Prepared by R.B. Toth Associates
Authors: Michael B. Toth, William Sellers, Sam Webb, Nick Edwards, Uwe Bergmann
Date: 22 April 2020
This data set includes captured and processed data from the x-ray fluorescence (XRF) imaging of the Hill Museum and Manuscript Library (HMML) Palimpsest on Beamline 10-2 at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory from 24 to 27 January 2020.
X-ray absorption spectroscopy imaging of the HMML Palimpsest was conducted at SLAC, a multi-program national laboratory user facility by Stanford University supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. This imaging was conducted as part of fundamental research which is published or shared broadly with the scientific and scholarly community. This builds on XRF imaging of the Archimedes and Syriac Galen Palimpsests, and uses some of the same techniques and the metadata extensions developed during the Archimedes Palimpsest XRF imaging at SLAC in 2006 and refined during the Syriac Galen Palimpsest XRF imaging in 2019 and 2020.
The SSRL SPEAR3 3-GeV, high-brightness third-generation storage ring was upgraded in 2004. It operates at 500 mA in top-off mode, with high reliability and low emittance.
SSRL’s extremely bright x-rays were used to image the HMML Palimpsest. Beamline10-2 is a wiggler end-station that is used for hard x-ray transmission x-ray imaging.
The x-ray fluorescence from the HMML Palimpsest was detected with multiple Vortex detectors, each collecting multiple elements. More information on the detectors is contained in Edwards et al, J. Synchrotron Rad, 25, 1565-73 (2018), DOI: 10.1107/S1600577518010202
The XRF image data are collected and saved at SSRL as HDF5 data files containing the raw data from a multichannel analyzer (MCA). Multiple channels of data are collected and stored, as cited in the metadata document. Data from scans in the original hdf5 and tar files are stored at SLAC and the Hill Museum and Manuscript Library for additional research. These are minimally processed data from the XRF detectors on each beam line and require special software (such as SMAK) for viewing.
Sam’s Microprobe Analysis Kit, or SMAK for short, is a data-processing toolkit for x-ray microprobes. This is used to view and analyze images both for textual analysis and for improvement in the imaging methods and techniques.
All images from HMML Palimpsest are in the public domain or released under Creative Commons license 4.0 with attribution. All significant results are to be publicly disseminated. Use of the SLAC SSRL facility must be acknowledged in all presentations and publications with the following “Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515.” SLAC SSRL should be informed of all publications, theses, awards, patents and other forms of recognition resulting from research conducted fully or partially with the results of this imaging.
Both the recto and verso sides of bifolio SJU MS 32 that comprise the HMML
Palimpsest were imaged. The XRF data files from this session all have the
prefix letters HMML and are in two folders, one for recto images and one for
verso images. Each folder contains 13 TIFF images from the XRF scans of each
side of the HMML Palimpsest. The data set contains the following folders:
Data: Data captured from XRF imaging of the HMML Palimpsest that have been
converted into TIFF images.
Processed: Digitally processed TIFF images from the captured XRF images of
the HMML Palimpsest to reveal unseen features.
ReadMe_XRF.txt: This description of the data set in txt form providing an
orientation to the data and rights management.
The directory structure, starting from the root is as follows for the XRF data:
|-- Data
| |-- Frag32r
| | |-- Frag32rXRF
| | | |-- HMML_SJU_Ms_F_32r_14500_0_001_Cu1.tiff
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-AsPb_001_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Ca_002_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Cl_003_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Cu_004_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Fe_005_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Hg_006_R.tiff
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-K_007_R.tiff
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA--01-pc02-pc03-pc05_PCAN-1--3_RGB.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA--01-pc02-pc03-pc07_PCAN-1--3_RGB.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA1.jpg
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA.jpg
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA--pc01-pc02-pc03-pc06_PCAN-1--3_RGB.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA--pc02-pc03-pc05-pc07_PCAN-1--3_RGB.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA--pc02-pc03-pc05-pc08_PCAN-1--3_RGB.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-_MBT_PCA.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Mn_008_R.tiff
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-S_009_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Scat_010_R.tif
| | | |-- HMML_SJUMsFrag32r14500-Frag32r-Ti_011_R.tif
| | | `-- HMML_SJUMsFrag32r14500-Frag32r-Zn_012_R.tif
| | `-- Processed
| `-- Frag32v
| |-- Frag32vXRF
| | |-- HMML_SJU_Ms_F_32v_14500_0_001_sPCAComp5.tiff
| | |-- HMML_SJUMsFrag32v14500-Frag32v-AsPb_001_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Ca_002_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Cl_003_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Cu_004_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Fe_005_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Hg_006_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-K_007_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA.jpg
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA--pc01-pc02-pc03-pc06_PCAN-1--3_RGB.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA--pc01-pc02-pc03-pc08_PCAN-1--3_RGB.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA--pc05-pc06-pc07-pc09_PCAN-1--3_RGB.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA--pc05-pc06-pc07-pc10_PCAN-1--3_RGB.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v_MBT_PCA.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Mn_008_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-S_009_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Scat_010_R.tif
| | |-- HMML_SJUMsFrag32v14500-Frag32v-Ti_011_R.tif
| | `-- HMML_SJUMsFrag32v14500-Frag32v-Zn_012_R.tif
| `-- Processed
|-- manifest-sha1.txt
|-- ReadMe_Multispectral.html
|-- ReadMe_Multispectral.txt
|-- ReadMe_XRF.html
`-- ReadMe_XRF.txt
For each palimpsest bifolio side, the data set provides captured scans converted to TIFF images and JPEG thumbnail images with metadata. These images should be retained as archival images and will be easiest to read with most image viewers.
.hdf5 format to 8-bit .TIF format.The core data includes:
Captured Image data consisting of captured XRF scans converted to TIFF. These are individual images from each of the scans created with specific elemental data.
Computer Processed images. Images that have been digitally produced through the application of computer algorithms to combine and enhance visibility of text. All processed images are TIFF images and jpegs.
Metadata are included in the overall metadata document.
The remainder of the file name, including the extension, indicates the SSRL ID code and file type. The latter are usually:
tifjpg