluor 594 tyramide). Nuclei were labeled with NucBlue Fixed Cell ReadyProbes Reagent. Images were acquired on a confocal microscope.

High- to medium-abundance protein targets

Secondary antibodies are used for the indirect detection of target antigens. While primary antibodies bind directly to the target, secondary antibodies bind indirectly by using the primary antibody as a bridge to the targeted biomolecule. This methodology serves to amplify signals and increase sensitivity to maximize detection.
Explore secondary antibodies

Medium- to low-abundance protein targets

Streptavidin conjugates can increase the number of fluorophores that label your target, and boost their signals. Streptavidin-based amplification techniques are widely used in fluorescence imaging for improved sensitivity of detection with primary and secondary antibodies.
Find out more about streptavidin signal amplification for imaging

Low-abundance protein targets

For low-abundance protein targets that are not detectable by conventional means, tyramide signal amplification (TSA, PerkinElmer) provides sensitive detection without compromising resolution. TSA technology employs an enzyme that releases reactive dyes in the presence of hydrogen peroxide to bring targets out of the background with definition and clarity.
Learn more about imaging low-abundance targets with TSA

3.1 Secondary antibody choice–Fixed cell imaging: 5 steps for publication-quality images
Step three of the five steps in making publishable images is to detect the label. That is, to detect with a secondary antibody, for instance, or an amplification technique, as well as to determine what controls to use. Your options are discussed.

3.2 Secondary antibody optimization–Fixed cell imaging: 5 steps for publication-quality images
Secondary antibody detection protocols also need to be optimized for each primary antibody used.

3.3 Amplification techniques–Fixed cell imaging: 5 steps for publication-quality images
If the signal is not strong enough using standard secondary detection schemes, you can increase the signal using amplification techniques. This is particularly important for low-expressing antigens, or rare-cell detection in samples.

3.4 Controls–Fixed cell imaging: 5 steps for publication-quality images
Researchers should conduct all necessary controls to rule out the possibility of non-specific binding or non-specific signal. Types of controls are described. Proper controls will boost your confidence in your final results.

3.5 Dye choice and special concerns–Fixed cell imaging: 5 steps for publication-quality images
There are many different dyes spanning the visible, far-red, and infrared wavelengths.Considerations for making the right choices for your experiment are presented.

Step 4. Protecting your samples

Fluorophores are ideal for high-quality cell imaging but are inevitably prone to photobleaching, a photochemical degradation or fading of fluorescence signals. Any reduction in photosensitivity can skew your data and yield false results. Antifade mountants are designed to protect the photostability of fluorescently labeled proteins and maintain image integrity for weeks to months.

Key benefits of ProLong antifade mountants for fixed cells include:

  • Inhibit photobleaching across the spectrum, even after prolonged storage
  • Low background across the spectrum
  • Hard-setting mountants
  • Available with or without DAPI
  • Ready-to-use benchtop formulations
  • Choice of refractive index based on your needs: 1.52 for ProLong Glass reagent and 1.47 for ProLong Diamond and ProLong Gold reagents

Explore Invitrogen ProLong antifades for fixed-cell imaging

multipanel image series showing fluorescence stained cell following repeated illumination

A 60-second time-lapse showing the enhanced resistance to photobleaching afforded by ProLong antifade mountants. Fixed HeLa cells were labeled with fluorescein phalloidin and mounted in ProLong Glass reagent, ProLong Diamond reagent, ProLong Gold reagent, or 50% PBS/glycerol. Images were acquired at 12-second intervals using a 20x objective with continuous illumination from a standard 100-watt Hg-arc lamp.

Featured Scientific Poster

Antifade mounting media to help improve image quality in 3D biological samples

Download poster

4.1 Mounting media–Fixed cell imaging: 5 steps for publication-quality images
Using the right mounting media can impact your experiment. Be sure to choose the right type of mountant for your set-up.

4.2 Photobleaching and antifades–Fixed cell imaging: 5 steps for publication-quality images
What is photobleaching and how can you prevent it from destroying your sample? Options for antifades are discussed.

Step 5. Imaging your samples

Capture research discoveries with maximum clarity and definition. In today’s competitive scientific environment, generating publication-quality images is critical to your success. To capture top-quality images, you need an imaging platform with top-of-the-line imaging components, including:

  • High-quality cameras and optics to capture high-resolution images
  • LED illumination to produce superior signal-to-noise ratios
  • Easy-to-use image capture and processing software for ready-to-publish images

Compare the systems below to find the one that fits your imaging needs.

Get more information on our entire line of microscopy cell imaging systems

Basic transmitted light-digital inverted system Advanced transmitted-light digital inverted system Basic fluorescence system Advanced fluorescence system Fully automated fluorescence system

EVOS XL Core
Perfect for cell culture and routine cell maintenance

EVOS XL
Perfect for more advanced colormetric assays

EVOS FLoid
Perfect for quick fluorescence visualization

EVOS FL
Perfect for multichannel fluorescence imaging and transfections


EVOS FL Auto 2
Perfect for a variety of advanced, automated applications

Microscopy reagent selection table for fixed-cell imaging

EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis

Get more information on our entire line of high-content analysis cell imaging systems

5-channel LED system 7-channel LED confocal system 7-channel laser confocal system

CellInsight CX5
Perfect for labs looking for a compact and affordable system to increase scale

See reagents

CellInsight CX7
Perfect for labs looking for additional choices of imaging mode


See reagents

CellInsight CX7 LZR
Perfect for labs looking for advanced performance in sensitivity and speed


See reagents

Get more information on our entire line of microscopy cell imaging systems

Basic transmitted light-digital inverted system Advanced transmitted-light digital inverted system Basic fluorescence system Advanced fluorescence system Fully automated fluorescence system

EVOS XL Core
Perfect for cell culture and routine cell maintenance

EVOS XL
Perfect for more advanced colormetric assays

EVOS FLoid
Perfect for quick fluorescence visualization

EVOS FL
Perfect for multichannel fluorescence imaging and transfections


EVOS FL Auto 2
Perfect for a variety of advanced, automated applications

Microscopy reagent selection table for fixed-cell imaging

EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis

Get more information on our entire line of high-content analysis cell imaging systems

5-channel LED system 7-channel LED confocal system 7-channel laser confocal system

CellInsight CX5
Perfect for labs looking for a compact and affordable system to increase scale

See reagents

CellInsight CX7
Perfect for labs looking for additional choices of imaging mode


See reagents

CellInsight CX7 LZR
Perfect for labs looking for advanced performance in sensitivity and speed


See reagents

5.1 Imaging platforms-hardware–Fixed cell imaging: 5 steps for publication-quality images
The fifth step of the process is the actual imaging. To capture top-quality images, you need an imaging platform with top-of-the-line imaging capabilities. Here we review considerations for getting the best image.

5.2 Imaging platforms-software–Fixed cell imaging: 5 steps for publication-quality images
Taking images on a microscope usually entails having some type of imaging software that aids in taking the image and assists in combining differing colors into one. There are some very important aspects to keep in mind to get a publishable image.

5.3 Image capture with EVOS FL Auto 2.0–Fixed cell imaging: 5 steps for publication-quality images
Here the advantages of using the EVOS FL Auto 2.0 imaging system to capture your images are discussed.

5.4 Image analysis with Celleste software–Fixed cell imaging: 5 steps for publication-quality images
The functionality of the Celleste softwis reviewed and considerations for processing the image in different software programs are described.

5.5 Ethical considerations–Fixed cell imaging: 5 steps for publication-quality images
Ethical imaging means trustworthy data, and thus, publishable data. How to treat your samples and data to preserve data integrity is presented.

Step 1. Cell and tissue preparation

To achieve optimal imaging quality, begin by setting up your study to spotlight proteins and cell structures of interest while keeping everything else out of the picture. Fixation and permeabilization prepare the cell samples for labeling—first by locking cellular structures, proteins, and nucleic acids in place, and then by making it possible for antibodies and fluorescent stains to permeate the interior of cells and label the targets of interest. Blocking prevents the fluorescent labels from nonspecifically binding to proteins that are not relevant to your research, thereby minimizing the signal-to-noise ratio.

Stained cell images, with and without optimized fixation

After fixation and permeabilization, U2OS cells were stained with NucBlue Live Cell Stain and ActinGreen 488 ReadyProbes Reagent. Treatment A used methanol-based solution for fixation, and Treatment B used the formaldehyde-based Image-iT Fixation/Permeabilization Kit. The methanol-based fixation in A results in fragmentation of the actin cytoskeleton and disruption of the cells. The Image-iT Fixation/Permeabilization Kit provides optimal fixation conditions for most cell types.

Product Description Cat. No.
Image-iT Fixation/Permeabilization Kit
  • Fixative: high-purity 4% formaldehyde in PBS, pH 7.3
  • Permeabilization solution: 0.5% Triton X-100
  • Blocking buffer: 3% BSA, fraction V, delipidated, New Zealand source, in DPBS
  • Wash solution: PBS, pH 7.4
R37602
BlockAid Blocking Solution 50 mL B10710
1.1 Culture conditions–Fixed cell imaging: 5 steps for publication-quality images
The first step in obtaining a good image is tissue preparation. For cultured cells, the cells must have good cell health and morphology, as well as good confluency. Healthy cells equal healthy data.

1.2 Fixation–Fixed cell imaging: 5 steps for publication-quality images
The next step of tissue preparation is fixation. Fixation refers to a chemical means of killing and preserving cells in a particular physiological state, and in many cases, to preserve morphology. Proper fixation equals preservation of target.

1.3 Permeabilization–Fixed cell imaging: 5 steps for publication-quality images
The next step is the permeabilization of the cells which is the key to opening intracellular compartments.

1.4 Blocking–Fixed cell imaging: 5 steps for publication-quality images
The next step after permeabilization is blocking, and there are a number of blocking techniques. Protein blocking equals specific antibody binding. Dye charge blocking means less non-specific binding.

1.5 Autofluorescence–Fixed cell imaging: 5 steps for publication-quality images
The last step in cell preparation is autofluorescence. Cells and tissue can have a certain degree of autofluorescence that can confuse the specific signal, and lower the signal-to-background. Overcoming autofluorescence means greater sensitivity.

Step 2. Labeling your sample

Labeling various targets with separate fluorescent colors allows you to visualize different structures or proteins within cells in the same sample. Ways to label your target fluorescently include fluorescent dyes, immunolabeling, and fluorescent fusion proteins—all of which provide a means to selectively mark structures and proteins within the cell and allow you to see them more easily when you image.Many fluorescence tools for cell biology are essentially fluorophores that have been modified in different ways or conjugated to various molecules to give them a certain function or allow them to bind to specific organelles or proteins.Through chemical modifications, a single fluorophore can be produced in a number of variant forms, each with a different specificity. For example, the green-fluorescent Invitrogen Alexa Fluor 488 dye molecule can be modified to target actin filaments, can be attached to an IgG for use in immunolabeling, or can act as a whole-cell stain.The Invitrogen portfolio offers more than 51,000 high-quality primary antibodies. Some of these antibodies are attached directly to a broad range of intensely fluorescent markers and labels, including Invitrogen Alexa Fluor dyes. Explore our extensive portfolio of antibodies at thermofisher.com/primaryantibodies.

ActinGreen488 mitoSecAbAF750

Cultured cells were prepared for staining using the Invitrogen Image-iT Fixation/Permeabilization Kit and were treated with Invitrogen BlockAid Blocking Solution. The sample was labeled with a primary antibody that recognizes mitochondria, followed by an Alexa Fluor 750 dye–conjugated secondary antibody (purple), Invitrogen NucBlue cell stain (blue), and Invitrogen ActinGreen 488 ReadyProbes Reagent (green). The image was captured on an Invitrogen EVOS FL Auto Imaging System.

2.1 Primary antibody choice–Fixed cell imaging: 5 steps for publication-quality images
After preparation, the second step to publishable images is to label the sample, usually involving primary antibodies to your specific targets of interest.

2.2 Primary antibody protocol optimization–Fixed cell imaging: 5 steps for publication-quality images
Every primary antibody must be optimized separately. There are many protocols available, and it is important to understand a “one size fits all” approach gives inferior results, as every antibody is slightly different.

Step 3. Detecting your samples

Detecting complex biological assemblies requires maximum clarity of fluorescence signals and separation of signals from background noise. Standard immunofluorescence labeling rarely provides the best signal-to-noise visibility. The difference between producing a good and a great publication-quality image requires fine-tuning your sample’s signal for peak specificity, definition, and amplification.

Quickly and easily choose the labeling solution you need

Lg superboost multiplex icc/ihc

Fixed and permeabilized HeLa cells, treated using the reagents in the Image-iT Fixation/Permeabilization Kit, were incubated with an anti-tubulin primary antibody and an Alexa Fluor 488 goat anti–mouse IgG (H+L) secondary antibody. Cells were then incubated with an anti–ATP synthase subunit IF1 antibody and labeled with the reagents in the Alexa Fluor 594 Tyramide SuperBoost Kit (goat anti–mouse IgG and Alexa Fluor 594 tyramide). Nuclei were labeled with NucBlue Fixed Cell ReadyProbes Reagent. Images were acquired on a confocal microscope.

High- to medium-abundance protein targets

Secondary antibodies are used for the indirect detection of target antigens. While primary antibodies bind directly to the target, secondary antibodies bind indirectly by using the primary antibody as a bridge to the targeted biomolecule. This methodology serves to amplify signals and increase sensitivity to maximize detection.
Explore secondary antibodies

Medium- to low-abundance protein targets

Streptavidin conjugates can increase the number of fluorophores that label your target, and boost their signals. Streptavidin-based amplification techniques are widely used in fluorescence imaging for improved sensitivity of detection with primary and secondary antibodies.
Find out more about streptavidin signal amplification for imaging

Low-abundance protein targets

For low-abundance protein targets that are not detectable by conventional means, tyramide signal amplification (TSA, PerkinElmer) provides sensitive detection without compromising resolution. TSA technology employs an enzyme that releases reactive dyes in the presence of hydrogen peroxide to bring targets out of the background with definition and clarity.
Learn more about imaging low-abundance targets with TSA

3.1 Secondary antibody choice–Fixed cell imaging: 5 steps for publication-quality images
Step three of the five steps in making publishable images is to detect the label. That is, to detect with a secondary antibody, for instance, or an amplification technique, as well as to determine what controls to use. Your options are discussed.

3.2 Secondary antibody optimization–Fixed cell imaging: 5 steps for publication-quality images
Secondary antibody detection protocols also need to be optimized for each primary antibody used.

3.3 Amplification techniques–Fixed cell imaging: 5 steps for publication-quality images
If the signal is not strong enough using standard secondary detection schemes, you can increase the signal using amplification techniques. This is particularly important for low-expressing antigens, or rare-cell detection in samples.

3.4 Controls–Fixed cell imaging: 5 steps for publication-quality images
Researchers should conduct all necessary controls to rule out the possibility of non-specific binding or non-specific signal. Types of controls are described. Proper controls will boost your confidence in your final results.

3.5 Dye choice and special concerns–Fixed cell imaging: 5 steps for publication-quality images
There are many different dyes spanning the visible, far-red, and infrared wavelengths.Considerations for making the right choices for your experiment are presented.

Step 4. Protecting your samples

Fluorophores are ideal for high-quality cell imaging but are inevitably prone to photobleaching, a photochemical degradation or fading of fluorescence signals. Any reduction in photosensitivity can skew your data and yield false results. Antifade mountants are designed to protect the photostability of fluorescently labeled proteins and maintain image integrity for weeks to months.

Key benefits of ProLong antifade mountants for fixed cells include:

  • Inhibit photobleaching across the spectrum, even after prolonged storage
  • Low background across the spectrum
  • Hard-setting mountants
  • Available with or without DAPI
  • Ready-to-use benchtop formulations
  • Choice of refractive index based on your needs: 1.52 for ProLong Glass reagent and 1.47 for ProLong Diamond and ProLong Gold reagents

Explore Invitrogen ProLong antifades for fixed-cell imaging

multipanel image series showing fluorescence stained cell following repeated illumination

A 60-second time-lapse showing the enhanced resistance to photobleaching afforded by ProLong antifade mountants. Fixed HeLa cells were labeled with fluorescein phalloidin and mounted in ProLong Glass reagent, ProLong Diamond reagent, ProLong Gold reagent, or 50% PBS/glycerol. Images were acquired at 12-second intervals using a 20x objective with continuous illumination from a standard 100-watt Hg-arc lamp.

Featured Scientific Poster

Antifade mounting media to help improve image quality in 3D biological samples

Download poster

4.1 Mounting media–Fixed cell imaging: 5 steps for publication-quality images
Using the right mounting media can impact your experiment. Be sure to choose the right type of mountant for your set-up.

4.2 Photobleaching and antifades–Fixed cell imaging: 5 steps for publication-quality images
What is photobleaching and how can you prevent it from destroying your sample? Options for antifades are discussed.

Step 5. Imaging your samples

Capture research discoveries with maximum clarity and definition. In today’s competitive scientific environment, generating publication-quality images is critical to your success. To capture top-quality images, you need an imaging platform with top-of-the-line imaging components, including:

  • High-quality cameras and optics to capture high-resolution images
  • LED illumination to produce superior signal-to-noise ratios
  • Easy-to-use image capture and processing software for ready-to-publish images

Compare the systems below to find the one that fits your imaging needs.

Get more information on our entire line of microscopy cell imaging systems

Basic transmitted light-digital inverted system Advanced transmitted-light digital inverted system Basic fluorescence system Advanced fluorescence system Fully automated fluorescence system

EVOS XL Core
Perfect for cell culture and routine cell maintenance

EVOS XL
Perfect for more advanced colormetric assays

EVOS FLoid
Perfect for quick fluorescence visualization

EVOS FL
Perfect for multichannel fluorescence imaging and transfections


EVOS FL Auto 2
Perfect for a variety of advanced, automated applications

Microscopy reagent selection table for fixed-cell imaging

EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis

Get more information on our entire line of high-content analysis cell imaging systems

5-channel LED system 7-channel LED confocal system 7-channel laser confocal system

CellInsight CX5
Perfect for labs looking for a compact and affordable system to increase scale

See reagents

CellInsight CX7
Perfect for labs looking for additional choices of imaging mode


See reagents

CellInsight CX7 LZR
Perfect for labs looking for advanced performance in sensitivity and speed


See reagents

Get more information on our entire line of microscopy cell imaging systems

Basic transmitted light-digital inverted system Advanced transmitted-light digital inverted system Basic fluorescence system Advanced fluorescence system Fully automated fluorescence system

EVOS XL Core
Perfect for cell culture and routine cell maintenance

EVOS XL
Perfect for more advanced colormetric assays

EVOS FLoid
Perfect for quick fluorescence visualization

EVOS FL
Perfect for multichannel fluorescence imaging and transfections


EVOS FL Auto 2
Perfect for a variety of advanced, automated applications

Microscopy reagent selection table for fixed-cell imaging

EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS RFP Light Cube (AMEP4652)
Excitation: 531/40 nm;
Emission: 593/40 nm
Step Application Key tools for RFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS Texas Red Light Cube (AMEP4655)
Excitation: 585/29 nm;
Emission: 624/40 nm
EVOS Cy5 Light Cube (AMEP4656)
Excitation: 628/40 nm;
Emission: 693/40 nm
Step Application Key tools for Cy5 channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis
EVOS DAPI Light Cube (AMEP4650)
Excitation: 357/44 nm;
Emission: 447/60 nm
EVOS GFP Light Cube (AMEP4651)
Excitation: 470/22 nm;
Emission: 510/42 nm
Step Application Key tools for GFP channel
Step 1. Fix, permeabilize, and block Buffers
Step 2. Label Mitochondria
Cytoskeleton
Plasma membrane
Nucleus
Step 3. Detect Antibody direct labeling kits
Zenon kits
Secondary antibodies
Streptavidin
SuperBoost TSA kits
Step 4. Protect and enhance Signal enhancer
Mountants and antifades
Step 5. Image Imaging and analysis