Imaris

Manufactured by Leica

Sourced in Germany

Imaris is a 3D/4D image analysis software designed for the visualization and analysis of complex data sets. It provides a comprehensive set of tools for segmentation, tracking, and quantification of biological structures. Imaris is compatible with a wide range of imaging modalities, including confocal, multiphoton, and light-sheet microscopy.

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Lab products found in correlation

Murine mscs, by Leica (2 mentions) Murine mscs, by Thermo Fisher Scientific (2 mentions) Penicillin streptomycin, by Thermo Fisher Scientific (2 mentions) Tcs sp8, by Leica (2 mentions) Dexamethasone (dex), by Merck Group (2 mentions) Imagej, by Leica (2 mentions) Matrigel, by Corning (1 mentions) Las af, by Leica (1 mentions) Tcs sp8 laser scanning microscope, by Leica (1 mentions) Prolong gold, by Thermo Fisher Scientific (1 mentions) On stage incubator, by Okolab (1 mentions) Chameleon vision 2, by Coherent Inc (1 mentions) Confocal microscopy, by Leica (1 mentions)

Close spelling variants of this product

Imaris 7.6 (2 citations)

6 protocols using imaris

Multipotent Differentiation Analysis of MSCs

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Live images were taken every 24 h until 96 h to assess tdT and H2B-eGFP signals. Anti-TPPP3 antibodies were used to determine the maintenance of endogenous TPPP3 expression (Extended Data 6b).
Tile scan images of each well were captured on the Leica TCS SP8 and the conversion index was calculated using automated filtering and thresholding in Imaris (Bitplane).
2) For multipotential differentiation assays, each sub-population was subjected to culturing and differentiation conditions per murine MSCs^{12 (link)}. murine MSCs (Invitrogen) were used as a positive control in parallel. For adipogenesis and chondrogenesis, cells were expanded in MSC growth media. For osteogenesis, cells were expanded in osteogenic growth media (αMEM, 20% MSC qualified FBS, 2 mM GlutaMax, 100 U/mL Penicillin-Streptomycin (Gibco), 10 nM Dexamethasone (Sigma)). At 80% confluency, cells were trypsinized, pelleted and seeded for assay.

Harvey T., Flamenco S, & Fan C.M. (2019). A Tppp3+Pdgfra+ tendon stem cell population contributes to regeneration and reveals a shared role for PDGF signalling in regeneration and fibrosis. Nature cell biology, 21(12), 1490-1503.

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Live Imaging of Embryonic Tagln-Cre Lineage

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E11.5-E14.5 Tagln-Cre:Rosa26-tdTom or Tagln-Cre:Rosa26-tdTom:PAX3-GFP embryos were decapitated and the trunk full circumference was maintained. The body wall explant was placed on a glass-bottom 35 mm tissue culture disc (WPI, FD3510-100), stabilised with Phenol Red-free growth factor-reduced Matrigel (Corning, 356231), then standard cell culture medium (DMEM with 10% FBS) was added and then cultured for 6-16 h. The explants were imaged in a laser scanning confocal microscopy system (Leica SP8 inverted gSTED) maintained at 37°C and 5% CO₂ with a humidiﬁer. z-slices were acquired using a ×10 objective every 10-20 min. Four-dimensional datasets were analysed with Leica confocal and Imaris (Bitplane) software.

Aldeiri B., Roostalu U., Albertini A., Wong J., Morabito A, & Cossu G. (2017). Transgelin-expressing myofibroblasts orchestrate ventral midline closure through TGFβ signalling. Development (Cambridge, England), 144(18), 3336-3348.

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Visualizing F-actin and Lysosomes in HeLa Cells

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To visualize F-actin and lysosomes, HeLa cells grown on coverslips were fixed with 4% p-formaldehyde in PBS for 30 min at room temperature, HeLa cells were treated with 50 mM NH₄Cl in PBS for 15 min, washed in PBS and then blocked for 1 h at room temperature in PGN-saponin (PBS containing 0.15% gelatin, 0.1% saponin, 0.1% sodium azide). Alexa Fluor 488 phalloidin or TRITC-phalloidin diluted 1:200 (v/v) in blocking solution plus 10 μg/ml DAPI (4′,6-diamidine-2′-phenylindole dihydrochloride), was used to detect F-actin and DNA, respectively. For lysosome visualization, the cells were processed as previously described, using anti-human LAMP2 antibody and Alexa Fluor 488-conjugated anti-mouse IgG (Rodrigues et al., 2017 (link)). Coverslips, mounted in ProLong Gold (Invitrogen) were analyzed at Leica TCS SP8 laser-scanning microscope (Leica, Germany), Instituto de Farmacologia e Biologia Molecular (INFAR), Universidade Federal de São Paulo, using Plan-Apochromat oil immersion and 63X objective. Images were processed and analyzed using Leica LAS AF (Leica, Germany) and Imaris (Bitplane) software.

Onofre T.S., Rodrigues J.P, & Yoshida N. (2019). Depletion of Host Cell Focal Adhesion Kinase Increases the Susceptibility to Invasion by Trypanosoma cruzi Metacyclic Forms. Frontiers in Cellular and Infection Microbiology, 9, 231.

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Multipotent Differentiation Analysis of MSCs

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Visualizing 3D Tumor Cell Invasion

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For time-lapse experiments, CAFs were stained with a lyophilic carbocyanine dye (Vybrant DiI-Cell Labeling Solutions; ThermoFisher) according to the manufacturer’s recommendation. Cells were embedded in collagen as described in the Invasion assay section. The dish was incubated at 5% CO₂ and 37°C in the on-stage incubator (Okolab). For fixed and live 3D samples, images were acquired with an inverted AOBS two-photon laser-scanning confocal microscope (SP8; Leica) coupled with a femtosecond laser (Chameleon Vision II; Coherent Inc.) using a 25×/1.0 NA water immersion objective. The microscope was equipped with three nondescanned HyD detectors: NDD1 (500–550 nm), NDD2 (≥590 nm), and NDD3 (405 nm). Fluorescence channels were recorded simultaneously using the excitation wavelength 980 nm. Collagen was visualized by either second harmonic generation using the excitation wavelength 910 nm or by confocal reflectance microscopy that does not interfere with DAPI staining, using light at a wavelength of 488 nm and a standard photomultiplier tube detector at a low gain (500 V). Images were recorded every 10 min up to 72 h. 3D stacks were obtained at a step size of 2-µm intervals. The images were processed with the Leica Application Suite, ImageJ, and Imaris (Bitplane).

Attieh Y., Clark A.G., Grass C., Richon S., Pocard M., Mariani P., Elkhatib N., Betz T., Gurchenkov B, & Vignjevic D.M. (2017). Cancer-associated fibroblasts lead tumor invasion through integrin-β3–dependent fibronectin assembly. The Journal of Cell Biology, 216(11), 3509-3520.

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Imaging NF-κB and CCL2 in LSV

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Briefly, segments of LSV were assessed for the cellular localisation of NF-κB and quantity of CCL2 after exposure to acute arterial WSS by immunostaining of en face prepared vessels (for detailed description, see Supplementary Methods). The LSV endothelium was imaged en face, using confocal microscopy (Leica, Germany) and image analysis was all performed in 3D, either using Imaris (Supplementary Figure 3) or ImageJ (Supplementary Figure 4).

Ward A.O., Angelini G.D., Caputo M., Evans P.C., Johnson J.L., Suleiman M.S., Tulloh R.M., George S.J, & Zakkar M. (2020). NF-κB inhibition prevents acute shear stress-induced inflammation in the saphenous vein graft endothelium. Scientific Reports, 10, 15133.

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