Imagej software

Manufactured by Zeiss

Sourced in Germany, United States

ImageJ is an open-source image processing software developed by the National Institutes of Health. It is designed for the visualization, analysis, and processing of digital images.

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Lab products found in correlation

Zen software, by Zeiss (8 mentions) Lsm 880 confocal microscope, by Zeiss (4 mentions) Lsm 710 confocal microscope, by Zeiss (3 mentions) Axio observer z1, by Zeiss (3 mentions) Dm3000, by Leica (2 mentions) Axio imager m2, by Zeiss (2 mentions) Zen image acquisition software package, by Zeiss (2 mentions) Lsm 510, by Zeiss (2 mentions) Lsm 780, by Zeiss (2 mentions) Lsm 700 confocal microscope, by Zeiss (2 mentions) Lsm 710, by Zeiss (2 mentions) Wheat germ agglutinin (wga), by Leica (1 mentions) Wheat germ agglutinin (wga), by Merck Group (1 mentions) Axiovert 40 cfl, by Zeiss (1 mentions) Axiovision software, by Zeiss (1 mentions) Anti 8 oxo dg antibody, by Bio-Techne (1 mentions) Alexafluor 488 nm antibody, by Thermo Fisher Scientific (1 mentions) Axiovert 200 widefield fluorescence microscope, by Zeiss (1 mentions) Observer a1 fluorescent microscope, by Zeiss (1 mentions) Pkh67, by Merck Group (1 mentions)

48 protocols using imagej software

Histological Techniques for Skeletal Muscle Analysis

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H&E staining and wheat germ agglutinin (WGA) staining were used to detect the cross-sectional area of mouse gastrocnemius muscle fibers, which has been described in detail in our previous study [10 (link)].
For H&E staining, each slide was imaged using a 20× magnification on a Leica microscope (Wetzlar, Germany, DM3000) to take 20-40 fields of view per sample. The area of the myofibers was analyzed using Image J software (NIH, USA), with a minimum of 400 fibers per mouse being analyzed.
WGA lectin staining was performed as it is a fast, reliable and an inexpensive method used for skeletal muscle fiber, compared to other antibody-based techniques[38 (link)]. The frozen tissue sections were stained with WGA (1:200, Sigma, MO, USA), and photographed with Carl Zeiss fluorescence microscope (Oberkochen, Germany, Axio Imager M2) at 20× magnification, and the area of the myofibers was analyzed with Image J software with a minimum of 400 fibers per mouse being counted.

Chen R., Yuan W., Zheng Y., Zhu X., Jin B., Yang T., Yan Y., Xu W., Chen H., Gao J., Li G., Gokulnath P., Vulugundam G., Li J, & Xiao J. (2022). Delivery of engineered extracellular vesicles with miR-29b editing system for muscle atrophy therapy. Journal of Nanobiotechnology, 20, 304.

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Histomorphometric Examination of Chicken Jejunum

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The removed chicken jejunum was fixed in 4% paraformaldehyde and embedded in paraffin. Then, a ZEISS microscope (Shanghai, China) and ImageJ software (Version 1.8.0.345 Chinese, Kunming, China) were employed to perform histomorphometric examinations of 5 μm thick serial sections of the jejunal sample that were stained with hematoxylin and eosin (HE). Villus height (VH), crypt depth (CD), and VH:CD ratio measurements were obtained from at least 3 slides, with a minimum of 6 well-oriented indices to calculate their respective averages.

Kang X., Li X.D., Luo C.Y., Xin W.G., Zhou H.Y., Wang F, & Lin L.B. (2023). Effects of Dietary Supplementation of Lacticaseibacillus Chiayiensis AACE3 on Hepatic Antioxidant Capacity, Immune Factors and Gut Microbiology in Nandan Yao Chicks. Antibiotics, 12(9), 1356.

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Quantitative Immunofluorescence Assessment of 8-OHdG

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8-Hydroxy-2'-deoxyguanosine (8-OhdG) is a mutation-prone (G:C to T:A tranversion) DNA base-modified product generated by reactive oxygen species or photodynamic action. It is one of the most commonly used markers for the evaluation of oxidative DNA damage. Immunofluorescence staining for 8-oxo-2′-deoxyguanosine (8-oxo-dG) was carried out using anti-8-oxo-dG antibody (Trevigen, Gaithersburg, MD, USA) and visualized with AlexaFluor 488-nm antibody (Invitrogen). The samples were analyzed by using an inverted fluorescence microscope equipped with a CCD camera (ZEISS Axiovert 40 CFL), image processing was performed using the ZEISS AxioVision software (Carl Zeiss AG) and the intensity of green fluorescence was measured by using the NIH-developed ImageJ software (Wayne Rasband, NIH).

Guo K., Lu J., Huang Y., Wu M., Zhang L., Yu H., Zhang M., Bao Y., He J.C., Chen H, & Jia W. (2015). Protective Role of PGC-1α in Diabetic Nephropathy Is Associated with the Inhibition of ROS through Mitochondrial Dynamic Remodeling. PLoS ONE, 10(4), e0125176.

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Immunofluorescence Protocol for Histone H3 Citrullination

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Fixed cells or vessels were washed with PBS and permeabilized (0.1% Triton X-100 and 0.1% sodium citrate) for 10 min at 4°C. Samples were blocked with 3% (w/v) BSA for 90 min at 37°C, rinsed, and then incubated overnight at 4°C or for 1 hour at 37°C in antibody dilution buffer containing 0.3% BSA, 0.1% Tween 20, and relevant antibodies (rabbit anti-histone H3 (citrulline 2, 8, and 17) (0.3 μg/ml; Abcam, ab5103), rat anti–PSGL-1 (1:1000; BD Biosciences). After several washes, samples were incubated for 2 hours at room temperature in antibody dilution buffer containing AF 488–conjugated secondary antibody (1.5 μg/ml) in 0.3% BSA in PBS. DNA was counterstained with Hoechst 33342 (1 μg/ml), and slides were coverslipped with Fluoromount gel (Electron Microscopy Sciences). Fluorescent images were acquired using an Axiovert 200 widefield fluorescence microscope (Zeiss) in conjunction with an Axiocam MRm monochromatic charge-coupled device camera (Zeiss) and analyzed with Zeiss AxioVision software. All channels were acquired in grayscale and pseudo-colored using Zeiss AxioVision or ImageJ software (National Institutes of Health). Exposure times are identical between LysM-Cre and K2KO tissue or neutrophils. Images were analyzed using ImageJ.

Bernal A, & Kimbrell D.A. (2000). Drosophila Thor participates in host immune defense and connects a translational regulator with innate immunity. Proceedings of the National Academy of Sciences of the United States of America, 97(11), 6019-6024.

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Embryonic GFP and Sox2 expression

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Embryos treated with rAAV CMV-GFP and scAAV1-Sox2-Str were imaged using a Zeiss Observer A1 fluorescent microscope 48 hours and 72 hours post-transduction, respectively. Images were processed using ZEN software (Zeiss), and fluorescence intensity was quantified for embryos transduced with rAAV-CMV-GFP using ImageJ software. Fluorescence intensity was calculated by the following equation: (total signal intensity – negative control background signal) / number of embryos.

Chen S., Sun S., Moonen D., Lee C., Yiu-Fai Lee A., Schaffer D.V, & He L. (2019). CRISPR-READI: Efficient generation of knock-in mice by CRISPR RNP Electroporation and AAV Donor Infection. Cell reports, 27(13), 3780-3789.e4.

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Live-Cell Imaging of NaD1 Effects

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Live imaging was performed on a Zeiss LSM 510 or LSM 780 confocal microscope using a 40× or 63× oil immersion objective in a 37°C/5% CO₂ atmosphere. Adherent cells were cultured on coverslips prior to imaging, while non-adherent cells were immobilized onto 10% poly-L-lysine-coated coverslips. All cell types were prepared for imaging in RPMI medium containing 0.1% BSA and 1–2 μg/ml PI. NaD1, BODIPY-NaD1, and FITC-Dextran (100 μg/ml) was added directly to the imaging chamber via a capillary tube. In certain experiments, cells were either stained with PKH67 (Sigma-Aldrich) or transfected with a plasmid construct for free GFP or GFP-PH(PLCδ) using Lipofectamine 2000 Reagent (Invitrogen) as per manufacturer’s instructions prior to imaging. The images were analyzed using ImageJ software or Zen software (Zeiss, Oberkochen, Germany). For quantification of CLSM experiments involving transfected cells, the effects of NaD1 on HeLa cells were observed over a 15 min timeframe from the time of NaD1 addition. Non-expressing cells were excluded from analysis.

Poon I.K., Baxter A.A., Lay F.T., Mills G.D., Adda C.G., Payne J.A., Phan T.K., Ryan G.F., White J.A., Veneer P.K., van der Weerden N.L., Anderson M.A., Kvansakul M, & Hulett M.D. (2014). Phosphoinositide-mediated oligomerization of a defensin induces cell lysis. eLife, 3, e01808.

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Immunohistochemical Analysis of Microglia

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IHC was performed according to our previous report [57 (link)]. The antibodies that were used are listed in Additional file 1: Table S1. Images were processed using the Zen image acquisition software package (Carl Zeiss, Oberkochen, Germany) and ImageJ software. The soma area was evaluated using images of Iba1 staining, and the amoeboid score was calculated by the following formula: (soma area/entire Iba1-stained area) × 100 (%). The Iba1- and CD68-costained areas were analyzed with ImageJ software (National Institutes of Health, Bethesda, MD, USA).

Tanaka M., Okuda T., Itoh K., Ishihara N., Oguro A., Fujii-Kuriyama Y., Nabetani Y., Yamamoto M., Vogel C.F, & Ishihara Y. (2023). Polycyclic aromatic hydrocarbons in urban particle matter exacerbate movement disorder after ischemic stroke via potentiation of neuroinflammation. Particle and Fibre Toxicology, 20, 6.

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Histological and Immunohistochemical Analysis of Wound Angiogenesis

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For H&E staining, slides with 5 μm tissue sections were baked at 60°C for 30 min and stained with an Autostainer XL (Leica Microsystems, Wetzlar, Germany) using an established protocol (Chen et al., 2020 (link); Chen et al., 2022 (link)). Immunohistochemistry of CD31 was performed in skin wound sections of db/db mice (6 mice per group) as described previously (Chen et al., 2022 (link)). Briefly, for wound tissue analysis of CD31 immunostaining, formalin-fixed paraffin-embedded sections were probed with a 1:50 dilution of anti-CD31 Ab overnight at 4°C, and then 1 h at room temperature with 1:500 dilution of a secondary antibody conjugated with Alexa-555. Images were obtained with a Zeiss LSM 880 confocal microscope. Vascular density, determined from 6 high-power fields per section and represented as a percentage of vascular tissue area occupied by CD31 relative to the total area of the field of view, was analyzed using Zeiss Zen and ImageJ software as described (Chen et al., 2022 (link)).

Chen Z., Haus J.M., DiPietro L.A., Koh T.J, & Minshall R.D. (2023). Neutralization of excessive CCL28 improves wound healing in diabetic mice. Frontiers in Pharmacology, 14, 1087924.

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Nicotine Modulates DAF-16 Localization

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A previously described protocol, modified slightly, was used to determine the effect of nicotine on the nuclear localization of DAF-16 in TJ356 zls356 [daf-16p::da16a/b::GFP + rol-6(su1006)] (DAF-16:: GFP fusion protein) transgenic L1 worms (Lee et al., 2018 (link)). Synchronized L1 larvae were put on nicotine-treated/untreated NGM plates incubated for 72 h at 20°C. In the following steps, C. elegans were washed three times with M-9 buffer, mounted on a glass slide containing 100 mM sodium azide, and covered with a coverslip. DAF-16::GFP nuclear localization was observed under a fluorescence microscope (Olympus BX53) based on the discrete fluorescence aggregation phenotype. ImageJ software was used for analyzing the images (Carl Zeiss, Gottingen, Germany). Each experiment was repeated three times.

Ullah I., Zhao L., Uddin S., Zhou Y., Wang X, & Li H. (2024). Nicotine-mediated therapy for Parkinson’s disease in transgenic Caenorhabditis elegans model. Frontiers in Aging Neuroscience, 16, 1358141.

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Eca109 Cell Scratch Assay

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Eca109 cell (5 × 10⁵) were seeded in 6-well plates for 24 h and scraped by a sterile pipette tip. Cells were cultured with DMSO or Ginsenoside CK in FBS-free medium. sh-NC and sh-VEGF-A cells were maintained with FBS-free medium. The Zen Imaging software (Carl Zeiss, Germany) was applied to observe images at 0 h, 24 h and 48 h. The Image J software (USA) was applied to calculate the scratch area.

Huang J., Pan D., Liu F., Hong Y., Huang G., Huang X., Wang X, & Lin Z. (2022). Ginsenoside compound K inhibits the proliferation, migration and invasion of Eca109 cell via VEGF-A/Pi3k/Akt pathway. Journal of Cardiothoracic Surgery, 17, 99.

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