README.md

In vmeasur: Quantify the Contractile Nature of Vessels Monitored under an Operating Microscope

vmeasur

The goal of vmeasur is to quantify the contractile nature of vessels monitored under an operating microscope.

Installation

You can install the released version of vmeasur from CRAN with:

install.packages("vmeasur")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("JamesHucklesby/vmeasur")

Calibrating the operating microscope

To calibrate an operating microscope, take an image of a gradiated ruler. You can then use this function to calculate the number of pixels per mm.

calibrate_pixel_size()

Measuring the vessel diameter

Once video data is collected, the region of interest can be selected using select_roi. This provides a wizard that will assist the user through image analysis.

select_roi()

Once selected, vmeasur can output a variety of important parameters and graphs

#> # A tibble: 4 x 12
#> # Rowwise: 
#>   event_maxima event_start event_end type     start_value end_value max_value
#>          <dbl>       <dbl>     <dbl> <chr>          <dbl>     <dbl>     <dbl>
#> 1          531         472       647 contract        12.9      12.3      3.76
#> 2          261         195       331 contract        14.7      14.2      5.67
#> 3          130          67       195 contract        14.6      14.7      5.95
#> 4          396         331       472 contract        14.2      12.9      6.02
#> # ... with 5 more variables: baseline_change <dbl>, event_duration <dbl>,
#> #   cont_duration <dbl>, fill_duration <dbl>, event_gradient <dbl>
#> # A tibble: 6 x 4
#>   variable   mean      sd overall           
#>   <chr>     <dbl>   <dbl> <chr>             
#> 1 CA       0.12   0.00645 0.12 (0.006448)   
#> 2 CD       2.77   0.136   2.774 (0.1358)    
#> 3 CS       0.0434 0.00390 0.04337 (0.003905)
#> 4 ED       6.36   0.908   6.36 (0.9081)     
#> 5 EDD      0.193  0.0112  0.1932 (0.0112)   
#> 6 EDD2     0.185  0.0152  0.1854 (0.01517)
#>   X.1 y p_width excluded filename
#> 1   1 1       0    FALSE        1
#> 2   2 2       0    FALSE        1
#> 3   3 3       0    FALSE        1
#> 4   4 4       0    FALSE        1
#> 5   5 5       0    FALSE        1
#> 6   6 6       0    FALSE        1

#> # A tibble: 6 x 15
#> # Groups:   source_file [6]
#>   ygroup event_maxima event_start event_end type     start_value end_value
#>   <chr>         <dbl>       <dbl>     <dbl> <chr>          <dbl>     <dbl>
#> 1 3               134          62       192 contract       13.2      13.2 
#> 2 4               130          62       193 contract       12.6      12.7 
#> 3 2               136          63       193 contract       12.3      12.1 
#> 4 5               128          63       194 contract        9.97      9.88
#> 5 1               132          65       191 contract       14.2      14.2 
#> 6 6               129          66       196 contract       10.5      10.6 
#> # ... with 8 more variables: max_value <dbl>, baseline_change <dbl>,
#> #   event_duration <dbl>, cont_duration <dbl>, fill_duration <dbl>,
#> #   event_gradient <dbl>, source_file <dbl>, cont_id <int>
#> # A tibble: 6 x 5
#>   ygroup variable   mean      sd overall          
#>   <chr>  <chr>     <dbl>   <dbl> <chr>            
#> 1 1      CA       0.104  0.0345  0.1038 (0.03449) 
#> 2 1      CD       2.96   0.0913  2.961 (0.0913)   
#> 3 1      CS       0.0349 0.0105  0.03486 (0.01051)
#> 4 1      ED       6.38   1.14    6.382 (1.145)    
#> 5 1      EDD      0.188  0.00948 0.1875 (0.009478)
#> 6 1      EDD2     0.177  0.0190  0.1768 (0.01904)

vmeasur documentation built on Nov. 12, 2021, 1:07 a.m.