Archimedes Palimpsest Supplemental Multispectral Imaging Read Me

Authors: Michael B. Toth
Doug Emery
Date: 22 April 2016


Archimedes Palimpsest Supplemental Multispectral Imaging

This data set includes captured and processed data from the narrowband multispectral imaging of designated folio sides in the Archimedes Palimpsest on 30 April 2015 in a private library by R.B. Toth Associates and Equipoise Imaging LLCs. Dr. Reviel Netz identified 22 key folio sides for follow-up imaging to support scholarly research and provide more insight into undertext that remained illegible. It follows multispectral imaging of all the palimpsest folios during the Archimedes Palimpsest multispectral imaging project. This comprises 23 multispectral image stacks (including a stack of “flats” images) and processed images with 355 files totaling about 40 Gigabytes of data.

The narrowband multispectral imaging system used for this project includes a medium-format, high-pixel-count camera that takes a series of high-quality digital images, each illuminated by a specific wavelength of light with two LED illumination panels. The resulting image set is then digitally processed and combined to reveal residues and features in the object that are not visible to the eye in natural light. These processed images clarify and reveal text that might not be seen in natural light

1 Narrowband Multispectral Imaging System

The narrowband multispectral imaging system used for this project includes commercial-off-the-shelf hardware and software for digital spectral image capture and viewing with the integrated system. The system operations are integrated with the Spectral XV system software that controls the camera, illumination panels and filters with a one-button user interface. It also includes customized image processing software for exploitation of the spectral images, provided in partnership by Equipoise Imaging LLC.

1.1 Camera System

The camera system utilizes a Phase One IQ260 60 Megapixel (MP) Achromatic back with an iXR body and 120mm lens producing over 1000 ppi resolution images. Image data were downloaded in at the end of each capture via USB 3.0 connection to a laptop computer and transferred to local drives and Google Drive for sharing.

1.2 Illumination System

The imaging system provides narrowband illumination with light in 10 specific wavelengths from low heat and low maintenance, long-lifetime light emitting diodes (LEDs). It includes two integrated illuminators, each with multiple LEDs, providing illumination for imaging in distinct ultraviolet, visible and infrared spectral bands (see wavelengths in “General File Conventions” below). It is integrated with software to allow simplified system operation and unified metadata capture.

1.3 Filter System

To capture fluorescence from an object, a 6-position motorized filter wheel contains 2-inch square optical glass filters, with control software and computer interface. Filtered images can increase the range of captured information to include both fluorescence emissions and UV reflectance. This allows the characteristic spectra of substrate, colorant, and contaminant materials to be more completely determined and analyzed. The filter wheel is driven by computer control with a removable carousel containing a selection of filters (UV bandpass; visible bandpass and longpass filters).

1.4 Image Capture Integration

The Spectral XV integrated image capture operating software provides integrated control of the digital camera back, filters and illumination as a single system. This software – based on the CaptureCore application engine developed by Phase One A/S to control camera capture operations and processing workflow – allows streamlined operation and metadata capture from a single interface with simple setup and imaging.

1.5 Spectral Imaging Processing

Images are initially processed with ImageJ open-source image processing software and a customized Paleo Toolbox – a spectral imaging toolkit created by Bill Christens-Barry of Equipoise Imaging, LLC, for applications in cultural heritage imaging. The Paleo toolkit comprises plugin modules that integrate into ImageJ, an open source image processing tool originally developed at the US National Institutes of Health. ImageJ has been widely adopted and extended by scientists working in remote sensing, biological science, and cultural heritage world-wide. It offers a wide range of digital operations for the enhancement and reproduction of non-visible features from the objects based on their spectral response in images captured with the full set of illumination wavelengths and emission bands.

2 Rights

Right to all images from Archimedes Palimpsest Supplemental Imaging are CC0. We request published images be credited to “The Owner of the Archimedes Palimpsest”.

3 Archimedes Palimpsest Supplemental Data Set Contents

The Archimedes Palimpsest Supplemental Imaging data set comprises a core content set of digital images of the sides of parchment folios imaged on 30 April 2015. It contains the following folders with multispectral image data. Each folder corresponds to a stack of 16 images of an Archimedes Palimpsest folio side, with each image captured using a different illumination and/or filter. A “Flats” image stack was also captured with a large white sheet of paper in the scene. The image data comprises:

  • 0000-171r
  • 0000-171v
  • 157r-160v
  • 157v-160r
  • 158r-159v
  • 158v-159r
  • 165r-168v
  • 168r-165v
  • 169r-164v
  • 169v-164r
  • 177r-172v
  • 177v-172r
  • Flats1058_2015-04-30

3.1 Core Data

For each side of a palimpsest leaf, the data set provides sequences or stacks of captured and registered images converted to TIFF and JPEG thumbnail images with metadata. These images should be retained as archival images and will be easiest to read with most image viewers. Images in IIQ format are working images that can be viewed with Phase One’s Capture One software. The data set includes:

  1. Multispectral images captured using Spectral XV were converted from .IIQ format to 16-bit .TIF format by use of Capture One Software and the “Linear Scie ntific” curve. Converted images have the "_R" at the end of the rootname.
  2. Reference "flats" images that were smoothed using a gaussian blur operation; smoothed flats images have the string "_H" at the end of the rootname.
  3. Subject images flattened using reference "_H" flats images; flattened images have the string "_F" at the end of the rootname. These flattened images serve as the archival images provided to the Archimedes Palimpsest Supplemental.

The core data includes:

  • Captured Image data consisting of those converted to TIFF. These are individual images from each of the imaging systems taken with different energy levels.
  • Computer Processed images. Images that have been digitally produced through the application of computer algorithms to combine and enhance captured images to enhance visibility of manuscripts artifacts and text. All processed images are TIFF or jpg images.

Sample multispectral image metadata is included in the file 177v-172r/177v_ARCH69v.json which gives the details of the image capture for the project, scene and sequence and processing methods used to generate integrated images from the various captured images. Descriptive metadata is provided in a JSON file giving details of the image capture for the project, scene and sequence.

This includes basic Archimedes Palimpsest Metadata Standard metadata, such as:

"Project": {
  "ProjectID": "Archimedes Reimaging",
  "ProjectName": "177v", [folio side number]
  "Copyright": "Creative Commons 4.0",
  "Publisher": " Owner of the Archimedes Palimpsest",
  "ProjectNickName": "177v",
  "ProjectCreator": "R.B. Toth Associates",
  "ProjectContributors": "Michael B. Toth, William A.  Christens-Barry, Vincent Carney, Doug Emery",
  "Comments": "",
  "Scenes": [
      "SceneID": "ARCH69v",
      "SceneNickName": "ARCH69v",
      "SceneStatus": "ToDo",
      "Sequences": [
          "SequenceID": "177v Archimedes 69v",
          "SequenceNickName": "177vArch69v",
          "Creator": "R.B. Toth Associates",
          "Contributors": "William A.  Christens-Barry Michael B. Toth Vincent Carney",
          "SeqNumShots": 16,
          "SequenceStatus": "ToDo",
          "ISO": 200.0,
          "Aperture": 8.0,
          "Shots": [
              "ShotIndex": 1,
              "ShotID": "448N",
              "ShotUID": "448N",
              "LightMode": "448",
              "ShotStatus": "Done",
              "Cameras": [
                  "CameraID": "IQ260 Achromatic",
                  "ISO": "200",
                  "Aperture": "8",
                  "ShutterTime": "1/2",
                  "IntegrationTime": "1/2"
              "Lights": [
                  "LightID": "Left-0171-Light1",
                  "WaveLength": "448 nm",
                  "Power": 100.0,
                  "PreShutterAdvance": 0.5,
                  "PostShutterDelay": 0.5
                  "LightID": "Right-0172-Light2",
                  "WaveLength": "448 nm",
                  "Power": 100.0,
                  "PreShutterAdvance": 0.5,
                  "PostShutterDelay": 0.5
              "FilterWheels": [
                  "FWID": "FilterName",
                  "FWPosition": "1",
                  "FilterName": "CLEAR",
                  "FilterLabel": "N"

4 General File Conventions

The unflattened and flattened captured images file names include six fields plus an extension. The initial three fields match the short forms of the project name, scene name, and sequence name. The first and second fields are delimited by "_", and the second and third fields are delimited by "-". The fourth field consists of a three digit number, indicating the illumination wavelength (in nm), plus a plus a single letter identifier for the camera filter. The illumination or illuminations used to produce each image cited in the filename of the flattened images include seventeen illumination types, with one symbol each. The illumination symbol is one of the following symbols, or a combination of multiple symbols for processed images:

Examples for unflattened and flattened captured images are respectively:

project_scene-sequence-<wavelength and filter>_<index number>_R.tif


project_scene-sequence-<wavelength and filter>_<index number>_F.tif

Processed images amend this naming convention to indicate the type of processing employed. The initials of the individual who created the processed images are (optionally) given in the fourth field of the filename of processed files. Since processing operations most often utilize all of the captured images of a sequence, identification of individual images used as inputs for processing operations are generally omitted. One or more following, underscore-delimited fields describe the processing operations and parameters that were used, appended in order of their application. Within an underscore-delimited field, single hyphens are used to delimit parameter values or image indices used during that processing operation. Usually the parameters refer to the index number of a component image.

A typical filename exemplifies the naming practices used for processed images:

Project name: Archimedes Reimaging
Scene name: [ManuscriptName]
Sequence name: [Sequencename]
Creator: Michael B. Toth (this field is sometimes not used)
  1. Principal Components Analysis (PCA)

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2. PCA components 05, 06, and 07 were used in the R, G, and B channels, respectively, of the final (synthetic) RGB TIFF image

In some case, two rounds of PCA processing were performed. Selected components from the first round of PCA processing were used during the second round of processing. In these cases, the string "PCAx2", followed by "-" delimited indices of the first round components that were used in the second round. For example, the file name:


This indicates that William Christens-Barry used components 2, 5, 8, 12, and 15 from the first PCA round in the second round, and used components 02, 03, and 09 from the second round of processing in the red, green, and blue channels, respectively, of the final RGB TIFF image.

Note that the use "--" as a delimiter indicates that a range of component images was used, e.g. "3--6" would indicate that components 3, 4, 5, and 6 were used.

Please note that the practice of including a leading "0" is not followed consistently, and that the use of "pc" in the front of a principal component used in an RGB channel is not followed consistently due to excessively long filenames.

Other strings in processed file names include:

dS8_BasicRGB an RGB image has been synthesized from flattened images and desaturated computationally by a factor of x0.8;
8gs a single channel (grayscale) image stored in 8-bit format
desat an RGB image has been synthesized from flattened images and desaturated visually by an unspecified factor
Combi multiple grayscale images (captured or processed) were use combinatorally to create many different synthetic RGB images. The resulting files are very large, and are frequently stored in the "AVI" movie format for viewing and selection of the best images.

The remainder of the file name, including the extension, indicates the file type. These are usually:

  1. TIFF still image files, ending in 'tif',
  2. JPEG still image files ending in 'jpg'
  3. AVI moving image files ending in ‘avi’