# HMML Palimpsest XRF Imaging ReadMe

**Prepared by R.B. Toth Associates**

## XRF Imaging for the Hill Museum & Manuscript Library

**Authors**: Michael B. Toth, William Sellers, Sam Webb, Nick Edwards, Uwe Bergmann

**Date**: 22 April 2020

## 1 HMML Palimpsest XRF Imaging

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.

### 1.1 SLAC Imaging

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.

### 1.2 Illumination System

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.

### 1.3 Detectors

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

### 1.4 XRF Data Integration and Image Capture

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.

### 1.5 XRF Imaging Processing

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.

## 2 Rights

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.

## 3 HMML Palimpsest XRF Data Set Contents

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


### 3.1 Core Data

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.

1. XRF images captured using SLAC SSRL operating systems and SMAK software
   were converted from `.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.

## 4 General File Conventions

The remainder of the file name, including the extension, indicates the SSRL ID
code and file type. The latter are usually:

1. TIFF still image files, ending in `tif`
2. JPEG still image files ending in `jpg`