diffusion data in matlab Search Results


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Diffusion Model Analysis Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Diffusion Data, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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MathWorks Inc fibronectin diffusion model
Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
Fibronectin Diffusion Model, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
Ca 2+ Diffusion Matlab Code, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
Matlab Frap Analysis Plugin, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
Matlab Version R2017b, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
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Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the <t>fibronectin</t> gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.
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Image Search Results


Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the fibronectin gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: Fibronectin1 gradient in mouse embryo cranial region and microfluidic chip for haptotaxis study. A) Immunofluorescence of FN1 was performed on the coronal section of the E13.5 mouse skull, with a yellow region‐of‐interest (ROI) line used to identify the fibronectin gradient in gray scale 16‐bits image. B) The fluorescent intensity line profile along the yellow ROI line was obtained after applying a Gaussian averaging filter. Four different ROI lines locations were chosen (image depicts only one), the averaged line profile (red) is plotted with standard deviation in shaded area (blue). Three biological replicates were conducted to conclude the 2–3‐fold changes in fluorescent intensity of fibronectin antibody staining, with only one depicted in the figure. C) Stitched bright field image of the chip with four food‐dye colors in all channels and chambers. The food dye was used to visually demonstrate the capability of the chip to generate multiple gradients in a high‐throughput manner. The chip dimension is ≈60 mm × 20 mm. Scale bar: 5 mm. Each unit comprises four chambers and a rinse channel. Open and close of the chambers and rinse channel is controlled by push‐down valves, which are placed at the inlet and outlet of each chamber and channel, and between the chambers. Scale bar: 500 µm.

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Immunofluorescence, Standard Deviation, Staining, High Throughput Screening Assay

MATLAB model for fibronectin diffusion gradient simulation and FITC‐dextran validation. A) Fibronectin was delivered by perfusion to chamber D as the source and diffuses to other chambers, creating a gradient. Fibronectin in the source chamber was refreshed every 30 min to maintain a constant concentration. B) The concentration changes of fibronectin over the y‐axis were simulated at various time points with source concentration of 100 µg mL −1 (0–48 h). The chip schematic was presented to match the fibronectin concentration gradients to the chip location. The chambers were labeled as upper, mid, and lower gradient chambers (area shaded in gray) to represent their respective gradient location. C) Time‐lapse images of 500 kDa 1000 µg mL −1 FITC‐dextran diffusion at 0, 2, 4, 8, 12, 24, and 48 h. Images were color‐coded: white indicates higher fluorescent intensity, while purple denotes lower intensity. D) Line profiles of FITC‐dextran fluorescent intensity at various time points were plotted. At each time point, 24 line profiles from eight technical replicates were averaged and plotted using custom MATLAB code. Intensities were normalized to the overall maximum. E) Profiles were magnified to evaluate chambers with lower and mid gradient chambers.

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: MATLAB model for fibronectin diffusion gradient simulation and FITC‐dextran validation. A) Fibronectin was delivered by perfusion to chamber D as the source and diffuses to other chambers, creating a gradient. Fibronectin in the source chamber was refreshed every 30 min to maintain a constant concentration. B) The concentration changes of fibronectin over the y‐axis were simulated at various time points with source concentration of 100 µg mL −1 (0–48 h). The chip schematic was presented to match the fibronectin concentration gradients to the chip location. The chambers were labeled as upper, mid, and lower gradient chambers (area shaded in gray) to represent their respective gradient location. C) Time‐lapse images of 500 kDa 1000 µg mL −1 FITC‐dextran diffusion at 0, 2, 4, 8, 12, 24, and 48 h. Images were color‐coded: white indicates higher fluorescent intensity, while purple denotes lower intensity. D) Line profiles of FITC‐dextran fluorescent intensity at various time points were plotted. At each time point, 24 line profiles from eight technical replicates were averaged and plotted using custom MATLAB code. Intensities were normalized to the overall maximum. E) Profiles were magnified to evaluate chambers with lower and mid gradient chambers.

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Diffusion-based Assay, Biomarker Discovery, Concentration Assay, Labeling

Validation of gradient formation through FITC‐fibronectin diffusion. A) Fluorescent images of 500 µg mL −1 FITC‐fibronectin diffusion at 24 h compared with a blank control. Images were color‐coded as previously described. B) The line profiles of averaged fluorescent intensity (red: 500 µg mL −1 FITC‐fibronectin; black: Blank control) across the y‐axis were generated for the lower, mid, and upper gradient chambers (shaded in gray), derived from multiple line profiles and utilizing eight technical replicates.

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: Validation of gradient formation through FITC‐fibronectin diffusion. A) Fluorescent images of 500 µg mL −1 FITC‐fibronectin diffusion at 24 h compared with a blank control. Images were color‐coded as previously described. B) The line profiles of averaged fluorescent intensity (red: 500 µg mL −1 FITC‐fibronectin; black: Blank control) across the y‐axis were generated for the lower, mid, and upper gradient chambers (shaded in gray), derived from multiple line profiles and utilizing eight technical replicates.

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Biomarker Discovery, Diffusion-based Assay, Control, Generated, Derivative Assay

Calvarial osteoblast progenitor migration and cell morphology in segmented fibronectin gradient compared with controls. A) Track plots (top row) provide visualization of cell migration direction. Cells migrating upward or toward the increasing fibronectin of the gradient are labeled in red, while those moving downward or toward decreasing fibronectin levels of the gradient are labeled in blue. The number of cells migrating upward or downward is annotated in the text. The rose plot (bottom row), resembling a circular histogram, visually depicts the distribution of cell migration angles, with the frequency of migration events in different directions labeled as percentages. B) Primary calvarial osteoblast progenitors exhibit distinct morphologies and sizes in segmented concentration gradients, as revealed by phalloidin staining of actin filaments (Green: Phalloidin; Blue: Hoechst; Scale bar: 100 µm). C) The quantification of percentage of cells migrating upward (toward the upper regions of the fibronectin gradient) or downward (toward the lower regions of the fibronectin gradient). D) Cell area quantification was performed using phalloidin images and compared across groups, including lower, mid, and upper gradient chambers, as well as blank and uniform fibronectin controls. N = 150 for all groups. Cells in the upper gradient chambers were found to be significantly larger in size.

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: Calvarial osteoblast progenitor migration and cell morphology in segmented fibronectin gradient compared with controls. A) Track plots (top row) provide visualization of cell migration direction. Cells migrating upward or toward the increasing fibronectin of the gradient are labeled in red, while those moving downward or toward decreasing fibronectin levels of the gradient are labeled in blue. The number of cells migrating upward or downward is annotated in the text. The rose plot (bottom row), resembling a circular histogram, visually depicts the distribution of cell migration angles, with the frequency of migration events in different directions labeled as percentages. B) Primary calvarial osteoblast progenitors exhibit distinct morphologies and sizes in segmented concentration gradients, as revealed by phalloidin staining of actin filaments (Green: Phalloidin; Blue: Hoechst; Scale bar: 100 µm). C) The quantification of percentage of cells migrating upward (toward the upper regions of the fibronectin gradient) or downward (toward the lower regions of the fibronectin gradient). D) Cell area quantification was performed using phalloidin images and compared across groups, including lower, mid, and upper gradient chambers, as well as blank and uniform fibronectin controls. N = 150 for all groups. Cells in the upper gradient chambers were found to be significantly larger in size.

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Migration, Labeling, Concentration Assay, Staining

Calvarial osteoblast progenitor haptotactic migration in mid FN1 gradient chamber. A) The forward migration index (yFMI), B) velocity, and C) Euclidean distance were compared across the groups using estimation plots to illustrate the distribution of the entire cell population. The swarmplot displays the underlying distribution, with differences compared to the blank control group plotted for all other groups as bootstrap 95% confidence intervals. Statistical analysis was performed using one‐way ANOVA test with Dunnett's multiple comparison test ( p < 0.05 significance threshold). N = 150 for all groups in Figure panel (A–C). D) The number of protrusions in migrating cells was counted for the lower, mid, and upper FN1 gradient condition and compared to blank and uniform fibronectin controls. The mean is indicated with 95% confidence intervals. Statistical analysis was performed using one‐way ANOVA test with Dunnett's multiple comparison test (All groups compared to blank control). N = 28–33 cells in (D).

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: Calvarial osteoblast progenitor haptotactic migration in mid FN1 gradient chamber. A) The forward migration index (yFMI), B) velocity, and C) Euclidean distance were compared across the groups using estimation plots to illustrate the distribution of the entire cell population. The swarmplot displays the underlying distribution, with differences compared to the blank control group plotted for all other groups as bootstrap 95% confidence intervals. Statistical analysis was performed using one‐way ANOVA test with Dunnett's multiple comparison test ( p < 0.05 significance threshold). N = 150 for all groups in Figure panel (A–C). D) The number of protrusions in migrating cells was counted for the lower, mid, and upper FN1 gradient condition and compared to blank and uniform fibronectin controls. The mean is indicated with 95% confidence intervals. Statistical analysis was performed using one‐way ANOVA test with Dunnett's multiple comparison test (All groups compared to blank control). N = 28–33 cells in (D).

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Migration, Control, Comparison

Effect of small molecules on cell migration and morphology. A) Tracking (top row) and rose plots (bottom row) illustrate changes in directional migration in small molecule groups compared to the haptotaxis control. B) All cell migration analysis in this and subsequent figures is conducted in the Mid FN1 gradient chamber. C) The quantification of percentage of cells migrating upward (toward the fibronectin gradient) or downward (away from the fibronectin gradient). D) Phalloidin‐stained cell areas for the mid fibronectin gradient condition were compared with small molecule groups, including 20 µ m CK666, 100 µ m CK666, and 50 µ m Y27632. N = 80 for all groups. Statistical analyses were performed using a one‐way ANOVA test with Dunnett's multiple comparison test.

Journal: Small (Weinheim an Der Bergstrasse, Germany)

Article Title: Lamellipodia‐Mediated Osteoblast Haptotaxis Guided by Fibronectin Ligand Concentrations on a Multiplex Chip

doi: 10.1002/smll.202401717

Figure Lengend Snippet: Effect of small molecules on cell migration and morphology. A) Tracking (top row) and rose plots (bottom row) illustrate changes in directional migration in small molecule groups compared to the haptotaxis control. B) All cell migration analysis in this and subsequent figures is conducted in the Mid FN1 gradient chamber. C) The quantification of percentage of cells migrating upward (toward the fibronectin gradient) or downward (away from the fibronectin gradient). D) Phalloidin‐stained cell areas for the mid fibronectin gradient condition were compared with small molecule groups, including 20 µ m CK666, 100 µ m CK666, and 50 µ m Y27632. N = 80 for all groups. Statistical analyses were performed using a one‐way ANOVA test with Dunnett's multiple comparison test.

Article Snippet: To validate the MATLAB fibronectin diffusion model, we conducted experiments using FITC‐dextran with a molecular weight similar to fibronectin (FITC‐dextran: 500 kDa; fibronectin: 440–530 kDa).

Techniques: Migration, Control, Staining, Comparison