From 92c7b418d614c0bcb31ede398420b0593a3155d7 Mon Sep 17 00:00:00 2001
From: Marta Girona Alarcon <marta.gironaalarcon@uzh.ch>
Date: Wed, 14 Aug 2024 13:38:49 +0200
Subject: [PATCH] detele duplicated folders
---
.../CLS_2023_November/Experiment_page.qmd | 50 ----
.../Data_organization_ESRF_v1.qmd | 28 --
.../Mouse_list_CLS_November_2023.csv | 3 -
.../Mouse_list_CLS_November_2023_codebook.csv | 13 -
.../metadata_tables/README.txt | 1 -
.../Scan_list_CLS_November_2023.csv | 3 -
.../Scan_list_CLS_November_2023_codebook.csv | 13 -
.../xlsx/Mouse_list_CLS_November_2023.xlsx | Bin 10822 -> 0 bytes
.../xlsx/Scan_list_ESRF_November_2021.xlsx | Bin 10914 -> 0 bytes
.../protocols/Protocol-A_Facility_v1.qmd | 17 --
.../protocols/Protocol-B_Facility_v1.qmd | 17 --
.../CLS_2023_November/protocols/README.txt | 1 -
.../ESRF_2021_November/Experiment_page.qmd | 50 ----
.../Data_organization_ESRF_v1.qmd | 28 --
.../Mouse_list_ESRF_November_2021.csv | 4 -
...Mouse_list_ESRF_November_2021_codebook.csv | 13 -
.../metadata_tables/README.txt | 1 -
.../Scan_list_ESRF_November_2021.csv | 4 -
.../Scan_list_ESRF_November_2021_codebook.csv | 13 -
.../xlsx/Mouse_list_ESRF_November_2021.xlsx | Bin 10914 -> 0 bytes
.../xlsx/Scan_list_ESRF_November_2021.xlsx | Bin 10914 -> 0 bytes
.../protocols/Protocol-A_Facility_v1.qmd | 17 --
.../protocols/Protocol-B_Facility_v1.qmd | 17 --
.../ESRF_2021_November/protocols/README.txt | 1 -
.../README_ESRF_2021_November.md | 5 -
.../ESRF_2022_June/Experiment_page.qmd | 50 ----
.../Data_organization_ESRF_v1.qmd | 28 --
.../Mouse_list_ESRF_June_2022.csv | 3 -
.../Mouse_list_ESRF_June_2022_codebook.csv | 13 -
.../ESRF_2022_June/metadata_tables/README.txt | 1 -
.../Scan_list_ESRF_June_2022.csv | 3 -
.../Scan_list_ESRF_June_2022_codebook.csv | 14 -
.../xlsx/Mouse_list_ESRF_June_2022.xlsx | Bin 10859 -> 0 bytes
.../xlsx/Scan_list_ESRF_June_2022.xlsx | Bin 10859 -> 0 bytes
.../protocols/Protocol-A_Facility_v1.qmd | 17 --
.../protocols/Protocol-B_Facility_v1.qmd | 17 --
.../ESRF_2022_June/protocols/README.txt | 1 -
.../Mice_Information_SPring-8_20230508.csv | 35 ---
.../SPring-8_BL20B2_2023A1208_Scanlist.csv | 259 ------------------
.../experiments/SPring-8_May_2023/index.qmd | 28 --
.../Mice_Information_SPring-8_20230508.csv | 35 ---
.../Mouse_list_SPring-8_May_2023.csv | 3 -
.../Mouse_list_SPring-8_May_2023_codebook.csv | 13 -
.../SPring-8_BL20B2_2023A1208_Scanlist.csv | 259 ------------------
.../Scan_list_SPring-8_May_2023.csv | 3 -
.../Scan_list_SPring-8_May_2023_codebook.csv | 13 -
.../xlsx/Mouse_list_SPring-8_May_2023.xlsx | Bin 10854 -> 0 bytes
.../xlsx/Scan_list_SPring-8_May_2023.xlsx | Bin 10854 -> 0 bytes
.../protocols/SPring-8_reconstruction.qmd | 189 -------------
49 files changed, 1283 deletions(-)
delete mode 100644 webpage_contents/experiments/CLS_2023_November/Experiment_page.qmd
delete mode 100644 webpage_contents/experiments/CLS_2023_November/data_organization/Data_organization_ESRF_v1.qmd
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023.csv
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023_codebook.csv
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/README.txt
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023.csv
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023_codebook.csv
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/xlsx/Mouse_list_CLS_November_2023.xlsx
delete mode 100644 webpage_contents/experiments/CLS_2023_November/metadata_tables/xlsx/Scan_list_ESRF_November_2021.xlsx
delete mode 100644 webpage_contents/experiments/CLS_2023_November/protocols/Protocol-A_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/CLS_2023_November/protocols/Protocol-B_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/CLS_2023_November/protocols/README.txt
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/Experiment_page.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/data_organization/Data_organization_ESRF_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021.csv
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021_codebook.csv
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/README.txt
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021.csv
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021_codebook.csv
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/xlsx/Mouse_list_ESRF_November_2021.xlsx
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/metadata_tables/xlsx/Scan_list_ESRF_November_2021.xlsx
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-A_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-B_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/protocols/README.txt
delete mode 100644 webpage_contents/experiments/ESRF_2021_November/test_monitoring/README_ESRF_2021_November.md
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/Experiment_page.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/data_organization/Data_organization_ESRF_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022.csv
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022_codebook.csv
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/README.txt
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022.csv
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022_codebook.csv
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/xlsx/Mouse_list_ESRF_June_2022.xlsx
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/metadata_tables/xlsx/Scan_list_ESRF_June_2022.xlsx
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-A_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-B_Facility_v1.qmd
delete mode 100644 webpage_contents/experiments/ESRF_2022_June/protocols/README.txt
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/Mice_Information_SPring-8_20230508.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/SPring-8_BL20B2_2023A1208_Scanlist.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/index.qmd
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mice_Information_SPring-8_20230508.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023_codebook.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/SPring-8_BL20B2_2023A1208_Scanlist.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023_codebook.csv
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/xlsx/Mouse_list_SPring-8_May_2023.xlsx
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/metadata_tables/xlsx/Scan_list_SPring-8_May_2023.xlsx
delete mode 100644 webpage_contents/experiments/SPring-8_May_2023/protocols/SPring-8_reconstruction.qmd
diff --git a/webpage_contents/experiments/CLS_2023_November/Experiment_page.qmd b/webpage_contents/experiments/CLS_2023_November/Experiment_page.qmd
deleted file mode 100644
index 648e137..0000000
--- a/webpage_contents/experiments/CLS_2023_November/Experiment_page.qmd
+++ /dev/null
@@ -1,50 +0,0 @@
----
-title: 'SPring-8'
-subtitle: 'Collection period: YYYY-Month-DD to YYYY-Month-DD'
-date: '2046-12-31'
-description: |
- Description: e.g., Synchrotron X-ray computed microtomography data of mouse cerebrospinal fluid spaces in vivo
-collection-date: 'x'
-author:
- - name: Firstname1 Lastname1
- orcid: 0000-0000-0000-0000
- email: bill@gates.com
- affiliations:
- - name: Center X, Department of XX, University of XXX
-
- - name: Firstname2 Lastname2
- orcid: 0000-0000-0000-0000
- affiliations:
- - name: Center X, Department of XX, University of XXX
-license: CC BY
-listing:
- - id: protocols
- contents: "protocols/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
- - id: organization
- contents: "data_organization/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
----
-
-
-# Protocols
-
-::: {#protocols}
-:::
-
-# Data organization
-
-::: {#organization}
-:::
-
-
-# Mouse list table
-
-# Scan list table
-
diff --git a/webpage_contents/experiments/CLS_2023_November/data_organization/Data_organization_ESRF_v1.qmd b/webpage_contents/experiments/CLS_2023_November/data_organization/Data_organization_ESRF_v1.qmd
deleted file mode 100644
index 81acde2..0000000
--- a/webpage_contents/experiments/CLS_2023_November/data_organization/Data_organization_ESRF_v1.qmd
+++ /dev/null
@@ -1,28 +0,0 @@
----
-title: Data organization
-date: last-modified
----
-
-# Folder and filename schema:
-
- <date>_<labID>_<experiment description>/
- └── subj<subjID>/
- └── sc<scanID>_<anat>_[<suffix>]/
- └── subj<subjID>_sc<scanID>_[<suffix>].<ext>
-
-Example:
-
- 20231013_HOME_TEST/subj001/sc12345_brain/subj001_sc12345.img
-
-
-# Name parts explanation:
-
-- <date>: date formatted YYYYMMDD
-- <labID> : str Shortname of the lab, e.g., DESY-P07
-- <experiment description>: Short title e.g. in-vivo-mouse-CSF-infusion.
-- subj<subjID> : num subject id (3 digits, leading zeroes; e.g., subj001)
-- sc<scanID> : num scan identifier (5 digits; e.g., sc12345).
-- <anat> : str anatomy descriptor (e.g., mousebrain)
-- <date> : num YYYYMM. At folder if a single recording date, else in file.
-- [<suffix>] : str | num mixed specifications e.g., state, version
-- <ext> : str [a-z] file extension
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023.csv b/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023.csv
deleted file mode 100644
index 2df98d5..0000000
--- a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-subjCA019,UZH,The Interface Group,2023,November,26/11/2023,synchrotron_microCT,in vivo CSF,38G13327,,Canada,CLS,BMIT
-,,,,,,,,,,,,
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023_codebook.csv b/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023_codebook.csv
deleted file mode 100644
index 13495b6..0000000
--- a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Mouse_list_CLS_November_2023_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRæCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/README.txt b/webpage_contents/experiments/CLS_2023_November/metadata_tables/README.txt
deleted file mode 100644
index 51e68ac..0000000
--- a/webpage_contents/experiments/CLS_2023_November/metadata_tables/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Month and Year (of data collection) are preserved in these tables so they are uniquely identified beyond the folder they are in (as there may be more tables from the same facility)
\ No newline at end of file
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023.csv b/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023.csv
deleted file mode 100644
index 4d0abcc..0000000
--- a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-subjCA019,UZH,The Interface Group,2023,November,26/11/2023,SRµCT,in vivo CSF,38G13327,,Canada,CLS,BMIT
-,,,,,,,,,,,,
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023_codebook.csv b/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023_codebook.csv
deleted file mode 100644
index 13495b6..0000000
--- a/webpage_contents/experiments/CLS_2023_November/metadata_tables/Scan_list_CLS_November_2023_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRæCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/CLS_2023_November/metadata_tables/xlsx/Mouse_list_CLS_November_2023.xlsx b/webpage_contents/experiments/CLS_2023_November/metadata_tables/xlsx/Mouse_list_CLS_November_2023.xlsx
deleted file mode 100644
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diff --git a/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-A_Facility_v1.qmd b/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-A_Facility_v1.qmd
deleted file mode 100644
index ce6b639..0000000
--- a/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-A_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures A
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-B_Facility_v1.qmd b/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-B_Facility_v1.qmd
deleted file mode 100644
index 6613dae..0000000
--- a/webpage_contents/experiments/CLS_2023_November/protocols/Protocol-B_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures B
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/CLS_2023_November/protocols/README.txt b/webpage_contents/experiments/CLS_2023_November/protocols/README.txt
deleted file mode 100644
index 6035ee1..0000000
--- a/webpage_contents/experiments/CLS_2023_November/protocols/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Here, it uses .qmd instead of .md so that we are able to include the 'last-modified' field in the YAML header of the file. When rendered it will automatically give us the last day it was modified.
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2021_November/Experiment_page.qmd b/webpage_contents/experiments/ESRF_2021_November/Experiment_page.qmd
deleted file mode 100644
index 648e137..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/Experiment_page.qmd
+++ /dev/null
@@ -1,50 +0,0 @@
----
-title: 'SPring-8'
-subtitle: 'Collection period: YYYY-Month-DD to YYYY-Month-DD'
-date: '2046-12-31'
-description: |
- Description: e.g., Synchrotron X-ray computed microtomography data of mouse cerebrospinal fluid spaces in vivo
-collection-date: 'x'
-author:
- - name: Firstname1 Lastname1
- orcid: 0000-0000-0000-0000
- email: bill@gates.com
- affiliations:
- - name: Center X, Department of XX, University of XXX
-
- - name: Firstname2 Lastname2
- orcid: 0000-0000-0000-0000
- affiliations:
- - name: Center X, Department of XX, University of XXX
-license: CC BY
-listing:
- - id: protocols
- contents: "protocols/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
- - id: organization
- contents: "data_organization/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
----
-
-
-# Protocols
-
-::: {#protocols}
-:::
-
-# Data organization
-
-::: {#organization}
-:::
-
-
-# Mouse list table
-
-# Scan list table
-
diff --git a/webpage_contents/experiments/ESRF_2021_November/data_organization/Data_organization_ESRF_v1.qmd b/webpage_contents/experiments/ESRF_2021_November/data_organization/Data_organization_ESRF_v1.qmd
deleted file mode 100644
index 81acde2..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/data_organization/Data_organization_ESRF_v1.qmd
+++ /dev/null
@@ -1,28 +0,0 @@
----
-title: Data organization
-date: last-modified
----
-
-# Folder and filename schema:
-
- <date>_<labID>_<experiment description>/
- └── subj<subjID>/
- └── sc<scanID>_<anat>_[<suffix>]/
- └── subj<subjID>_sc<scanID>_[<suffix>].<ext>
-
-Example:
-
- 20231013_HOME_TEST/subj001/sc12345_brain/subj001_sc12345.img
-
-
-# Name parts explanation:
-
-- <date>: date formatted YYYYMMDD
-- <labID> : str Shortname of the lab, e.g., DESY-P07
-- <experiment description>: Short title e.g. in-vivo-mouse-CSF-infusion.
-- subj<subjID> : num subject id (3 digits, leading zeroes; e.g., subj001)
-- sc<scanID> : num scan identifier (5 digits; e.g., sc12345).
-- <anat> : str anatomy descriptor (e.g., mousebrain)
-- <date> : num YYYYMM. At folder if a single recording date, else in file.
-- [<suffix>] : str | num mixed specifications e.g., state, version
-- <ext> : str [a-z] file extension
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021.csv b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021.csv
deleted file mode 100644
index 1dbb91e..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-Mouse17,UZH,The Interface Group,2021,November,19/11/2021,synchrotron_microCT,in vivo CSF,md1230,,France,ESRF,ID17
-Mouse19,UZH,The Interface Group,2021,November,19/11/2021,synchrotron_microCT,in vivo CSF,md1230,,France,ESRF,ID17
-Mouse21,UZH,The Interface Group,2021,November,20/11/2021,synchrotron_microCT,in vivo CSF,md1230,,France,ESRF,ID17
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021_codebook.csv b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021_codebook.csv
deleted file mode 100644
index 13495b6..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Mouse_list_ESRF_November_2021_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRæCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/README.txt b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/README.txt
deleted file mode 100644
index 51e68ac..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Month and Year (of data collection) are preserved in these tables so they are uniquely identified beyond the folder they are in (as there may be more tables from the same facility)
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021.csv b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021.csv
deleted file mode 100644
index ad82ffe..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-Mouse17,UZH,The Interface Group,2021,November,19/11/2021,SRµCT,in vivo CSF,md1230,,France,ESRF,ID17
-Mouse19,UZH,The Interface Group,2021,November,19/11/2021,SRµCT,in vivo CSF,md1230,,France,ESRF,ID17
-Mouse21,UZH,The Interface Group,2021,November,20/11/2021,SRµCT,in vivo CSF,md1230,,France,ESRF,ID17
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021_codebook.csv b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021_codebook.csv
deleted file mode 100644
index 13495b6..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/Scan_list_ESRF_November_2021_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRæCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/ESRF_2021_November/metadata_tables/xlsx/Mouse_list_ESRF_November_2021.xlsx b/webpage_contents/experiments/ESRF_2021_November/metadata_tables/xlsx/Mouse_list_ESRF_November_2021.xlsx
deleted file mode 100644
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diff --git a/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-A_Facility_v1.qmd b/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-A_Facility_v1.qmd
deleted file mode 100644
index ce6b639..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-A_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures A
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-B_Facility_v1.qmd b/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-B_Facility_v1.qmd
deleted file mode 100644
index 6613dae..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/protocols/Protocol-B_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures B
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/ESRF_2021_November/protocols/README.txt b/webpage_contents/experiments/ESRF_2021_November/protocols/README.txt
deleted file mode 100644
index 6035ee1..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/protocols/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Here, it uses .qmd instead of .md so that we are able to include the 'last-modified' field in the YAML header of the file. When rendered it will automatically give us the last day it was modified.
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2021_November/test_monitoring/README_ESRF_2021_November.md b/webpage_contents/experiments/ESRF_2021_November/test_monitoring/README_ESRF_2021_November.md
deleted file mode 100644
index 7492ad2..0000000
--- a/webpage_contents/experiments/ESRF_2021_November/test_monitoring/README_ESRF_2021_November.md
+++ /dev/null
@@ -1,5 +0,0 @@
-This folder contains monitoring data (e.g., heart rate, pulse oximetry, etc).
-LabChart collected ECG, ventilator on/off, tracheal pressure, camera on/off.
-The files from LabChart and LabVIEW are in .txt format, while files from Physiosuite are in .log format.
-Monitoring files contain the whole monitored period, which includes additional image acquisitions with the camera which are not available in the repository.
-Each scan contains an info file with the acquisition time, which serves to find the monitoring data of the selected subject in the selected scan.
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2022_June/Experiment_page.qmd b/webpage_contents/experiments/ESRF_2022_June/Experiment_page.qmd
deleted file mode 100644
index 648e137..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/Experiment_page.qmd
+++ /dev/null
@@ -1,50 +0,0 @@
----
-title: 'SPring-8'
-subtitle: 'Collection period: YYYY-Month-DD to YYYY-Month-DD'
-date: '2046-12-31'
-description: |
- Description: e.g., Synchrotron X-ray computed microtomography data of mouse cerebrospinal fluid spaces in vivo
-collection-date: 'x'
-author:
- - name: Firstname1 Lastname1
- orcid: 0000-0000-0000-0000
- email: bill@gates.com
- affiliations:
- - name: Center X, Department of XX, University of XXX
-
- - name: Firstname2 Lastname2
- orcid: 0000-0000-0000-0000
- affiliations:
- - name: Center X, Department of XX, University of XXX
-license: CC BY
-listing:
- - id: protocols
- contents: "protocols/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
- - id: organization
- contents: "data_organization/*.qmd"
- type: grid
- fields: [title, date]
- grid-columns: 1
-
----
-
-
-# Protocols
-
-::: {#protocols}
-:::
-
-# Data organization
-
-::: {#organization}
-:::
-
-
-# Mouse list table
-
-# Scan list table
-
diff --git a/webpage_contents/experiments/ESRF_2022_June/data_organization/Data_organization_ESRF_v1.qmd b/webpage_contents/experiments/ESRF_2022_June/data_organization/Data_organization_ESRF_v1.qmd
deleted file mode 100644
index 81acde2..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/data_organization/Data_organization_ESRF_v1.qmd
+++ /dev/null
@@ -1,28 +0,0 @@
----
-title: Data organization
-date: last-modified
----
-
-# Folder and filename schema:
-
- <date>_<labID>_<experiment description>/
- └── subj<subjID>/
- └── sc<scanID>_<anat>_[<suffix>]/
- └── subj<subjID>_sc<scanID>_[<suffix>].<ext>
-
-Example:
-
- 20231013_HOME_TEST/subj001/sc12345_brain/subj001_sc12345.img
-
-
-# Name parts explanation:
-
-- <date>: date formatted YYYYMMDD
-- <labID> : str Shortname of the lab, e.g., DESY-P07
-- <experiment description>: Short title e.g. in-vivo-mouse-CSF-infusion.
-- subj<subjID> : num subject id (3 digits, leading zeroes; e.g., subj001)
-- sc<scanID> : num scan identifier (5 digits; e.g., sc12345).
-- <anat> : str anatomy descriptor (e.g., mousebrain)
-- <date> : num YYYYMM. At folder if a single recording date, else in file.
-- [<suffix>] : str | num mixed specifications e.g., state, version
-- <ext> : str [a-z] file extension
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022.csv b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022.csv
deleted file mode 100644
index bf0bbb3..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-mouse50,UZH,The Interface Group,2022,June,05/06/2022,synchrotron_microCT,in vivo CSF,md1324,,France,ESRF,ID17
-mouse63,UZH,The Interface Group,2022,June,07/06/2022,synchrotron_microCT,in vivo CSF,md1324,,France,ESRF,ID17
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022_codebook.csv b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022_codebook.csv
deleted file mode 100644
index 29bfc17..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Mouse_list_ESRF_June_2022_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/README.txt b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/README.txt
deleted file mode 100644
index 51e68ac..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Month and Year (of data collection) are preserved in these tables so they are uniquely identified beyond the folder they are in (as there may be more tables from the same facility)
\ No newline at end of file
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022.csv b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022.csv
deleted file mode 100644
index 92b6298..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-mouse50,UZH,The Interface Group,2022,June,05/06/2022,SRµCT,in vivo CSF,md1324,,France,ESRF,ID17
-mouse63,UZH,The Interface Group,2022,June,07/06/2022,SRµCT,in vivo CSF,md1324,,France,ESRF,ID17
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022_codebook.csv b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022_codebook.csv
deleted file mode 100644
index d714134..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/Scan_list_ESRF_June_2022_codebook.csv
+++ /dev/null
@@ -1,14 +0,0 @@
-Variable,Description
-SubjectID," ""Mice unique identifier"""
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year," ""Year of collection YYYY"""
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition," ""DD/MM/YYYY"""
-Data_type,"Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution," ""Name or acronym of the institution hosting the main facility (it can be the same as University)"""
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/ESRF_2022_June/metadata_tables/xlsx/Mouse_list_ESRF_June_2022.xlsx b/webpage_contents/experiments/ESRF_2022_June/metadata_tables/xlsx/Mouse_list_ESRF_June_2022.xlsx
deleted file mode 100644
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diff --git a/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-A_Facility_v1.qmd b/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-A_Facility_v1.qmd
deleted file mode 100644
index ce6b639..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-A_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures A
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-B_Facility_v1.qmd b/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-B_Facility_v1.qmd
deleted file mode 100644
index 6613dae..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/protocols/Protocol-B_Facility_v1.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
----
-title: Procedures B
-date: last-modified
----
-
-# Section 1
-
-## Subsection
-
-``` powershell
-# This is some code for you to copy paste
-
-cd ..
-'hello world'
-
-
-```
diff --git a/webpage_contents/experiments/ESRF_2022_June/protocols/README.txt b/webpage_contents/experiments/ESRF_2022_June/protocols/README.txt
deleted file mode 100644
index 6035ee1..0000000
--- a/webpage_contents/experiments/ESRF_2022_June/protocols/README.txt
+++ /dev/null
@@ -1 +0,0 @@
-Here, it uses .qmd instead of .md so that we are able to include the 'last-modified' field in the YAML header of the file. When rendered it will automatically give us the last day it was modified.
\ No newline at end of file
diff --git a/webpage_contents/experiments/SPring-8_May_2023/Mice_Information_SPring-8_20230508.csv b/webpage_contents/experiments/SPring-8_May_2023/Mice_Information_SPring-8_20230508.csv
deleted file mode 100644
index 137dff1..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/Mice_Information_SPring-8_20230508.csv
+++ /dev/null
@@ -1,35 +0,0 @@
-SubjectID,Sex,Body weight [g],Cannula length (mm),Dilution,Concentration,Withdrawn CA in syringe (uL),Infused CA in mannitol (uL),Injection 1 rate (uL/min),Injection 1 volume (uL) ,Injection 1 JP time (HH:MM),Injection 2 rate (uL/min),Injection 2 volume (uL) ,Injection 2 JP time (HH:MM),Bubbles?,Comments, anything different in the protocol?
-JP01,Male,27.5,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,15:05,,,,,scanned dead,
-JP02,Male,26.6,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,18:16,,,,,scanned dead,
-JP03,Male,27.5,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,20:55,,,,,probably not full volume injected, scanned dead
-JP04,Female,20.2,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,11:15,,,,,scanned dead,
-JP05,Female,20.2,2.2,1.5x,480 mg Ba/ml,5,,0.1,2.5,15:01,,,,,scanned dead,
-JP06,Female,20.3,2.2,1.5x,480 mg Ba/ml,5,,0.1,2.5,,,,,,scanned dead,
-JP07,Male,26.4,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,17:00,,,,,scanned dead,
-JP08,Male,24.6,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,12:45,,,,,injection post mortem, scanned dead
-JP09,Male,26.8,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,13:56,,,,,not all 17ul withdrawn (air?),
-JP10,Male,25.7,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,16:33,,,,,not all 17ul withdrawn, air bubbles
-JP11,Male,24.4,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,18:45,,,,,injection post mortem,
-JP12,Male,25.3,2.3,1x,320 mg Ba/ml,17,0.2,0.5,5,20:44,,,,,injection post mortem,
-JP13,Male,24.7,2.2,1x,320 mg Ba/ml,17,0.5,0.5,5,11:14,0.5,5,12:15,,poor life signs after first injection; mouse dies within 6 min of second injection,
-JP14,Male,27,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,13.38,0.5,2.5,14:49,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; between injections 0.02 ul/min; mouse recovers better after start of injection,
-JP15,Male,24,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,16:24,0.5,2.5,17:26,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s,
-JP16,Male,25.8,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,20:10,0.5,2.5,21:14,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; second injection in the dead mouse,
-JP17,Male,26.4,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,22:58,0.5,2.5,23:40,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; at second injection mouse was already dying; injection killed it quickly,
-JP18,Male,26.6,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,10:01,,,,,mouse starts dying 15 min after injection,
-JP19,Male,26.9,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,12:54,,,,,mouse starts dying 16 min after injection,
-JP20,Male,26.2,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,15:39,0.5,2.5,16:35,,mouse starts dying 20 min after second injection,
-JP21,Female,21,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,17:53,,,,,ramp up from 0.02 ul/min to 0.25 ul/min during 60 s; between injections 0.02 ul/min,
-JP22,Female,19.5,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,20:48,0.25,2.5,22:31,,second injection no ramp up, observed in the spine
-JP23,Female,19.6,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,23:28,,,,,injection in parenchyma,
-JP24,Female,19.56,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,11:20,,,,,contrast agent didn't go in,
-JP25,Female,19.63,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,13:10,,,,,injection in parenchyma,
-JP26,Female,19.71,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,16:58,,,,,best animal so far,
-JP27,Female,19.2,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,20:04,,,,,mouse dead at mounting; inject post mortem,
-JP28,Female,20.2,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,22:19,0.25,5,00:06,,good; second injection interrupted,
-JP29,Female,18.6,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,09:53,,,,,good,
-JP30,Female,19.03,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,12:11,0.25,ca. 2.5,13:47,,good; not all of second injection covered by scans,
-JP31,Female,20.5,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,14:42,,,,,good; but mouse died 25 min. after injection,
-JP32,Female,20.2,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,16:49,0.25,ca. 2.5,18:28,,good,
-JP33,Female,21.2,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,19:11,0.25,ca. 2.5,20:47,,good,
-JP34,Female,19.21,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,,no contrast agent,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/SPring-8_BL20B2_2023A1208_Scanlist.csv b/webpage_contents/experiments/SPring-8_May_2023/SPring-8_BL20B2_2023A1208_Scanlist.csv
deleted file mode 100644
index 5109abc..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/SPring-8_BL20B2_2023A1208_Scanlist.csv
+++ /dev/null
@@ -1,259 +0,0 @@
-SPring-8 BL20B2 Beamtime 2023A1208 May 2023,,,,
-Scan name,Number of subscans,ECG data,On Disk No.,Notes
-CA-dilution-1scan-afterJP15standing,,,Disk 1,
-CA-dilution-1scan-afterJP15standingVortex2min,,,Disk 1,
-CA-dilution-1scan-V2US15standing,,,Disk 1,
-CA-dilution-1scan-vortex2min,,,Disk 1,
-CA-dilution-1scan-vortex2min-v2,,,Disk 1,
-CA-dilution-1sca-vortex2minUSbath15min,,,Disk 1,
-Calib01_033_perc_v2,,,Disk 1,
-Calib01_033perc,,,Disk 1,
-Calib01_050perc,,,Disk 1,
-Calib01_050perc_v2,,,Disk 1,
-Calib01_050perc_v3,,,Disk 1,
-Calib01_050perc_v4,,,Disk 1,
-Calib01_050perc_v5,,,Disk 1,
-Calib01_067perc,,,Disk 1,
-Calib01_070perc,,,Disk 1,
-Calib01_100perc,,,Disk 1,
-Calib02_010perc_standing01,,,Disk 1,
-Calib02_010perc_standing02,,,Disk 1,
-Calib02_010perc_vortex2min01,,,Disk 1,
-Calib02_010perc_vortex2min02,,,Disk 1,
-Calib02_025perc_standing01,,,Disk 1,
-Calib02_025perc_standing02,,,Disk 1,
-Calib02_025perc_vortex2min01,,,Disk 1,
-Calib02_025perc_vortex2min02,,,Disk 1,
-Calib02_033perc_standing01,,,Disk 1,
-Calib02_033perc_standing02,,,Disk 1,
-Calib02_033perc_vortex2min01,,,Disk 1,
-Calib02_033perc_vortex2min02,,,Disk 1,
-Calib02_050perc_standing01,,,Disk 1,
-Calib02_050perc_standing02,,,Disk 1,
-Calib02_050perc_vortex2min01,,,Disk 1,
-Calib02_050perc_vortex2min01_v2,,,Disk 1,
-Calib02_050perc_vortex2min02,,,Disk 1,
-Calib03_000perc_abso,,,Disk 1,
-Calib03_010perc_abso,,,Disk 1,
-Calib03_025perc_abso,,,Disk 1,
-Calib03_033perc_abso,,,Disk 1,
-Calib03_050perc_abso,,,Disk 1,
-Calib03_050perc_abso_standing,,,Disk 1,shutter was open for dark-fields. Copied dark.img from JP14-invivo-1prescan-h1-bulbs
-Calib03_pureH2O_abso,,,Disk 1,
-cut-implant-01,,,Disk 1,
-cut-implant-01-v2,,,Disk 1,
-cut-implant-02,,,Disk 1,
-drilled-implant-01,,,Disk 1,
-ear-bar-left01,,,Disk 1,
-earbar-right01,,,Disk 1,
-flat_series_001ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_002ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_003ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_004ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_005ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-Implant01,,,Disk 1,
-implant01_dremel,,,Disk 1,
-implant02_dremel,,,Disk 1,
-JP01-dead-1scan,,,Disk 1,
-JP02-dead-1scan,,,Disk 1,scan failed
-JP02-dead-1scan-v2,,,Disk 1,scan failed
-JP02-dead-1scan-v3,,,Disk 1,
-JP03-dead-1scan,,,Disk 1,
-JP04-dead-1scan,,,Disk 1,scan failed
-JP04-dead-1scan-v2,,,Disk 1,
-JP04-dead-1scan-v3,,,Disk 1,
-JP05-dead-1scan,,,Disk 1,
-JP06-dead-1scan,,,Disk 1,
-JP07-dead-1scan,,,Disk 1,
-JP08-dead-1scan,,,Disk 1,
-JP09-invivo-1scan-head,,yes,Disk 1,
-JP09-invivo-1scan-neck,,yes,Disk 1,
-JP09-invivo-1scan-nose,,yes,Disk 1,
-JP09-invivo-1scan-nose-v2,,yes,Disk 1,
-JP09-invivo-20scan-phase1-injection,20 scan,yes,Disk 1,
-JP10-invivo-14scan-phase1-injection,14 scan,yes,Disk 1,
-JP10-invivo-1prescan-brain,,yes,Disk 1,
-JP10-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP10-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP10-invivo-5scan-maintain,5 scan,issues at scans 1 and 5,Disk 1,
-JP10-invivo-5scan-maintain2,5 scan,yes,Disk 1,
-JP11-dying-10scan-phase1-injection,10 scan,no,Disk 1,
-JP12-dying-10scan-phase1-injection,10 scan,yes,Disk 1,
-JP12-dying-10scan-phase2-injection,10 scan,no,Disk 1,
-JP13-dead-14scan-phase4-maintain,14 scan,dying! ECG reducing from 5,Disk 1,
-JP13-invivo-10scan-phase2-maintain,10 scan,issues at scans 7 and 8,Disk 1,
-JP13-invivo-10scan-phase2-maintain2,10 scan,yes,Disk 1,
-JP13-invivo-10scan-phase2-maintain3,10 scan,yes,Disk 1,
-JP13-invivo-14scan-phase1-injection,14 scan,yes,Disk 1,
-JP13-invivo-14scan-phase3-injection,14 scan,yes,Disk 1,
-JP13-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP13-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP14-dead-10scan-phase3-injection,10 scan,dead,Disk 1,
-JP14-invivo-10scan-phase2-maintain2,10 scan,yes,Disk 1,
-JP14-invivo-14scan-phase1pinjection,14 scan,yes,Disk 1,
-JP14-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP14-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP14-invivo-55scan-phase2-maintain,55 scan,yes,Disk 1,
-JP15-invivo-10scan-phase1-injection,10 scan,yes,Disk 1,
-JP15-invivo-10scan-phase2-maintain,10 scan,yes,Disk 1,motion artifacts
-JP15-invivo-10scan-phase3-injection,10 scan,yes,Disk 1,
-JP15-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP15-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP15-invivo-20scan-phase4-maintain,20 scan,yes,Disk 1,
-JP15-invivo-30scan-phase4-maintain2,30 scan,yes,Disk 1,
-JP16-dead-10scan-phase3-injection,10 scan,,Disk 2,
-JP16-invivo-10scan-phase1-injection,10 scan,,Disk 2,
-JP16-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP16-invivo-1prescan-h2-spine,,,Disk 2,
-JP16-invivo-50scan-phase2-maintain,50 scan,,Disk 2,"File incomplete, 1001 projections missing at the end. Used spl_c2 to extract the projections of scan 1 - 49. Scans 3 - 49 did not determine center of rotation correctly (last projection mirrored?). All scans were reconstructed with constant center of rotation = 1026"
-JP17-invivo-10scan-phase1-infusion,10 scan,,Disk 2,
-JP17-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP17-invivo-1prescan-h2-spine,,,Disk 2,
-JP17-invivo-20scan-phase2-maintain,20 scan,,Disk 2,
-JP17-invivo-20scan-phase3-infusion,20 scan,,Disk 2,
-JP18-invivo-10scan-phase1-injection,10 scan,,Disk 2,
-JP18-invivo-1prescan-h1-bulbs,,,Disk 2,capnograph tubing in flat-field
-JP18-invivo-1prescan-h1-bulbs-v2,,,Disk 2,
-JP18-invivo-1prescan-h2-spine,,,Disk 2,
-JP19-invivo-10scan-phase1-wait,10 scan,,Disk 2,
-JP19-invivo-1postscan-h1-bulbs,,,Disk 2,
-JP19-invivo-1postscan-h2-spine,,,Disk 2,
-JP19-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP19-invivo-1prescan-h2-spine,,,Disk 2,
-JP19-invivo-1scan-phase2-preinjection,,,Disk 2,
-JP19-invivo-1scan-phase3-postinjection,,,Disk 2,
-JP19-invivo-1scan-phase4-10min,,,Disk 2,
-JP19-invivo-1scan-phase4-20min,,,Disk 2,
-JP19-invivo-1scan-phase4-30min,,,Disk 2,
-JP19-invivo-1scan-phase5-preinjection,,,Disk 2,
-JP19-invivo-1scan-phase6-postinjection,,,Disk 2,
-JP19-invivo-1scan-phase7-10min,,,Disk 2,
-JP19-invivo-30scan-phase1-wait2,30 scan,,Disk 2,"Shutter was deliberately closed for scan 11 – 29, after it became clear that radiation dose was the issue"
-JP20-invivo-1prescan-h1-bulbs,,,Disk 2,scan failed
-JP20-invivo-1prescan-h1-bulbs-v2,,,Disk 2,
-JP20-invivo-1prescan-h2-spine,,,Disk 2,scan failed
-JP20-invivo-1prescan-h2-spine-v2,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-1,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-2,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-3,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-4-preinjection,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-5-postinjection,,,Disk 2,
-JP20-invivo-1scan-h2-spine-1,,,Disk 2,
-JP20-invivo-1scan-h2-spine-2,,,Disk 2,
-JP20-invivo-1scan-h2-spine-3,,,Disk 2,
-JP20-invivo-1scan-h2-spine-4-preinjection,,,Disk 2,
-JP20-invivo-1scan-h2-spine-5-postinjection,,,Disk 2,
-JP20-invivo-3scan-phase1-injection,3 scan,,Disk 2,
-JP21-invivo-1scan-phase1-preinjection,,,Disk 2,
-JP21-invivo-1scan-phase2-injection-brain-10min,,,Disk 2,
-JP21-invivo-1scan-phase2-injection-nose,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-100min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-110min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-120min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-20min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-30min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-40min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-50min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-60min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-nose-120min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP22-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP22-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP22-invivo-1scan-phase2-injection-nose-60min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP22-invivo-1scan-phase4-injection-spine-90min,,,Disk 2,
-JP22-invivo-1scan-phase4-injection-spine-95min,,,Disk 2,
-JP22-invivo-6scan-phase2-injection-brain,6 scan,,Disk 2,
-JP23-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP23-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP23-invivo-1scan-phase2-injection-brain-10min,,,Disk 2,
-JP23-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP23-invivo-2scan-phase3-postinjection-brain-70-80min,2 scan,,Disk 2,
-JP23-invivo-5scan-phase3-postinjection-brain-20-60min,5 scan,,Disk 2,
-JP24-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP24-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP24-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP24-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP24-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP25-invivo-1scan-phase1-injection-brain,,,Disk 2,
-JP25-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP25-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-100min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-110min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP25-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP26-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP26-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP26-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP26-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP26-invivo-2scan-phase3-postinjection-brain-80-90min,1 scan,,Disk 2,is actually only one scan
-JP26-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-jp27-dead-1scan-phase1-preinjection-brain,,,Disk 2,
-jp27-dead-1scan-phase1-preinjection-nose,,,Disk 2,
-JP27-dead-1scan-phase2-injection1-brain,,,Disk 2,
-JP27-dead-30scan-phase2-injection2-brain,30 scan,,Disk 2,
-JP28-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP28-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP28-invivo-1scan-phase2-injection-brain-v2,,,Disk 2,
-JP28-invivo-1scan-phase2-injection-nose,,,Disk 2,
-JP28-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP28-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP28-invivo-30scan-phase4-reinjection-brain-continuous-110min,30 scan,,Disk 2,
-JP28-invivo-3scan-phase3-postinjection-brain-80-100min,3 scan,,Disk 2,
-JP28-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP29-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP29-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP29-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP29-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP29-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP29-invivo-2scan-phase3-postinjection-brain-70min-80min,2 scan,,Disk 2,
-JP29-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP30-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP30-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP30-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP30-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP30-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP30-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP30-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-brain-65min,,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-spine-80min,,,Disk 2,"missing a.HIS file, was never recorded"
-JP31-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP31-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP31-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP31-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP32-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP32-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP32-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP32-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP32-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP32-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP32-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP33-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP33-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP33-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP33-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP33-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP33-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP33-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP34-invivo-scan1-brain,,,Disk 2,
-JP34-invivo-scan2-nose,,,Disk 2,
-JP34-invivo-scan3-spine,,,Disk 2,
-JP34-invivo-scan4-60scans-brain,60 scan,,Disk 2,
-purified_water_eppendorf01,,,Disk 1,
-purified_water_eppendorf02,,,Disk 1,
-test01,,,Disk 1,
-test02,,,Disk 1,
-test03,,,Disk 1,
-test04,,,Disk 1,
-test05,,,Disk 1,
-test06,,,Disk 1,
-test07,,,Disk 1,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/index.qmd b/webpage_contents/experiments/SPring-8_May_2023/index.qmd
deleted file mode 100644
index 1b8e26f..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/index.qmd
+++ /dev/null
@@ -1,28 +0,0 @@
----
-title: 'SPring-8'
-date: '2023-05-01'
-listing:
- type: grid
- grid-columns: 1
- contents: protocols
- id: protolist
- fields: [title, description, date]
-
----
-
-# Protocol
-
-
-::: {#protolist}
-:::
-
-
-## TO BE FILLED
-
-### Mouse list table
-
-### Scan list table
-
-### Links to protocol pages for this beamtime
-
-- TO CREATE: Link to ./protocols/SPring-8_reconstruction.qmd
\ No newline at end of file
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mice_Information_SPring-8_20230508.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mice_Information_SPring-8_20230508.csv
deleted file mode 100644
index 137dff1..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mice_Information_SPring-8_20230508.csv
+++ /dev/null
@@ -1,35 +0,0 @@
-SubjectID,Sex,Body weight [g],Cannula length (mm),Dilution,Concentration,Withdrawn CA in syringe (uL),Infused CA in mannitol (uL),Injection 1 rate (uL/min),Injection 1 volume (uL) ,Injection 1 JP time (HH:MM),Injection 2 rate (uL/min),Injection 2 volume (uL) ,Injection 2 JP time (HH:MM),Bubbles?,Comments, anything different in the protocol?
-JP01,Male,27.5,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,15:05,,,,,scanned dead,
-JP02,Male,26.6,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,18:16,,,,,scanned dead,
-JP03,Male,27.5,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,20:55,,,,,probably not full volume injected, scanned dead
-JP04,Female,20.2,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,11:15,,,,,scanned dead,
-JP05,Female,20.2,2.2,1.5x,480 mg Ba/ml,5,,0.1,2.5,15:01,,,,,scanned dead,
-JP06,Female,20.3,2.2,1.5x,480 mg Ba/ml,5,,0.1,2.5,,,,,,scanned dead,
-JP07,Male,26.4,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,17:00,,,,,scanned dead,
-JP08,Male,24.6,2.3,1.5x,480 mg Ba/ml,5,,0.1,2.5,12:45,,,,,injection post mortem, scanned dead
-JP09,Male,26.8,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,13:56,,,,,not all 17ul withdrawn (air?),
-JP10,Male,25.7,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,16:33,,,,,not all 17ul withdrawn, air bubbles
-JP11,Male,24.4,2.3,1.5x,480 mg Ba/ml,17,0.2,0.5,5,18:45,,,,,injection post mortem,
-JP12,Male,25.3,2.3,1x,320 mg Ba/ml,17,0.2,0.5,5,20:44,,,,,injection post mortem,
-JP13,Male,24.7,2.2,1x,320 mg Ba/ml,17,0.5,0.5,5,11:14,0.5,5,12:15,,poor life signs after first injection; mouse dies within 6 min of second injection,
-JP14,Male,27,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,13.38,0.5,2.5,14:49,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; between injections 0.02 ul/min; mouse recovers better after start of injection,
-JP15,Male,24,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,16:24,0.5,2.5,17:26,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s,
-JP16,Male,25.8,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,20:10,0.5,2.5,21:14,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; second injection in the dead mouse,
-JP17,Male,26.4,2.2,1x,320 mg Ba/ml,17,0.5,0.5,2.5,22:58,0.5,2.5,23:40,,ramp up from 0.02 ul/min to 0.5 ul/min during 60 s; at second injection mouse was already dying; injection killed it quickly,
-JP18,Male,26.6,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,10:01,,,,,mouse starts dying 15 min after injection,
-JP19,Male,26.9,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,12:54,,,,,mouse starts dying 16 min after injection,
-JP20,Male,26.2,2.2,0.75x,240 mg Ba/ml,17,0.5,0.5,2.5,15:39,0.5,2.5,16:35,,mouse starts dying 20 min after second injection,
-JP21,Female,21,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,17:53,,,,,ramp up from 0.02 ul/min to 0.25 ul/min during 60 s; between injections 0.02 ul/min,
-JP22,Female,19.5,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,20:48,0.25,2.5,22:31,,second injection no ramp up, observed in the spine
-JP23,Female,19.6,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,23:28,,,,,injection in parenchyma,
-JP24,Female,19.56,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,11:20,,,,,contrast agent didn't go in,
-JP25,Female,19.63,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,13:10,,,,,injection in parenchyma,
-JP26,Female,19.71,2.3,0.75x,240 mg Ba/ml,10,0.5,0.25,5,16:58,,,,,best animal so far,
-JP27,Female,19.2,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,20:04,,,,,mouse dead at mounting; inject post mortem,
-JP28,Female,20.2,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,22:19,0.25,5,00:06,,good; second injection interrupted,
-JP29,Female,18.6,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,09:53,,,,,good,
-JP30,Female,19.03,2.2,0.75x,240 mg Ba/ml,10,0.5,0.25,5,12:11,0.25,ca. 2.5,13:47,,good; not all of second injection covered by scans,
-JP31,Female,20.5,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,14:42,,,,,good; but mouse died 25 min. after injection,
-JP32,Female,20.2,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,16:49,0.25,ca. 2.5,18:28,,good,
-JP33,Female,21.2,2.2,0.75x,240 mg Ba/ml,10,1,0.25,5,19:11,0.25,ca. 2.5,20:47,,good,
-JP34,Female,19.21,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,N/A,,no contrast agent,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023.csv
deleted file mode 100644
index 42edcf9..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-JP28,UZH,The Interface Group,2023,May,14/05/2023,synchrotron_microCT,in vivo CSF,2023A1208,,Japan,SPring-8,BL20B2
-,,,,,,,,,,,,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023_codebook.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023_codebook.csv
deleted file mode 100644
index 29bfc17..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Mouse_list_SPring-8_May_2023_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/SPring-8_BL20B2_2023A1208_Scanlist.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/SPring-8_BL20B2_2023A1208_Scanlist.csv
deleted file mode 100644
index 5109abc..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/SPring-8_BL20B2_2023A1208_Scanlist.csv
+++ /dev/null
@@ -1,259 +0,0 @@
-SPring-8 BL20B2 Beamtime 2023A1208 May 2023,,,,
-Scan name,Number of subscans,ECG data,On Disk No.,Notes
-CA-dilution-1scan-afterJP15standing,,,Disk 1,
-CA-dilution-1scan-afterJP15standingVortex2min,,,Disk 1,
-CA-dilution-1scan-V2US15standing,,,Disk 1,
-CA-dilution-1scan-vortex2min,,,Disk 1,
-CA-dilution-1scan-vortex2min-v2,,,Disk 1,
-CA-dilution-1sca-vortex2minUSbath15min,,,Disk 1,
-Calib01_033_perc_v2,,,Disk 1,
-Calib01_033perc,,,Disk 1,
-Calib01_050perc,,,Disk 1,
-Calib01_050perc_v2,,,Disk 1,
-Calib01_050perc_v3,,,Disk 1,
-Calib01_050perc_v4,,,Disk 1,
-Calib01_050perc_v5,,,Disk 1,
-Calib01_067perc,,,Disk 1,
-Calib01_070perc,,,Disk 1,
-Calib01_100perc,,,Disk 1,
-Calib02_010perc_standing01,,,Disk 1,
-Calib02_010perc_standing02,,,Disk 1,
-Calib02_010perc_vortex2min01,,,Disk 1,
-Calib02_010perc_vortex2min02,,,Disk 1,
-Calib02_025perc_standing01,,,Disk 1,
-Calib02_025perc_standing02,,,Disk 1,
-Calib02_025perc_vortex2min01,,,Disk 1,
-Calib02_025perc_vortex2min02,,,Disk 1,
-Calib02_033perc_standing01,,,Disk 1,
-Calib02_033perc_standing02,,,Disk 1,
-Calib02_033perc_vortex2min01,,,Disk 1,
-Calib02_033perc_vortex2min02,,,Disk 1,
-Calib02_050perc_standing01,,,Disk 1,
-Calib02_050perc_standing02,,,Disk 1,
-Calib02_050perc_vortex2min01,,,Disk 1,
-Calib02_050perc_vortex2min01_v2,,,Disk 1,
-Calib02_050perc_vortex2min02,,,Disk 1,
-Calib03_000perc_abso,,,Disk 1,
-Calib03_010perc_abso,,,Disk 1,
-Calib03_025perc_abso,,,Disk 1,
-Calib03_033perc_abso,,,Disk 1,
-Calib03_050perc_abso,,,Disk 1,
-Calib03_050perc_abso_standing,,,Disk 1,shutter was open for dark-fields. Copied dark.img from JP14-invivo-1prescan-h1-bulbs
-Calib03_pureH2O_abso,,,Disk 1,
-cut-implant-01,,,Disk 1,
-cut-implant-01-v2,,,Disk 1,
-cut-implant-02,,,Disk 1,
-drilled-implant-01,,,Disk 1,
-ear-bar-left01,,,Disk 1,
-earbar-right01,,,Disk 1,
-flat_series_001ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_002ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_003ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_004ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-flat_series_005ms,,,Disk 1,Flat fields recorded at different exposure times to model detector response
-Implant01,,,Disk 1,
-implant01_dremel,,,Disk 1,
-implant02_dremel,,,Disk 1,
-JP01-dead-1scan,,,Disk 1,
-JP02-dead-1scan,,,Disk 1,scan failed
-JP02-dead-1scan-v2,,,Disk 1,scan failed
-JP02-dead-1scan-v3,,,Disk 1,
-JP03-dead-1scan,,,Disk 1,
-JP04-dead-1scan,,,Disk 1,scan failed
-JP04-dead-1scan-v2,,,Disk 1,
-JP04-dead-1scan-v3,,,Disk 1,
-JP05-dead-1scan,,,Disk 1,
-JP06-dead-1scan,,,Disk 1,
-JP07-dead-1scan,,,Disk 1,
-JP08-dead-1scan,,,Disk 1,
-JP09-invivo-1scan-head,,yes,Disk 1,
-JP09-invivo-1scan-neck,,yes,Disk 1,
-JP09-invivo-1scan-nose,,yes,Disk 1,
-JP09-invivo-1scan-nose-v2,,yes,Disk 1,
-JP09-invivo-20scan-phase1-injection,20 scan,yes,Disk 1,
-JP10-invivo-14scan-phase1-injection,14 scan,yes,Disk 1,
-JP10-invivo-1prescan-brain,,yes,Disk 1,
-JP10-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP10-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP10-invivo-5scan-maintain,5 scan,issues at scans 1 and 5,Disk 1,
-JP10-invivo-5scan-maintain2,5 scan,yes,Disk 1,
-JP11-dying-10scan-phase1-injection,10 scan,no,Disk 1,
-JP12-dying-10scan-phase1-injection,10 scan,yes,Disk 1,
-JP12-dying-10scan-phase2-injection,10 scan,no,Disk 1,
-JP13-dead-14scan-phase4-maintain,14 scan,dying! ECG reducing from 5,Disk 1,
-JP13-invivo-10scan-phase2-maintain,10 scan,issues at scans 7 and 8,Disk 1,
-JP13-invivo-10scan-phase2-maintain2,10 scan,yes,Disk 1,
-JP13-invivo-10scan-phase2-maintain3,10 scan,yes,Disk 1,
-JP13-invivo-14scan-phase1-injection,14 scan,yes,Disk 1,
-JP13-invivo-14scan-phase3-injection,14 scan,yes,Disk 1,
-JP13-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP13-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP14-dead-10scan-phase3-injection,10 scan,dead,Disk 1,
-JP14-invivo-10scan-phase2-maintain2,10 scan,yes,Disk 1,
-JP14-invivo-14scan-phase1pinjection,14 scan,yes,Disk 1,
-JP14-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP14-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP14-invivo-55scan-phase2-maintain,55 scan,yes,Disk 1,
-JP15-invivo-10scan-phase1-injection,10 scan,yes,Disk 1,
-JP15-invivo-10scan-phase2-maintain,10 scan,yes,Disk 1,motion artifacts
-JP15-invivo-10scan-phase3-injection,10 scan,yes,Disk 1,
-JP15-invivo-1prescan-h1-bulbs,,yes,Disk 1,
-JP15-invivo-1prescan-h2-spine,,yes,Disk 1,
-JP15-invivo-20scan-phase4-maintain,20 scan,yes,Disk 1,
-JP15-invivo-30scan-phase4-maintain2,30 scan,yes,Disk 1,
-JP16-dead-10scan-phase3-injection,10 scan,,Disk 2,
-JP16-invivo-10scan-phase1-injection,10 scan,,Disk 2,
-JP16-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP16-invivo-1prescan-h2-spine,,,Disk 2,
-JP16-invivo-50scan-phase2-maintain,50 scan,,Disk 2,"File incomplete, 1001 projections missing at the end. Used spl_c2 to extract the projections of scan 1 - 49. Scans 3 - 49 did not determine center of rotation correctly (last projection mirrored?). All scans were reconstructed with constant center of rotation = 1026"
-JP17-invivo-10scan-phase1-infusion,10 scan,,Disk 2,
-JP17-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP17-invivo-1prescan-h2-spine,,,Disk 2,
-JP17-invivo-20scan-phase2-maintain,20 scan,,Disk 2,
-JP17-invivo-20scan-phase3-infusion,20 scan,,Disk 2,
-JP18-invivo-10scan-phase1-injection,10 scan,,Disk 2,
-JP18-invivo-1prescan-h1-bulbs,,,Disk 2,capnograph tubing in flat-field
-JP18-invivo-1prescan-h1-bulbs-v2,,,Disk 2,
-JP18-invivo-1prescan-h2-spine,,,Disk 2,
-JP19-invivo-10scan-phase1-wait,10 scan,,Disk 2,
-JP19-invivo-1postscan-h1-bulbs,,,Disk 2,
-JP19-invivo-1postscan-h2-spine,,,Disk 2,
-JP19-invivo-1prescan-h1-bulbs,,,Disk 2,
-JP19-invivo-1prescan-h2-spine,,,Disk 2,
-JP19-invivo-1scan-phase2-preinjection,,,Disk 2,
-JP19-invivo-1scan-phase3-postinjection,,,Disk 2,
-JP19-invivo-1scan-phase4-10min,,,Disk 2,
-JP19-invivo-1scan-phase4-20min,,,Disk 2,
-JP19-invivo-1scan-phase4-30min,,,Disk 2,
-JP19-invivo-1scan-phase5-preinjection,,,Disk 2,
-JP19-invivo-1scan-phase6-postinjection,,,Disk 2,
-JP19-invivo-1scan-phase7-10min,,,Disk 2,
-JP19-invivo-30scan-phase1-wait2,30 scan,,Disk 2,"Shutter was deliberately closed for scan 11 – 29, after it became clear that radiation dose was the issue"
-JP20-invivo-1prescan-h1-bulbs,,,Disk 2,scan failed
-JP20-invivo-1prescan-h1-bulbs-v2,,,Disk 2,
-JP20-invivo-1prescan-h2-spine,,,Disk 2,scan failed
-JP20-invivo-1prescan-h2-spine-v2,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-1,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-2,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-3,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-4-preinjection,,,Disk 2,
-JP20-invivo-1scan-h1-bulbs-5-postinjection,,,Disk 2,
-JP20-invivo-1scan-h2-spine-1,,,Disk 2,
-JP20-invivo-1scan-h2-spine-2,,,Disk 2,
-JP20-invivo-1scan-h2-spine-3,,,Disk 2,
-JP20-invivo-1scan-h2-spine-4-preinjection,,,Disk 2,
-JP20-invivo-1scan-h2-spine-5-postinjection,,,Disk 2,
-JP20-invivo-3scan-phase1-injection,3 scan,,Disk 2,
-JP21-invivo-1scan-phase1-preinjection,,,Disk 2,
-JP21-invivo-1scan-phase2-injection-brain-10min,,,Disk 2,
-JP21-invivo-1scan-phase2-injection-nose,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-100min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-110min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-120min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-20min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-30min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-40min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-50min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-60min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-nose-120min,,,Disk 2,
-JP21-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP22-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP22-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP22-invivo-1scan-phase2-injection-nose-60min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP22-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP22-invivo-1scan-phase4-injection-spine-90min,,,Disk 2,
-JP22-invivo-1scan-phase4-injection-spine-95min,,,Disk 2,
-JP22-invivo-6scan-phase2-injection-brain,6 scan,,Disk 2,
-JP23-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP23-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP23-invivo-1scan-phase2-injection-brain-10min,,,Disk 2,
-JP23-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP23-invivo-2scan-phase3-postinjection-brain-70-80min,2 scan,,Disk 2,
-JP23-invivo-5scan-phase3-postinjection-brain-20-60min,5 scan,,Disk 2,
-JP24-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP24-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP24-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP24-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP24-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP25-invivo-1scan-phase1-injection-brain,,,Disk 2,
-JP25-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP25-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-100min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-110min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-80min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP25-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP25-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP26-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP26-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP26-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP26-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP26-invivo-2scan-phase3-postinjection-brain-80-90min,1 scan,,Disk 2,is actually only one scan
-JP26-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-jp27-dead-1scan-phase1-preinjection-brain,,,Disk 2,
-jp27-dead-1scan-phase1-preinjection-nose,,,Disk 2,
-JP27-dead-1scan-phase2-injection1-brain,,,Disk 2,
-JP27-dead-30scan-phase2-injection2-brain,30 scan,,Disk 2,
-JP28-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP28-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP28-invivo-1scan-phase2-injection-brain-v2,,,Disk 2,
-JP28-invivo-1scan-phase2-injection-nose,,,Disk 2,
-JP28-invivo-1scan-phase3-postinjection-brain-70min,,,Disk 2,
-JP28-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP28-invivo-30scan-phase4-reinjection-brain-continuous-110min,30 scan,,Disk 2,
-JP28-invivo-3scan-phase3-postinjection-brain-80-100min,3 scan,,Disk 2,
-JP28-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP29-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP29-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP29-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP29-invivo-1scan-phase3-postinjection-brain-90min,,,Disk 2,
-JP29-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP29-invivo-2scan-phase3-postinjection-brain-70min-80min,2 scan,,Disk 2,
-JP29-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP30-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP30-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP30-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP30-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP30-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP30-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP30-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-brain-65min,,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP31-dead-1scan-phase3-postinjection-spine-80min,,,Disk 2,"missing a.HIS file, was never recorded"
-JP31-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP31-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP31-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP31-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP32-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP32-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP32-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP32-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP32-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP32-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP32-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP33-invivo-10scan-phase4-reinjection-brain-continuous,10 scan,,Disk 2,
-JP33-invivo-1scan-phase1-preinjection-brain,,,Disk 2,
-JP33-invivo-1scan-phase1-preinjection-nose,,,Disk 2,
-JP33-invivo-1scan-phase2-injection-brain,,,Disk 2,
-JP33-invivo-1scan-phase3-postinjection-nose-60min,,,Disk 2,
-JP33-invivo-3scan-phase3-postinjection-brain-70min-90min,3 scan,,Disk 2,
-JP33-invivo-5scan-phase3-postinjection-brain,5 scan,,Disk 2,
-JP34-invivo-scan1-brain,,,Disk 2,
-JP34-invivo-scan2-nose,,,Disk 2,
-JP34-invivo-scan3-spine,,,Disk 2,
-JP34-invivo-scan4-60scans-brain,60 scan,,Disk 2,
-purified_water_eppendorf01,,,Disk 1,
-purified_water_eppendorf02,,,Disk 1,
-test01,,,Disk 1,
-test02,,,Disk 1,
-test03,,,Disk 1,
-test04,,,Disk 1,
-test05,,,Disk 1,
-test06,,,Disk 1,
-test07,,,Disk 1,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023.csv
deleted file mode 100644
index 96a9af5..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-SubjectID,University,Research_group,Year,Month,Date_acquisition,Data_type,Dataproject_ID,Facility_proposal_ID,Facility_institution,Facility_country,Facility_name,Facility_sub
-JP28,UZH,The Interface Group,2023,May,14/05/2023,SRµCT,in vivo CSF,2023A1208,,Japan,SPring-8,BL20B2
-,,,,,,,,,,,,
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023_codebook.csv b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023_codebook.csv
deleted file mode 100644
index 29bfc17..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/Scan_list_SPring-8_May_2023_codebook.csv
+++ /dev/null
@@ -1,13 +0,0 @@
-SubjectID,Mice unique identifier
-University,"University affiliation of the group who collected the data (e.g., UZH; see glossary)"
-Research_group,"Abbreviation describing the group who collected the data (e.g., TIG; see glossary)"
-Year,Year of collection YYYY
-Month,"Month of collection (Jan, Feb, Mar, etc)"
-Date_acquisition,DD/MM/YYYY
-Data_type,"Abbreviation describing the type of data collected (e.g., SRµCT; see glossary)"
-Dataproject_ID,"(optional) Identifier of the project from which the data package derives, e.g., In Vivo CSF"
-Facility_proposal_ID,"(optional) Number of the proposal for facility usage e.g., the beamline numbers"
-Facility_institution,Name or acronym of the institution hosting the main facility (it can be the same as University)
-Facility_country,Country where the facility is located
-Facility_name,"Name or acronym of the main facility (e.g., CLS, SPring-8,etc)"
-Facility_sub,"(optional) Additional facility information (e.g., beamline)"
diff --git a/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/xlsx/Mouse_list_SPring-8_May_2023.xlsx b/webpage_contents/experiments/SPring-8_May_2023/metadata_tables/xlsx/Mouse_list_SPring-8_May_2023.xlsx
deleted file mode 100644
index f0c40137a9deee6c0142506b3e459f5d79fb5075..0000000000000000000000000000000000000000
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diff --git a/webpage_contents/experiments/SPring-8_May_2023/protocols/SPring-8_reconstruction.qmd b/webpage_contents/experiments/SPring-8_May_2023/protocols/SPring-8_reconstruction.qmd
deleted file mode 100644
index ea7d71b..0000000
--- a/webpage_contents/experiments/SPring-8_May_2023/protocols/SPring-8_reconstruction.qmd
+++ /dev/null
@@ -1,189 +0,0 @@
----
-date: last-modified
----
-
-# SPring-8 BL20B2 Reconstruction How-to
-
-## Setup
-
-Reconstruction is performed on **Windows** machines in the **cmd command terminal**. If using PowerShell, commands may differ, I.e. `bbb.bat` has to be invoked with `.\bbb.bat` Instead.
-
-## Installation of the software
-
-### Downloads
-
-The software relies on CUDA, you can download that here: https://developer.nvidia.com/cuda-downloads
-
-The software itself was custom-written and is available at:<http://www-bl20.spring8.or.jp/xct/index-e.html>
-
-### Adding the path to the reconstruction software executables to the terminal
-
-The path to the folder with the executables needs to be added to the environment variables in Windows, so that they can be called via terminal directly.
-
-**On Windows 10:**
-
-In **Start Menu:** `View Advanced System Settings > Tab: Advanced > Button: Environment Variables`
-
-In the upper part of the window, it will show the variables for a single user, in the lower part, the variables for all users.
-
-Then do `Select Path > Edit… > New` . Add the folder where you are keeping the .exe files from SPring-8 (I.e. “C:\\Program Files\\SPring-8\\ct-rec\\exeâ€) to the paths.
-
-## Extracting images from a.HIS file
-
-**!WARNING: The reconstruction pipeline differs if during acquisition, “Skip IO†was turned on or off!**
-
-**“Skip IO†= on** means that flat-field acquisition between consecutive scans was skipped, in order to shorten the scan time and increase time resolution.
-
-**“Skip IO†= off** means that separate flat-field acquisitions were performed for each scan, as per standard procedure
-
-For reconstructing individual scans, skip to the last section.
-
-### With “Skip IO†= On
-
-Change to raw directory in scan:
-
-``` plaintext
-cd G:\<scan location>\raw
-```
-
-Execute `spl_c` to write a batch-script, designed to split the Hamamatsu-Format a.HIS file to multiple files. Executing `spl_c` without arguments will display the required arguments. The arguments are:
-
-``` plaintext
-spl_c <number of projections> <number of flat-fields/dark-fields = “DIRECT†in acquisition window> <number of scans in a.HIS file>
-```
-
-``` plaintext
-spl_c 1801 30 3 > bbb.bat
-```
-
-Execute bbb.bat:
-
-``` plaintext
-bbb.bat
-```
-
-### **With “Skip IO†= Off**
-
-Change to raw directory in scan:
-
-``` plaintext
-cd G:\<scan location>\raw
-```
-
-Execute `spl` to write a batch-script, designed to split the Hamamatsu-Format **a.HIS file** to multiple files. Executing `spl` without arguments will display the required arguments. The arguments are:
-
-``` plaintext
-spl <N-Shots> <number of scans>
-```
-
-\<N-Shots\> is the number of all projections + all flat-fields + all dark-fields. In our scans, this is 1801 + 2\*30 + 30 = 1891:
-
-``` plaintext
-spl 1891 2 > bbb.bat
-```
-
-Execute bbb.bat:
-
-``` plaintext
-bbb.bat
-```
-
-## Reconstruction
-
-### Reconstruct single scan
-
-Enter the raw-folder of the individual scan:
-
-``` plaintext
-cd G:\<scan location>\raw\001\raw
-```
-
-Execute `conv.bat`. This creates a0001.img to a1891.img, which are all projections, flat-fields and dark-fields. It further creates:
-
-- dark.img = averaged flat-field
-- q0001.img = averaged flat-field from scan start
-- q1804.img = averaged flat-fields from scan end
-
-``` plaintext
-conv
-```
-
-Reconstruct a single slice to determine center of rotation. The arguments are the slice number (indexed from zero) and the manual center of rotation. If no second argument is provided, center of rotation will be calculated automatically. A single .tiff file will be written into the scan directory. New reconstructions will overwrite old ones without warning.
-
-``` plaintext
-ct_rec_g_c 750
-```
-
-This program will provide the center of rotation value as an output as the third variable on the second line. This will be required as argument for the full reconstruction. (The first variable is the file name, the second is the pixel size, which will be 1.0 since it’s not set up)
-
-To reconstruct the whole volume, one has to go up one folder from raw.
-
-``` plaintext
-cd ..
-```
-
-Make a new folder for where the reconstruction will be stored
-
-``` plaintext
-mkdir rec
-```
-
-Use the `hp_tg_g_c` command to reconstruct the whole volume. Arguments are:
-
-``` plaintext
-hp_tg_g_c <source folder> <pixel size> <center of rotation> <rotation angle of the reconstructed volume> <destination folder>
-```
-
-``` plaintext
-hp_tg_g_c raw 7.99 1023.0 0 rec
-```
-
-### PowerShell script to reconstruct multiple single scans
-
-The following script can be run in Windows PowerShell to automatize reconstruction after splitting the datasets. `spl` and `spl_c` do not work in PowerShell, and would need their own implementation (probably not difficult. Look at `bbb.bat`, it’s quite simple).
-
-``` powershell
-# Execute in scan/raw, not in scan/raw/001/raw
-
-$NumberOfScans = 5
-
-$SingleSliceRecoSlice = 750
-
-$PixelSize = 7.99
-
-$RotationAngleRecoVolume = 0
-
-for ($i = 1; $i -le $NumberOfScans; $i++)
-
-{
-
-# Convert 1, 2, 3 etc. to 001, 002, 003 etc.
-
-$FolderNumber = '{0:d3}' -f $i
-
-cd $FolderNumber
-
-cd raw
-
-./conv
-
-# Reconstruct a single slice (1st argument of ct_rec_g_c, slice 750 in this case, zero-indexed), and stores each line as an element in an array $SingleRecoTerminalOutput
-
-$SingleRecoTerminalOutput = ct_rec_g_c $SingleSliceRecoSlice
-
-# Calls the 2nd element of $SingleRecoTerminalOutput, splits the tab-separated values in the string to a new array and stores it in a variable
-
-$SingleRecoTerminalOutputSecondLine = $SingleRecoTerminalOutput[1].Split()
-
-$CenterOfRotation = $SingleRecoTerminalOutputSecondLine[2]
-
-cd ..
-
-mkdir rec
-
-hp_tg_g_c raw $PixelSize $CenterOfRotation $RotationAngleRecoVolume rec
-
-cd ..
-
-}
-```
--
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