In vivo Mouse Imaging of the Central Nervous System Fluid Spaces with High Spatiotemporal Resolution using Synchrotron Radiation Computed Tomography

IEEE2024

Authors
Affiliation

Marta Girona Alarcón (first author)

The Interface Group, Institute of Physiology, University of Zurich

Vartan Kurtcuoglu (last author)

The Interface Group, Institute of Physiology, University of Zurich

Published

January 1, 2024

Code
# EDIT INPUTS HERE ---------------------------

# Define the rows of the input table, each row is c('input1','input2','input',....). Separate the rows by comma except the last row
inputs <- data.frame(
      rbind(
        c("synchrotron_microCT","SPring-8_May_2023","Mice_Information_SPring-8_20230508.csv","JP21","Experiment 1"),
        c("synchrotron_microCT","SPring-8_May_2023","Mice_Information_SPring-8_20230508.csv","JP28","Experiment 2"),
        c("synchrotron_microCT","SPring-8_May_2023","Mice_Information_SPring-8_20230508.csv","JP23","Experiment 3")
      )
)

# Assign column names
colnames(inputs) <- c("EXPERIMENT_TYPE", "FACILITY", "FILE","SUBJECT","ADD_INFO")

Supplemental Results

Note: Supplemental Methods are supposed to go to beamtime pages

Synchrotron µCT Data

Code
# | warning: false 
# --- Do NOT EDIT --- 
# This code chunk gathers the rows from tables specified in the inputs
library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
Code
# Loop thru the input rows
data_used <- list()
for (i in 1:nrow(inputs)){ 
  row_filepath <- file.path(here::here(), 'experiments',inputs$EXPERIMENT_TYPE[i], inputs$FACILITY[i], inputs$FILE[i]) 
  data_used[[i]] <- read.csv(row_filepath) %>% filter(SubjectID == inputs$SUBJECT[i]) # read table and filter subject
}

# Gather list elements in a table 
data_used <- do.call(rbind,data_used) 
data_used$experiment <- inputs$ADD_INFO # Add additional input column 

#Display 
DT::datatable(data_used, filter = 'top')
  • Experiment 1: ESRF, FR019
  • Experiment 2: ESRF, FR021
  • Experiment 3: SPring-8, JP028
  • Experiment 4: ESRF, FR063
  • Experiment 5: ESRF, FR050
  • Experiment 6: ESRF, FR017
  • Experiment 7: CLS, CA019
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