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Image j

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ImageJ is an open-source image processing and analysis software. It provides a platform for viewing, editing, analyzing, and processing digital images. The software supports a variety of image file formats and offers a wide range of tools for tasks such as measuring, enhancing, and processing images.

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Lab products found in correlation

Vh e500, by Keyence (2 mentions) Vb 7010, by Keyence (1 mentions) Prism 7, by GraphPad (1 mentions) Clampfit 10, by Molecular Devices (1 mentions) Bz x analyzer, by Keyence (1 mentions) Alexa fluor 488 goat anti rabbit igg, by Thermo Fisher Scientific (1 mentions) Alexa fluor 488 goat anti rat igg, by Thermo Fisher Scientific (1 mentions) Bz x710 microscope, by Keyence (1 mentions) Fluoromount g with dapi, by Thermo Fisher Scientific (1 mentions) Gram staining kit, by Merck Group (1 mentions) Alexa fluor 594 goat anti rabbit igg, by Thermo Fisher Scientific (1 mentions) Trilogy buffer, by Cell Marque (1 mentions)

7 protocols using image j

1

Genital Rotation Patterns in Myo31DF Mutant Males

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In the majority of Myo31DFK2 homozygous males, the genitalia rotate 360° counterclockwise, which is the left-right inversed direction of their wild-type counterpart12 (link),14 (link). However, the rest of the males had genitalia whose rotation stopped before it was completed. The deviation in the rotation angle of the male genitalia (angle deviation) was defined as previously described with slight modifications14 (link). The angle formed by the midline of the abdomen and the dorsoventral line that passes though the anus and penis (middle of the claspers) was measured with Image J (http://rsb.info.nih.gov/ij/) on a photograph of the genitalia of each male (VB-7010, Keyence) (Fig. 2a,b). Based on this angle, the angle deviations were classified into eight groups: 0° (Left 22°-Right 22°), Right 45° (Right 22°-Right 67°), Right 90° (Right 67°-Right 112°), Right 135° (Right 112°-Right 157°), 180° (Right 157°- Left 157°), Left 135° (Left 157°-Left 112°), Left 90° (Left 112°-Left 67°), and Left 45° (Left 67°-Left 22°) (Fig. 2c).
Inatomi M., Shin D., Lai Y.T, & Matsuno K. (2019). Proper direction of male genitalia is prerequisite for copulation in Drosophila, implying cooperative evolution between genitalia rotation and mating behavior. Scientific Reports, 9, 210.
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2

Image Analysis and Statistical Methods

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Images were analyzed and processed using Photoshop (Adobe), ImageJ, the Keyence BZ-II viewer software, and Image Access Enterprise 6. Graphs were plotted and statistical analysis was performed with GraphPad Prism 7 software using Student's unpaired two-tailed t test when comparing two groups, one-way ANOVA followed by Tukey post-hoc test when comparing multiple groups and a χ2 test for genotype frequencies. Results are shown as mean and standard deviation (SD). Group and sample sizes were empirically determined and the number of biological repetitions (n) is stated in each figure legend. No randomization or blinding protocol was used for experimental grouping.
Labi V., Peng S., Klironomos F., Munschauer M., Kastelic N., Chakraborty T., Schoeler K., Derudder E., Martella M., Mastrobuoni G., Hernandez-Miranda L.R., Lahmann I., Kocks C., Birchmeier C., Kempa S., Quintanilla-Martinez de Fend L., Landthaler M., Rajewsky N, & Rajewsky K. (2019). Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat. Genes & Development, 33(23-24), 1673-1687.
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3

Droplet-based Characterization Techniques

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During cleaning efficiency evaluation, all the fluorescence intensity measurements were acquired via ImageJ (NIH, Bethesda, MD, USA) and analyzed via Origin (Electronic Arts, Redwood City, CA, USA). For evaluating the dead volumes of the TESLI, the total volume of the generated droplets was acquired by multiplying the droplet area obtained from ImageJ with the actual channel height measured by VK-X100K laser microscope (Keyence Corporation, Osaka, Japan). The images captured for correlation between microvalve opening time and droplet volume were also measured via ImageJ to acquire the droplet area to be multiplied with the channel height to obtain the droplet volume. The comparison, further data analysis, and plotting were done via Origin. The recorded fluorescence signal from the LABVIEW program were all analyzed via MATLAB and Excel and plotted via Origin. The distribution of the droplet size was normalized to its average and plotted via Origin.
Shao F., Hsieh K., Zhang P., Kaushik A.M, & Wang T.H. (2022). Facile and scalable tubing-free sample loading for droplet microfluidics. Scientific Reports, 12, 13340.
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4

Quantitative Analysis of Immunostaining and Electrophysiology

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Immunostaining data were quantified, analyzed with ImageJ (United States National Institutes of Health) and BZ-X Analyzer (Keyence BZ-X710 microscope, Itasca, IL, United States) software. Electrophysiological data were analyzed by Clampfit10 (Molecular Devices, San Jose, CA, United States). Statistical analyses were performed using OriginPro 2020 software. Graphs were generated using Canvas X (Canvas GFX Inc., Boston, MA, United States). Simple comparisons of the means and standard errors of the mean (SEMs) were performed using a Student’s t-test. Multiple comparisons of means and SEMs were performed by a one-way ANOVA (with/without repeated measures) analysis followed by Tukey’s test. p values < 0.05 were considered significant.
Rahaman S.M., Chowdhury S., Mukai Y., Ono D., Yamaguchi H, & Yamanaka A. (2022). Functional Interaction Between GABAergic Neurons in the Ventral Tegmental Area and Serotonergic Neurons in the Dorsal Raphe Nucleus. Frontiers in Neuroscience, 16, 877054.
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5

Optimization of Bioassay Platform Pretreatment

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Optimization of the analytical platform was carried out by experimentally investigating the effects of various surface pre-treatment methods. First, the disc-chips were washed to remove the releasing agent used in injection molding of the discs. Next, a water repellent treatment agent (FS-1060TH-0.5, Fluorotechnology, Japan) was applied to the reservoirs and the flow channels (Fig. 4). Then, the effects of three different blocking agents, BSA-PBS-T (B), milk protein (M), and IgG polymer (I), were analyzed. Each was applied to both the pad and the disc-chip. The concentrations of the blocking agents applied to the disc-chip were 20 mg/mL, 4 mg/mL and 40 μg/mL for B, M and I, respectively. The concentrations applied to the pads were 2.5 times those applied to the disc-chips.
The contact angles of the three blocking agents on the plate were measured using μL of distilled water on an acrylic resin made from the same material as the disc-chips. A microscope (VH-E500, Keyence Co., Japan) and image-analysis software (Image J, Open source) were used to measure the contact angles. At the same time, the intensities of the optical reader were measured for each pre-treatment condition using standard cortisol solutions with concentrations of 1 and 3 ng/mL.
Yamaguchi M., Katagata H., Tezuka Y., Niwa D, & Shetty V. (2014). Automated-immunosensor with centrifugal fluid valves for salivary cortisol measurement. Sensing and Bio-Sensing Research, 1, 15-20.
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6

Immunofluorescence Staining of Skin Samples

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Skin samples were fixed in 4% paraformaldehyde (PFA) in PBS overnight and submitted to the Johns Hopkins Oncology Tissue Services where they were embedded in paraffin, sliced into 4 μm sections, mounted and stained with hematoxylin and eosin (H&E). Gram stain was performed using the Gram Staining Kit (Sigma Aldrich) according to manufacturer’s instructions. For immunofluorescence labeling, paraffin sections were deparaffinized, underwent heat-mediated antigen retrieval in either Trilogy buffer (Cell Marque) or Tris-EDTA buffer (10mM Tris Base, 1 mM EDTA Solution, 0.05% Tween 20, pH 9.0), blocked in blocking buffer (PBS with 10% goat serum) for 1 hour at room temperature, and then incubated at 4° C overnight with 1 μg/mL rabbit anti-mBD14, rat anti-mouse Ly6G or rabbit anti-S.aureus primary antibodies in blocking buffer. The next day, sections were incubated for 1 hour at room temperature with 1 μg/mL of either AlexaFluor-488 goat anti-rabbit IgG (ThermoFisher, for mBD14 staining), AlexaFluor-488 goat anti-rat IgG (ThermoFisher, for Ly6G staining) or AlexaFluor-594 goat anti-rabbit IgG (ThermoFisher, for S. aureus staining). All slides were washed and mounted with Fluoromount-G with DAPI (ThermoFisher). All microscopy were performed on a Keyence BZ-X710 microscope (Keyence) and analyzed with Image J (National Institutes of Health Research Services Branch).
Dong X., Limjunyawong N., Sypek E.I., Wang G., Ortines R.V., Youn C., Alphonse M.P., Dikeman D., Wang Y., Lay M., Kothari R., Vasavda C., Pundir P., Goff L., Miller L.S., Lu W., Garza L.A., Kim B.S., Archer N.K, & Dong X. (2022). Keratinocyte-derived defensins activate neutrophil-specific receptors Mrgpra2a/b to prevent skin dysbiosis and bacterial infection. Immunity.
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7

Optimization of Bioassay Platform Pretreatment

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Optimization of the analytical platform was carried out by experimentally investigating the effects of various surface pre-treatment methods. First, the disc-chips were washed to remove the releasing agent used in injection molding of the discs. Next, a water repellent treatment agent (FS-1060TH-0.5, Fluorotechnology, Japan) was applied to the reservoirs and the flow channels (Fig. 4). Then, the effects of three different blocking agents, BSA-PBS-T (B), milk protein (M), and IgG polymer (I), were analyzed. Each was applied to both the pad and the disc-chip. The concentrations of the blocking agents applied to the disc-chip were 20 mg/mL, 4 mg/mL and 40 μg/mL for B, M and I, respectively. The concentrations applied to the pads were 2.5 times those applied to the disc-chips.
The contact angles of the three blocking agents on the plate were measured using μL of distilled water on an acrylic resin made from the same material as the disc-chips. A microscope (VH-E500, Keyence Co., Japan) and image-analysis software (Image J, Open source) were used to measure the contact angles. At the same time, the intensities of the optical reader were measured for each pre-treatment condition using standard cortisol solutions with concentrations of 1 and 3 ng/mL.
Yamaguchi M., Katagata H., Tezuka Y., Niwa D, & Shetty V. (2014). Automated-immunosensor with centrifugal fluid valves for salivary cortisol measurement. Sensing and Bio-Sensing Research, 1, 15-20.
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