Readme.txt
Data set for 'Using High Resolution X-ray Computed Tomography to Create an Image Based Model of a Lymph Node'
Laura Cooper
17th April 2018

File name: Gridrec_Subvolumes.zip
Description: Compressed .raw image data. Tomographic data acquired at TOMCAT beamline, Swiss Light Source (Villigen, Switzerland), The imaging was carried out using an energy of 14 keV, using a propagation distance between sample and detector of 60 mm. The exposure time was 180 ms and 1601 projections were taken over 180 degrees (with additional 32 dark field and 160 flat field images). The resulting voxel size was (0.65 um)^3. The images were reconstructed using the in-house implementation at TOMCAT of the Gridrec algorithm. Two scans were made to capture the full volume of the murine lymph node, were concatenated which have been concatenated, converted to an 8 bit range and binned x2 so the final voxel size is (1.3 um)^3. Three subvolumes were selected for comparion which are contained in three folders in the .zip file:
Gridrec_CC2LNChannels100
Gridrec_CC2LNDense100
Gridrec_CC2LNMedium100
Each folder contains 100 .png image files that correspond to 'Channels', 'Dense' and 'Medium' subvolumes, repectively, described in the paper for use in the COMSOL model.

File name: Paganin_Subvolumes.zip
Description: Compressed .raw image data. Tomographic data acquired at TOMCAT beamline, Swiss Light Source (Villigen, Switzerland), The imaging was carried out using an energy of 14 keV, using a propagation distance between sample and detector of 60 mm. The exposure time was 180 ms and 1601 projections were taken over 180 degrees (with additional 32 dark field and 160 flat field images). The resulting voxel size was (0.65 um)^3. The images were reconstructed using the in-house implementation at TOMCAT of the Paganin phase retrieval algorithm with Gridrec. Two scans were made to capture the full volume of the murine lymph node, which have been concatenated, converted to an 8 bit range and binned x2 so the final voxel size is (1.3 um)^3. Three subvolumes were selected for comparion and are contained in three folders in the .zip file:
CC2LNPagChannels
CC2LNPagDense
CC2LNPagMiddle
Each folder contains 100 .png image files that correspond to 'Channels', 'Dense' and 'Medium' subvolumes, respectively, as described in the paper for use in the COMSOL model.

File name: Paganin_CC2LN_8bt_2187x1329x2458.zip
Description: Compressed .raw image data. Tomographic data acquired at TOMCAT beamline, Swiss Light Source (Villigen, Switzerland), The imaging was carried out using an energy of 14 keV, using a propagation distance between sample and detector of 60 mm. The exposure time was 180 ms and 1601 projections were taken over 180 degrees (with additional 32 dark field and 160 flat field images). The resulting voxel size was (0.65 um)^3. The images were reconstructed using the in-house implementation at TOMCAT of the Paganin phase retrieval algorithm with Gridrec. Two scans were made to capture the full volume of the murine lymph node, which have been concatenated and converted to an 8 bit range.

Uncompressed file size: 6,976,971 kb
File bit depth: 8-bit unsigned
File dimensions: 2187x1329x2458 voxels

File name: DataFiles_XCTLymphNode.zip
Description: .csv files containing data from figures presented in 'Using High 
Resolution X-ray Computed Tomography to Create an Image Based Model of a Lymph 
Node'. Files are named by the figure number.