Journal: STAR Protocols

Article Title: Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

doi: 10.1016/j.xpro.2022.101542

Figure Lengend Snippet: Examples of good and bad brain explant and analysis (A and B) Good (B) and bad (A) examples of the adult brain explant. Dotted circles are the areas that experimenters should be careful. Small letters mark each dotted circle that show bad (a)-c)) and good examples (d)-f)). Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift. Refer to the MATLAB CBF analysis from the aligned recording file ( Figure 4 D2). Note that there are lots of artefacts (appearing at the frequency of circa 10 Hz, blue in the ‘CBF raw’ and ‘CBF masked’ plots) visible on the mean power spectrum, CBF histogram and CBF heatmaps. (D) Remaining drifts in an aligned recording file. Images of the first (D1), middle (D2) and last (D3) frame of the 30s recording file. Each black arrow indicates an identical pixel site on the image. Note the loss of sharpness of the image at the arrow locations reflecting z drift. (E) Example of an unsuccessful fluorescent particle injection. The yellow arrow marks accumulated fluorescent particle in the brain parenchyma. Scale bar: 50 μm.

Article Snippet: Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift.

Techniques: Injection

Journal: STAR Protocols

Article Title: Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

doi: 10.1016/j.xpro.2022.101542

Figure Lengend Snippet: Data analysis for ciliary beating images using a MATLAB script (A) The diagrams show the principle underlying the analysis for ciliary beating using the provided MATLAB scripts. (B) The interface of MATLAB. (C) The partial screenshot of “step 1” (C1) and “step 3” (C2) in the MATLAB script. The numbers with red lines can be modified to reflect the experimental or analyzing conditions. (D) Expected outcome of data analysis. (D1) Diagram of the brain explant (dorsal view). (D2) The PNG file output after analysis. The file contains the raw image, mean power spectrum, histogram of ciliary beating frequency (CBF) and color-coded raw/masked CBF. Red dotted circles with red arrows indicate difference between the results by the MATLAB script and FreQ plugin. Abbreviation: (D1) anterior (A), posterior (P), left (L) and right (R). (D2) Peak Frequency (Peak Freq) and Hertz (Hz). Scale bars are 50 μm.

Article Snippet: Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift.

Techniques: Modification

Journal: STAR Protocols

Article Title: Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

doi: 10.1016/j.xpro.2022.101542

Figure Lengend Snippet: Comparison of the data analysis for ciliary beating from the MATLAB script and FreQ plugin (A and B) Color-coded masked CBF plots from the MATLAB script (A) and the FreQ plugin (B). (C and D) The differences between the MATLAB and FreQ outputs are shown as a heat map of masked CBF (C) and histogram (D). Scale bars are 50 μm.

Article Snippet: Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift.

Techniques:

Journal: STAR Protocols

Article Title: Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

doi: 10.1016/j.xpro.2022.101542

Figure Lengend Snippet: Data analysis for ciliary beating using the FreQ plugin (A) The screenshots show various setup conditions on the parameters of the analysis in the FreQ plugin. (B) Expected outcome of the analysis. (B1) Diagram of the brain explant (dorsal view). (B2) The output PNG files after analysis. The files are color-coded raw/masked CBF, power spectrum of primary/secondary peak frequency, histogram of ciliary beating frequency (CBF). Red dotted circles with red arrows indicate difference between the results by the MATLAB script and FreQ plugin.

Article Snippet: Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift.

Techniques:

Journal: STAR Protocols

Article Title: Measurement of ciliary beating and fluid flow in the zebrafish adult telencephalon

doi: 10.1016/j.xpro.2022.101542

Figure Lengend Snippet:

Article Snippet: Scale bar: 50 μm. (C) The PNG output file of a MATLAB CBF analysis on a non-aligned recording file with some drift.

Techniques: Recombinant, Software, Microscopy, Imaging

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: An example of a right eye of a 21-year-old male subject where the corneal pre (a) and post (b) Ortho-K wear tangential refractive power maps were determined by a custom-built MATLAB code.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques:

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential power map of left eye of a 30-year-old male subject (a) as measured by Medmont, (b) as calculated then smoothed by a custom-built MATLAB software code.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 0 to S = 1.1.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 2.4 to S = 3.5.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 3.6 to S = 4.7.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 4.8 to S = 5.9.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 6 to S = 28.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software

Journal: Heliyon

Article Title: Investigation of the relationship between contact lens design parameters and refractive changes in Ortho-K

doi: 10.1016/j.heliyon.2022.e11699

Figure Lengend Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 30 to S = 140.

Article Snippet: Tangential refractive power map of a 30 years male subject as calculated then smoothed by a custom-built MATLAB software code with smoothing factor S = 1.2 to S = 2.3.

Techniques: Software