Processing Notes 2017

Jubilees Palimpsest Project

December 12, 2017
December 5, 2017
November 14, 2017
October 31, 2017
October 17, 2017
October 3, 2017
September 26, 2017
September 19, 2017
September 5, 2017
August 29, 2017
August 3, 2017
July 6, 2017
June 29, 2017
June 8, 2017
June 1, 2017
May 11, 2017
May 4, 2017
April 27, 2017
April 20, 2017
April 6, 2017
March 30, 2017
March 23, 2017
March 1, 2017

December 12, 2017

First attempt at Laplacian Eigenmaps on C73inf

Next steps

More background on non-linear transformations

Progress toward expanding access

December 5, 2017

Last call of 2017

Plan for spring 2018

Update on registration correction for filter magnification

Questions about non-linear transformations



November 14, 2017

Today's processing call was mostly concerned with preparing for the Society of Biblical Literature in Boston (where Mike, Keith, Roger, and I will be presenting), and the subsequent conference in Athens (including Ken, Keith, Roger, and Mike).

Keith's registration correction for magnification due to filters is still in debugging mode and will not resume until after Athens. We discussed the baseline to which other images are corrected. For Keith's processing it is the main bank 365 nanometer reflectance because it tends to have the most detail. The hemisphere captures should be fine without any registration correction because they are visible spectrum only, heavy on the blue (since they are white LED). Some of the images Roger created with the opposite side of the folio registered to the first side are cropped. It sounds like a simple transposition (without rotation) should suffice to align that data with the hemisphere captures, accurate color, etc. Roger may have a way to avoid cropping in the first place.

Once we have registration corrected data for filter magnification and for opposite side it may be worth another push to non-linear transformations.

The next call will be December 5 at the normal time and medium. Mike and Damian expect to be able to join from Sinai, perhaps using cell phone network. We'll reevaluate the time for 2018.

October 31, 2017

Today's processing call included Keith, Roger, and Todd. We're going to sit out next week and resume at the usual time on November 13 (after daylight savings). Here are some notes:

Opposite side of folio


2018 Scholars Workshop

Registration correction

October 17, 2017

Show-through from opposite side issue in general

What's next with c73inf

Next R-CHIVE working date is June 7-8, 2018

Milan summer 2018?

SBL, Boston, November 20, 9:00 am

Next call will be October 31 (skipping 10/24)

October 3, 2017


Registration correction




We will speak again at the usual time one way or the other. The agenda may shift toward topics from Mike.

September 26, 2017

We had a light day on the processing call, partly because Keith and I have been otherwise occupied lately. The progress was from Roger's work on Ambrosiana_S36sup. It is an odd specimen. Reading the undertext seems to go quickly from very easy to very hard. Rubrication may explain some of this, but not all. Separation is a challenge as well. Spectral angle maps can be helpful as an enhancement when there is a lead, but less so for pure discovery where nothing can be seen. It is worthwhile to run through advanced processing for the remaining pages, but not to get too bogged down if success is not forthcoming. Once we round out our tour of the supplemental samples we can return to the flagship, C73inf, equipped with lessons learned and registration-corrected data.

September 19, 2017

We had an extensive processing call today driven by Keith’s development of Hoku and news from Manusciences in Nice, France. My notes are below. Next week we will continue the regular schedule and will almost certainly have more questions for Keith about Hoku.

Ambrosiana S36sup (Gothic Bible)

Update on affordable ENVI

Report and miscellanea from Manusciences

Demo from Keith on Hoku

September 5, 2017

Registration correction and supervised processing plans

Schedule adjustments

Processing software options and long-term planning

August 29, 2017

Update from Keith on registration correction software

Update on C73inf

Update on S36sup (Gothic Bible)

R-CHIVE call on Friday, September 8, 9am EDT

Update on pan-sharpening as a way to deliberately reduce exposure time or increase depth of field, or correct depth-of-field focus issues after the fact

Resources for people at Manusciences to work on the Milan data (not all this was discussed in the call but was requested by Keith and I thought I would share with the whole team)

Update on calendar

August 3, 2017

Fall schedule

Using pan-sharpening to correct for out-of-focus or low-resolution captures

Scholars meeting around March

H190inf (unidentified erased texts)

Nicole is ending her program at RIT with a big presentation tomorrow. We are all grateful for her work and hope she can remain involved in our projects and the field to the extent most beneficial for her.


From: Damianos Kasotakis

The aperture that we use doesn't drop bellow f5.6 (Ken could confirm or correct me on this) yet again this is pretty wide open aperture, when compered to f8. I guess it could be wrong value reported by Photoshoot? Or vise versa, a wrong value that appears on Photoshoot as f5.6, when in reality its closer to f4.3.

Focus stacking is a very nice technique, but is also very much time consuming. Considering a project where you already have 100+shots and 15-20 min of exposures in total.

A more realistic approach would be to shoot everything with a higher aperture (f11-f16?) and get STRONGER lights (yes Ken, MORE LIGHT) to cut down the exposures or make them equal as now, since we will be getting less light with that narrower f11 . There is no way that in that aperture you would have any kind of focusing problems. During our project in OKC, we were almost consistent with an f8.5 but we had longer exposures since the lights had to be moved way back for the RTI.

From: Ken Boydston

More Light! Indeed.

We doubled again the 365nm in both Auxiliaries and Mains, and increased by 50% 385 and 400 in the Auxiliaries. If the Auxiliaries are positioned optimally, the benefit is significant. We did not quite have time to implement the new Auxiliaries at MOTB. Optimal position and new lights would have made nearly 2 stop improvement at MOTB.

PhotoShoot includes a feature we should put to use. There is button on the main window which reports "100". This is the ISO setting Push this button once, it goes to 200. Push it again, it goes to 400. Push it again, back to 100. . It could be set always to 400; the increase in noise for the short shots would be just noticeable on close inspection. I would shoot the short shots at 100, long shots at 400. The ISO button is not active during pause, so long shot shot table should not be linked to short shot table. 10 second exposures at ISO400 would be a lot quicker and produce better results than 30 second exposures at ISO100.

With new more powerful lights and 4X ISO, we should have much improved images with much shorter exposures.

Maybe "pan-sharpening, which is using a high-resolution capture to sharpen a low-resolution capture" could be implemented to possible benefit in a couple scenarios:

  1. Bin a high res chip for the long exposure shots. This results in lower resolution image with correlated increase in sensitivity and faster captures. The lower res image might be easily interpolated for use with a higher res luminescence-like image.
  2. Capture a [functionally] low res image with lots of bands (maybe mostly out of focus), then focus stack using a high res capture of only luminescence (or rgb) at each of the focus planes, then combine.

BTW, I think max aperture is about 4.8; if shutter is programmed correctly, correct values are reported in PhotoShoot.

July 6, 2017

Embossing effect


Option for what's next: Ambrosiana_H190inf

Option for what's next: Ambrosiana_S36sup

Option for what's next: go back to Ambrosiana_C73inf

Next week's call

June 29, 2017

Update from Keith on software correction of registration errors in filter captures

Results of focused processing based on comments from Origen Hexapla scholar Ben Kantor (BPK).

Gioberti Tincture

What’s next for processing after O39sup

Plans for next two weeks

June 8, 2017

Keith’s work correcting registration errors from filters

Nicole Polglaze has been doing some work on O39sup (Origen’s Hexapla) at RIT with Roger.

Texture imaging (raking and RTI)


Next call

June 1, 2017

Welcome Nicole

Keith’s Registration Correction Software


International programs

Next week continue on Skype at same time and format before in-person meeting in Rochester the following week.

May 11, 2017

Updated processing guides


Better processing through alignment of both sides of transmissive

Better processing through PCA

Better processing through ICA

Better processing through blur and divide

Better processing through correcting registration of captures with filters

Better capture by identifying fluorescence in IR from visible light

Better processing through slave labor

Better scholarship through functional user interface

May 4, 2017

Correction for registration loss from UVB and UVP filters (and eventually Wratten).

Viewing environments

Machine learning

May schedule for this call

Related calls

April 27, 2017

Correcting for registration distortion from UVB and UVP Filters

Ambrosiana_O39sup (Origen’s Hexapla)

Applying machine learning, neural nets, deep learning, etc. to palimpsests

Quality time in Rochester

Mirador, and what it will take before it helps us

Miscellaneous notes

April 20, 2017

The processing calls had a two-week hiatus due to conflicts, and will resume next Thursday, April 27 at the usual time.

In the meantime, work is continuing on the palimpsests we captured after C73 inf. Keith’s Pseudos and Sharpies have been added to the archive, along with some new files from Roger ( The archive also includes the semi-annual report I submitted to the NEH (http://palimpsest.stmarytx. edu/AmbrosianaArchive/Reports/ Performance-20170331.html). Images are also being added to the IIIF repository ( The squashing of bugs is ongoing…

Also, the first publication to utilize our images has already appeared in print. The cover of this book was captured by us. A8/%d7%93%d7%a7%d7%93%d7%95% d7%a7-%d7%94%d7%a2%d7%91%d7% a8%d7%99%d7%aa-%d7%a9%d7%9c-% d7%aa%d7%a2%d7%aa%d7%99%d7%a7% d7%99-%d7%90%d7%95%d7%a8%d7% 99%d7%92%d7%a0%d7%a1/

April 6, 2017

Lost registration from filters

Keith’s batch processing

Roger’s focused processing

Conversation about coordinating for sustainable collaborations

March 30, 2017

Keith is still working on using graph paper to correct for distortion from the filters. The problem is they distort inconsistently from one sequence to the next as the filters move about.

The Ruby technique that worked on C73inf may or may not work on other palimpsests. That too is on the list of ways for Keith to not be bored.

Roger has had some interesting results focusing on the hardest portions of C73inf that Ceriani could not read. The next step will be to work on some pages that are less difficult to read but more important to scholars. Page 67 and the relevant coordinates are described on the guide to unread regions: http://palimpsest.stmarytx. edu/AmbrosianaArchive/ GuidesUnreadRegions/ Unreadlines-LatinMoses.html It would be interesting to verify or falsify the reading of Taxo in the specified region. A paleography chart may come in handy: http://palimpsest.stmarytx. edu/AmbrosianaArchive/ GuidesUnreadRegions/ LatinMosesPaleography.html

We’re not returning to Milan this summer, but we haven’t given up. One approach is to resubmit to the NEH. We can make improvements based on new information gathered in January-February. We might be able to secure a better calendar position by planning with don Federico further in advance. This also gives us a window to think more broadly about what we would like to coordinate in northern Italy, and what funding partners may be interested in supporting one or more portions thereof. We can think more broadly than NEH and Mellon, including more regionally focused sources (e.g., sources/IN/top). Mike and Josephine will try to organize a conference call to begin brainstorming and note sharing about possibilities. We will try to include Todd, Mike, Josephine, Roger, Keith, Ken, Greg, and Julia Schneider (

The processing calls will continue next week as usual, except Mike will initiate on Skype because Todd’s Internet connection is in limbo.

March 23, 2017

Following some more work in Oklahoma City, Keith has made progress on using graph paper to correct for registration distortion from UV fluorescence filters. One thought is to disseminate the script for performing the correction rather than the complete set of corrected data. If anyone has a desire to download rather than generate the corrected data, Todd can run the correction on a supercomputer attached to One challenge will be to get the rotation correct, as the folios are either 90° or 270° rotated.

Roger and Todd have been trading notes on targeted processing of lines unreadable in the 1861 edition of Latin Moses. The notes are available here: http://palimpsest.stmarytx. edu/AmbrosianaArchive/ GuidesUnreadRegions/ Unreadlines-LatinMoses.html. Roger’s work has been using blur, divide, and ICA on the transmissive captures. Corrected fluorescence and Ruby images may profitably be added to the mix. So far it looks like a few words are readable beyond what Ceriani could read. More significantly for scholars, it seems likely we will be able to correct some of Ceriani’s claims, which potentially calls all his readings into question. This line of thinking is preliminary and needs verification especially from ruling out the possibility that the letters seen are from the other side. Roger’s images are on the LoadingDock, which is accessible by SFTP but not HTTP. Let me (Todd) know if you need an account.

We can continue with the document based on what Ceriani did not claim to read from Latin Moses. Other paths on the horizon:

Hopefully next week we will know whether another trip to Milan will take place this summer. If so, there may be a case for leaving the Arc of the Firmament in Italy. Don Federico prefers mid-May to mid-June for when such a session would take place.

March 1, 2017



Data Management