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webpage_contents/publications/beta__20240528_MartaGironaAlarcon.qmd

----
-title: 'In vivo Mouse Imaging of the Central Nervous System Fluid Spaces with High Spatiotemporal Resolution using Synchrotron Radiation Computed Tomography'
-date: '2024-05-28'
-First author: 'Marta Girona Alarcón'
-Last author: 'Vartan Kurtcuoglu'
-author: 
-  - name: 'Marta Girona Alarcón (first author)'
-    orcid: 0009-0006-2111-2716     
-    affiliations:
-      - name: The Interface Group, Institute of Physiology, University of Zurich
-
-  - name: 'Vartan Kurtcuoglu (last author)'
-    orcid: 0000-0003-2665-0995
-    affiliations:
-      - name: The Interface Group, Institute of Physiology, University of Zurich
-code-fold: true
----
-
-```{r userinputs}
-#| output: false
-#| echo: false
-library(dplyr)
-
- columns <- c("EXPERIMENT_TYPE", "FACILITY", "FILE","SUBJECT","ADD_INFO")
-
-# EDIT INPUTS For the columns 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"),
-        c("synchrotron_microCT","ESRF_01_Jan_0000","Mice_Information_dummy.csv","JP23","Experiment 4")
-      )
-)
-
- 
-# -- Do not edit code below this line ----------------------------------------------------------------------------
-# Assign column names
-colnames(inputs) <- columns 
- 
- 
-# --- Do NOT EDIT --- 
-# This code chunk gathers the rows from tables specified in the inputs
-# 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 
-
-```
-
-
-# Supplemental Results
-
-Note: Supplemental Methods are supposed to go to beamtime pages
-
-## Links to protocol pages
-
-```{r}
-# | warning: false 
-
-folders <- unique(cbind(inputs$EXPERIMENT_TYPE,inputs$FACILITY)) #unique combination of experiment type and facility
-paths <-  as.data.frame(file.path(apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')) #put together the paths rowwise
-colnames(paths) <- 'path'
-
-
-# Add location 
-paths$link <- paste0('<a href=\'',paths$path,'\' target=\'_blank\'>', 'protocol folder >>','</a>')
-file.path(here::here(), apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')
-
-DT::datatable(paths, escape = FALSE)
-
-```
-
-## Synchrotron µCT Data
-
-
-
-```{r}
-# | warning: false 
-
-#Display  table 
-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