Live Staining of Mitochondria Using MitoTracker® Fluorescent Dyes

EP144 v1.0


Key Steps:

Other Required Materials:

Visualize mitochondria in live cells via fluorescent imaging in Organ-Chips

  • Live staining and fluorescent imaging of Organ-Chips
  • MitoTracker® Orange CMTMRos (Thermo ScientificTM M7510), Mitotracker® Red CM-H2XROS (Thermo ScientificTM M7513), or Mitotracker ® Deep Red FM (Thermo Scientific TM M22426)
  • Cell culture medium (serum-free)
  • Dimethyl sulfoxide (DMSO)
  • Fluorescence microscope


  • PBS
  • 4% paraformaldehyde (PFA)


MitoTracker® is a fluorescent dye that stains mitochondria in live cells. Its accumulation is dependent upon membrane potential. This endpoint is used as a marker of cell viability.


Sample type

Live Organ-Chip

See Protocol EP155 Live Staining.

Recommended reagent dilution and incubation time

Prepare 1 mM stock solution in DMSO.

Dilute stock 1:5000 in serum-free media. Incubate for 30 minutes at 37C.

Fixative (optional)

Chips can be fixed immediately after staining: 4% PFA for 15 minutes at room temperature.

The signal remains for up to 24 hours after fixation.

Note: Do not fix cells before MitoTracker® staining.

See Emulate Fixation and Immunofluorescence (IF) Staining for Organ-Chips (#6137).

Representative image

Image of mitochondria (red) and nuclei (blue) in human hepatocytes in the Liver-Chip, stained by the MitoTracker® reagent (top channel).

More information on vendor site

Organs-Chips in which the staining has been validated

MitoTracker® (Thermo Fisher Scientific TM M7510) has been validated on Liver-Chips.

MitoTracker® (Thermo Fisher Scientific TM M7513 and M22426) have been validated on Caco-2 Intestine-Chips.



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Emulate® and the Emulate logo are registered trademarks for Emulate, Inc.

MitoTracker® is a registered trademark of Thermo Fisher Scientific.

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