From cac755841997d030298aa00ed39fc1a81aea87bb Mon Sep 17 00:00:00 2001
From: Willy Kuo <willy.kuo@physiol.uzh.ch>
Date: Mon, 30 Sep 2024 19:10:37 +0200
Subject: [PATCH] Rename Preview_Image_LowQuality to Preview_Image

---
 .../metadata_tables/Scan_list_CLS_2023_November.csv           | 2 +-
 .../metadata_tables/Scan_list_ESRF_2021_November.csv          | 2 +-
 .../metadata_tables/Scan_list_ESRF_2022_June.csv              | 2 +-
 .../metadata_tables/Scan_list_SPring-8_2023_May.csv           | 2 +-
 .../20240901_Marta_GironaAlarcon/Publication_page.qmd         | 4 ++--
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/Scan_list_CLS_2023_November.csv b/webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/Scan_list_CLS_2023_November.csv
index fee9271..f2ee97f 100644
--- a/webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/Scan_list_CLS_2023_November.csv
+++ b/webpage_contents/experiments/synchrotron_microCT/CLS_2023_November/metadata_tables/Scan_list_CLS_2023_November.csv
@@ -1,2 +1,2 @@
-Preview_Image_LowQuality,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
+Preview_Image,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
 ,490,2023-11-26,CA019,N/A,brain,subjCA019/scan002_time-steps,N/A,50,,in vivo,C57BL/6J,wild-type,healthy,standard tomography,time series,N/A,N/A,37.8 keV,Double crystal monochromator,8 µm,2048,1200,16.4 mm,9.6 mm,15 ms,2 ms,2000,180 °,N/A,N/A,600 mm,pco.edge 5.5,6.5 µm,2560,2160,Macro lens,,N/A,,2 Gy/s,CLS,BMIT,N/A,Canada,2023-11-21,38G13327,CSF time-resolved,CLS_Nov2023_Disk1,CLS_Nov2023_Disk3,laboratory cupboard,office cupboard,Y23 J78; Box 1; Slots 3 & 5 ,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
diff --git a/webpage_contents/experiments/synchrotron_microCT/ESRF_2021_November/metadata_tables/Scan_list_ESRF_2021_November.csv b/webpage_contents/experiments/synchrotron_microCT/ESRF_2021_November/metadata_tables/Scan_list_ESRF_2021_November.csv
index cf760b6..9e81253 100644
--- a/webpage_contents/experiments/synchrotron_microCT/ESRF_2021_November/metadata_tables/Scan_list_ESRF_2021_November.csv
+++ b/webpage_contents/experiments/synchrotron_microCT/ESRF_2021_November/metadata_tables/Scan_list_ESRF_2021_November.csv
@@ -1,4 +1,4 @@
-Preview_Image_LowQuality,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
+Preview_Image,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
 ,408,2021-11-19,Mouse17,N/A,brain,All_2k/Mouse17_male_live_23p7_0p5ulmin_5ul_2k_h2,N/A,1,,in vivo,C57BL/6J,wild-type,healthy,standard tomography,height steps,ESRF Data Repository,https://data.esrf.fr/investigation/534173041/datasets,37.95 keV,Double crystal monochromator,6.3 µm,2560,780,16.5 mm,4.9 mm,5 ms,5 ms,2000,180 °,N/A,4.4 mm,3000 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2021-11-18,MD1230,CSF gated,ESRF_ID17_inVivo_MD1230,esrf_id17_invivo_reco,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
 ,408,2021-11-19,Mouse17,N/A,brain,Mouse17_male_live_23p7_0p5ulmin_5ul_60k360_h2,N/A,1,20 reconstructed time delays,in vivo,C57BL/6J,wild-type,healthy,standard tomography,gated scan,ESRF Data Repository,https://data.esrf.fr/investigation/534173041/datasets,37.95 keV,Double crystal monochromator,6.3 µm,2560,780,16.5 mm,4.9 mm,5 ms,5 ms,60000,360 °,N/A,N/A,3000 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2021-11-18,MD1230,CSF gated,ESRF_ID17_inVivo_MD1230,esrf_id17_invivo_reco,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
 ,536,2021-11-19,Mouse19,N/A,brain ,All_2k/Mouse19_male_live_26p9_noCA_2k_h1,N/A,1,2 reconstructed delta/beta,in vivo,C57BL/6J,wild-type,healthy,standard tomography,height steps,ESRF Data Repository,https://data.esrf.fr/investigation/534173041/datasets,37.95 keV,Double crystal monochromator,6.3 µm,2560,780,16.5 mm,4.9 mm,5 ms,5 ms,2000,180 °,N/A,4.4 mm,3000 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2021-11-18,MD1230,CSF gated,ESRF_ID17_inVivo_MD1230,ESRF_MD1230_disk2,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
diff --git a/webpage_contents/experiments/synchrotron_microCT/ESRF_2022_June/metadata_tables/Scan_list_ESRF_2022_June.csv b/webpage_contents/experiments/synchrotron_microCT/ESRF_2022_June/metadata_tables/Scan_list_ESRF_2022_June.csv
index 3c27058..11bf43c 100644
--- a/webpage_contents/experiments/synchrotron_microCT/ESRF_2022_June/metadata_tables/Scan_list_ESRF_2022_June.csv
+++ b/webpage_contents/experiments/synchrotron_microCT/ESRF_2022_June/metadata_tables/Scan_list_ESRF_2022_June.csv
@@ -1,4 +1,4 @@
-Preview_Image_LowQuality,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
+Preview_Image,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
 cisternaMagna_timeseries2_001_1282_000500.tif,500,2022-06-05,mouse50,N/A,cisterna magna,mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved/cisternaMagna_timeseries2_001_,Original folder name on ESRF Data Repository is mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved; infusion rate is incorrect and should be 0p5ulmin.,1,,in vivo,C57BL/6J,wild-type,healthy,standard tomography,time series,ESRF Data Repository,https://data.esrf.fr/investigation/790329040/datasets,37.5 keV,Double crystal monochromator,6.45 µm,2560,698,16.5 mm,4.5 mm,4 ms,1 ms,2000,360 °,N/A,N/A,2500 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2022-06-03,MD1324,CSF time-resolved,ESRF_ID17_inVivo_MD1231,esrf_id17_invivo_reco,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
 cisternaMagna_timeseries2_002_1282_000500.tif,500,2022-06-05,mouse50,N/A,cisterna magna,mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved/cisternaMagna_timeseries2_002_,Original folder name on ESRF Data Repository is mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved; infusion rate is incorrect and should be 0p5ulmin.,1,,in vivo,C57BL/6J,wild-type,healthy,standard tomography,time series,ESRF Data Repository,https://data.esrf.fr/investigation/790329040/datasets,37.5 keV,Double crystal monochromator,6.45 µm,2560,698,16.5 mm,4.5 mm,4 ms,1 ms,2000,360 °,N/A,N/A,2500 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2022-06-03,MD1324,CSF time-resolved,ESRF_ID17_inVivo_MD1231,esrf_id17_invivo_reco,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-27
 cisternaMagna_timeseries2_003_1282_000500.tif,500,2022-06-05,mouse50,N/A,cisterna magna,mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved/cisternaMagna_timeseries2_003_,Original folder name on ESRF Data Repository is mouse50_male_alive_23p7g_0p1ulmin_2p5ul_2KTimeResolved; infusion rate is incorrect and should be 0p5ulmin.,1,,in vivo,C57BL/6J,wild-type,healthy,standard tomography,time series,ESRF Data Repository,https://data.esrf.fr/investigation/790329040/datasets,37.5 keV,Double crystal monochromator,6.45 µm,2560,698,16.5 mm,4.5 mm,4 ms,1 ms,2000,360 °,N/A,N/A,2500 mm,pco.edge 5.5,6.5 µm,2560,2160,Camera lens Hasselblad 100 mm f/2.2,2.2,N/A,250 µm LuAG,3.4 Gy/s,ESRF,ID17,N/A,France,2022-06-03,MD1324,CSF time-resolved,ESRF_ID17_inVivo_MD1231,esrf_id17_invivo_reco,laboratory cupboard,office cupboard,Y23 J78,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-27
diff --git a/webpage_contents/experiments/synchrotron_microCT/SPring-8_2023_May/metadata_tables/Scan_list_SPring-8_2023_May.csv b/webpage_contents/experiments/synchrotron_microCT/SPring-8_2023_May/metadata_tables/Scan_list_SPring-8_2023_May.csv
index 70725bc..789dc1a 100644
--- a/webpage_contents/experiments/synchrotron_microCT/SPring-8_2023_May/metadata_tables/Scan_list_SPring-8_2023_May.csv
+++ b/webpage_contents/experiments/synchrotron_microCT/SPring-8_2023_May/metadata_tables/Scan_list_SPring-8_2023_May.csv
@@ -1,2 +1,2 @@
-Preview_Image_LowQuality,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
+Preview_Image,Preview_Image_Slice_Number,Date,Subject_ID,Tissue_ID,Anatomical_location,Filename,Filename_changes,Number_of_subscans_in_file,Comments,Preparation,Strain,Genetic_strain_type,Pathology,Tomography_acquisition_scheme,Tomography_scan_type,Repository,Repository_URL,Mean_photon_energy,Monochromator,Effective_voxel_size,Projections_width_in_pixel,Projections_height_in_pixel,Projections_width,Projections_height,Exposure_time,Overhead_time_per_projection,Number_of_projections,Stage_rotation_angle_range,Stage_position_z,Height_step_size,Propagation_distance,Detector_model,Detector_pixel_size,Detector_width_in_pixel,Detector_height_in_pixel,Lens_type,Lens_f-number,Lens_numerical_aperture,Scintillator,Radiation_dose_rate,Facility_name,Facility_subunit,Facility_institution,Facility_country,Beamtime_start_date,Beamtime_proposal_number,Beamtime_project_description,Disk_ID_Projections,Disk_ID_Reconstructions,Disk_Basel_Physical_Location,Disk_Bern_Physical_Location,Disk_Zurich_Physical_Location,Research_group_institution,Research_group,Table_date_csv_export
 ,1060,2023-05-14,JP28,N/A,brain,JP28-invivo-5scan-phase3-postinjection-brain,N/A,5,,in vivo,C57BL/6JJmsSlc,wild-type,healthy,standard tomography,time series,N/A,N/A,40 keV,Double crystal monochromator,7.99 µm,2048,1500,16.4 mm,12 mm,5 ms,8 ms,1800,180 °,N/A,N/A,1000 mm,Hamamatsu Orca Flash 4.0,6.5 µm,2048,2048,Tandem Lens System 105 mm f/2.4 & 85 mm f/1.4,2.4,N/A,500 µm LuAG,22 Gy/s,SPring-8,BL20B2,RIKEN,Japan,2023-05-11,2023A1208,CSF time-resolved,SPring-8_May2023_Disk2,SPring-8_May2023_Disk2,laboratory cupboard,office cupboard,Y23 J78; Box 1; Slot 2,Unibas & Unibe & UZH,BMC & TKI & TIG,2024-09-30
diff --git a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
index 0c01917..4a5c32f 100644
--- a/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
+++ b/webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd
@@ -159,7 +159,7 @@ for (i in 1:nrow(inputs)){
   # Providing the preview images
   # ------------------------------------------------
   # Build URL based on the REpo URL (retrieved from _quarto.yml file)
-  image_url <- file.path(repo_url_basepath,'experiments',inputs$Data_type[i], inputs$Facility_name_YYYY_month[i],'preview_images',tmp_tbl_scans$Preview_Image_LowQuality)
+  image_url <- file.path(repo_url_basepath,'experiments',inputs$Data_type[i], inputs$Facility_name_YYYY_month[i],'preview_images',tmp_tbl_scans$Preview_Image)
   
   # Find relative path to image and COPY it into the publication folder
   source_images_relativepath <- gsub(repo_url_basepath,file.path('..','..'),image_url)
@@ -169,7 +169,7 @@ for (i in 1:nrow(inputs)){
  
 "C:/Users/gorka/Gitlab_crs/fdcns/webpage_contents/publications/20240901_Marta_GironaAlarcon/images"
 # Add HTML to display images in table and make them clickable link
- tmp_tbl_scans$Preview_Image_LowQuality <- paste0('<a href=\'', image_url,'\' target=\'_blank\'>','<img src=\'',  source_images_relativepath, '\' height=\'70\'></a>')
+ tmp_tbl_scans$Preview_Image <- paste0('<a href=\'', image_url,'\' target=\'_blank\'>','<img src=\'',  source_images_relativepath, '\' height=\'70\'></a>')
 
   # ------------------------------------------------
   
-- 
GitLab