Tag Archive | Historic Southern Naturalists

What Now? Digitization In An Age of Uncertainty

Fresh off her home computer, Linda Smith, our HSN Project Manager, brings you this month’s HSN update.

Small sandwich board that has "Keep Calm and Get the Disaster Plan" written on it with three disaster icons at the top.

Wow! What a difference a month makes, right?

We were working right along, making up lost time….and BOOM! Covid-19 makes its presence known.

“WHAT NEXT?” was my first reaction when the campus closed for an extra week of spring break. I shouldn’t have asked…Fast forward a week and a half and campus is closed for at least the remainder of the Spring 2020 term.

But we are in the middle of a multi-year, nearly half a million dollar grant and we have to keep working. Our grant employees need to continue to receive paychecks. So, “WHAT DO WE DO NOW?” became our next question. How does one convert an ongoing digitization project housed in a museum, where access to the collection is integral to the process, to a remote work project?

Answering this question has been our focus for about a week and a half now.

The first step in the process was to access. Access where we are in the project. Access the connectivity of the group, who has access to a computer, the correct software, etc…

The most important piece of the puzzle was figuring out how we can access the collection remotely. Thankfully, our brilliant and compassionate Curator of Collections converted an off-campus office where one of our students could continue to photograph the remainder of the shells in the Gibbes shell collection.

Eric sits in front of the lightbox while petting two greyhounds.
Eric works on photographing shells with his new coworkers

Next, we needed to assign different aspects of the process to various student employees in order to get these images processed. Once we photograph and process to DNG’s, we file share the photos to a student for descriptions and to another student for processing.

We have other students working on metadata, spreadsheets, and entering objects into our Past Perfect database as well.

Easy? No. Necessary for the circumstances we find ourselves in? Yes. Not the way we would chose to work on our project, but necessity breeds ingenuity…is that the right saying? Oh well…it definitely applies to this situation.

So you may see some rather odd blog posts as the response to Covid-19 continues to unfold, but know that we are working hard to be flexible, and truthfully, just happy to be working.

Stay tuned…as the Historic Southern Naturalists project continues marching on…ok baby steps but progress is progress.

Daniel S. Martin: Professor, Collector, Geologist, and Curator.

February’s update comes from Matt Gibson at The Charleston Museum. Our Historic Southern Naturalists Project continues to uncover key players in the preservation of natural history in the South, like Daniel S. Martin.

Professor Daniel S. Martin served as Honorary Curator of Geology at The Charleston Museum in the early 1900s. Prof. Martin was responsible for all rock and mineral samples as well as invertebrate fossils. Formerly a Professor of Geology at Rutgers Female College, and a geologist of renown, Martin helped reorganize the geological collections at the Museum which at the time were in disarray.  As Martin himself notes, “In the department of mineralogy and geology … little has been done since the time of Prof. Holmes” who had resigned his curator position with the Museum in 1869.

As curator, Prof. Martin took on the task of organizing the geological and paleontological specimens in the Museum and took particular note of two subsets of the Museum’s collection: A collection of minerals from the Ural Mountains (located in Western Russia) and a collection of phosphate rocks collected by Dr. C. U. Shepard. The Ural mountain collection was representative of the mining efforts in the area and included many semi-precious stones used in jewelry making such as emerald, topaz, garnet, and azurite, among others. Martin described this collection in Museum bulletin as truly exceptional and that “No such exhibit of Russian minerals can probably be found in any other Museum in the United States.” Dr. Shepard’s collection of phosphate rocks were collected from all over the world with the primary goal of being used comparison to the phosphates known from South Carolina.

While with the Museum, Martin also donated some of his own specimens to the collection. There are currently over 100 specimens within the Museum’s collection collected by Prof. Martin. Most are geology specimens, like samples of the metamorphic rock, gneiss. A high grade metamorphic rock, gneiss is formed from igneous rock (such as granite or schist) or sedimentary rock (such as sandstone) that has been exposed to high levels of heat and pressure. This process causes the minerals to align into distinct foliations, appearing as stripes or bands on the rock. Common minerals seen in gneiss include quartz and feldspar which are hard minerals. This in addition to the changes brought on through metamorphosis result in gneiss being a particularly hard material and results in gneiss commonly being used in industry as building material, as ornamental stone, and tabletops.

hand holding sample of gneiss
One of the gneiss samples donated by Prof. Martin

Prof. Martin also collected some paleontological material from the Charleston area. This includes two fossil whale teeth. Collectors have been uncovering fossil whale material from James Island to as far inland as Orangeburg, with specimens recovered inland being from older layers compared to those found closer to the present coastline. The two teeth are from an extinct species of odontocete, or toothed whale, and were collected from an old phosphate mine. These two specimens represent two more data points in fossil whale research in the Lowcountry. Specimens like the ones Prof. Martin collected over a century age help build our understanding of our natural world and we aim to continue his legacy of preserving these important objects.

two fossil whale teeth with historical label
These two fossil whale teeth were collected from the Lowcountry region of South Carolina

Natural History, Digitized

Our first blog of 2020 is brought to you by our fantastic Digital Collections Librarian Mēgan A. Oliver

Digitizing natural history collections is quickly becoming a specialty of ours, over at the Digital Collections department at the University of South Carolina Libraries. We’ve partnered with McKissick Museum for the past few years on their nationally grant-funded digitization project entitled ‘Historic Southern Naturalists’ (HSN); many thanks to the Institute of Museum and Library Services for the grant. This digital project has been highly collaborative and has produced a useful and beautiful web portal from which to access myriad museum collections of fossils, rocks, dried botanicals, and minerals, as well as the library’s collection of early naturalist manuscripts.

Since the HSN digital collaboration yielded such great results in providing museum and library users with fantastic historical resources, we’re excited to be back at the beginning of a new natural history digital collection.

In 2019, UofSC officially established the Mark Catesby Centre, a collective of scientists, librarians, curators, rare book experts, and naturalists, with invested personnel spread across the United States and the United Kingdom. The Catesby Centre’s work revolves around researching and promoting the ever-important findings and illustrative records of Mark Catesby, a naturalist that came to study biology in the Carolinas, Florida, and the Bahamas almost three centuries ago. Catesby’s seminal work predates that of Swedish botanist Carl Linnaeus by 29 years, with Catesby’s first edition of natural history findings published in 1729. Linnaeus would not release his now-famous biological classification system until 1758. The entirety of Catesby’s work in his multivolume set “The natural history of Carolina, Florida and the Bahama Islands” was published over the course of 18 years, beginning in May of 1729 and ending in July of 1747.

Illustration of the Bahamas Titmous[e].
The Bahamas Titmous[e], first edition of Mark Catesby’s “The natural history of Carolina, Florida and the Bahama Islands”, 1731.

Digitizing these rare and sometimes delicate natural history items requires specialty scanners and camera equipment, fully trained staff, and a great deal of time and patience. We strive to ensure that the color balance and tone distribution captured with our digitization equipment is as true to the physical, original item as possible. Calibrating and staging a single shot or scan can take up to 30 minutes, or the process could involve multiple scans of the same item in order to get the digital facsimile just right. In our department, this attention to detail often captures the iridescence and depth of the pigments used to hand color illustrations, as well as the texture of paper and the organic signs of age that rare books exhibit. Our staff, often graduates of the School of Library and Information Science here at UofSC, take great pride in producing such detailed work, as digital collections like these provide researchers with the next best thing to seeing a rare item in person; seeing it anywhere in the world at any time, online.  

Last year alone, we digitized and helped to format metadata (data that describes the digitized items online) for about 12,000 items for the Historic Southern Naturalists digital collection, and we scanned a little over 2,500 pages and prints from our Catesby rare books.  In creating yet another stunning natural history digital collection for students, scholars, and historians to peruse, we hope to create a diverse wealth of natural history primary resources online.


Historic Southern Naturalists, http://digitalussouth.org/historicsouthernnaturalists/index.php

The Mark Catesby Centre, https://digital.library.sc.edu/markcatesbycentre/mark-catesby/

The Centre’s announcement, https://sc.edu/about/offices_and_divisions/university_libraries/exhibits_events_news/news/catesby.php

Mark Catesby, https://cdn.lib.unc.edu/dc/catesby/about.html

Catesby’s multivolume publication dates and information, personal communication (email) with Catesby Centre curator Dr. Michael Weisenburg

Carolus [Carl] Linnaeus, https://www.anbg.gov.au/biography/linnaeus.html

A Look Back: 2019

Photo of Cepaea nemoralis
Cepaea nemoralis

Over the past year, we have introduced you to our grant, our institutions, some of our staff, and the world of digitization. We have cataloged more than 4,000 shells, taken over 2,000 photos, processed each photo multiple times, and captured the metadata for each file.

Well…now what?

As with any project of this magnitude, there are inevitably a couple of bumps along the way, but there’s one bump in particular that we’re currently working on.

How do we use all of the information and files we have amassed?

To answer this question, we have to refer back to the goals of the project which are:

1. To increase the availability of the collection to the public.

2. To increase access without the risk of damage to the objects.

3. To cross reference objects, archives, etc. across University organizations and across South Carolina.

In the first iteration of the grant, from 2016-2018, the digitized information was sent across campus to our digital libraries team. There, the information and files were uploaded to a digital collection management software, CONTENTdm. Digital Collections of the University of South Carolina displays the information in a searchable database. At that point the information was harvested into our Historic Southern Naturalists website. And now is where we expect you’re asking the obvious question: Why don’t we continue with the same procedures, right?

Screenshot of the Historic Southern Naturalist website database
Snapshot of our database on the HSN website

 Well…remember that bump we talked about before? We hit it, and it just might be the biggest bump yet. Our website was originally created by students and by now the students that built the original website have graduated, which is absolutely to be expected when working on projects in a university setting. (Congrats guys!) We planned to another student to work on the website…and then…we found out the University has stopped teaching the code in which the website was written.

OH NO!!!!!! (There really isn’t enough room for all of the exclamations needed to accurately express this sentiment.) So, this is where we find ourselves going into winter break and year two of our biggest IMLS grant ever: Looking for a new way to make our website accept information without having to completely rebuild it.

Not to worry dear readers, we are supported by the greatest University in the nation and we will navigate this road…bumps and all…

To Be Continued in 2020.

Have a Safe and Happy Holiday Season!

To Conference we go! Key takeaways and resources from our trip to the Southeastern Museum Conference

Digitization is the driving force behind the Historic Southern Naturalists project. In January 2019, McKissick staff members proposed a session describing the nuts and bolts of digitization projects for the upcoming Southeastern Museums Conference (SEMC) scheduled for October. In March we were notified that our proposal was accepted, and last month representatives from three institutions, McKissick Museum, South Carolina State Museum (IMLS recipient), and the Charleston Museum gave a 75-minute presentation on digitization.

Since the beginning of our project we have been discussing digitization, but what exactly is digitization? Is it necessary? Who pays for it? And how does a museum get started?

Digitization vs Photography: Is there a difference? YES!

Photography is the act of capturing an image of an object. Digitization refers to the creation of a digital image, with the inclusion of metadata and long-term, organized digital file storage. The term Digital Preservation describes an additional step that involves creating a digital master file: a photo file with no processing stored for future access.

WHY Digitize?

As an institution, McKissick digitizes objects from our permanent collection to increase access to our collection (with searchable databases like https://mckissick.pastperfectonline.com/ and http://www.digitalussouth.org/historicsouthernnaturalists/), to produce online exhibitions, to reduce the handling of objects, to document the condition of objects, and to produce quality images for marketing purposes. In short, it makes our jobs quicker, easier, and more professional.

Our Curator of Collections, Christian Cicimurri, presenting at the Southeastern Museums Conference, Oct. 2019.

What do we have to do? Plan, plan, plan…

If digitization is on your radar, planning is key. Organizations need to plan the scope of the project, the amount of time and personnel to work on the project, space available for use, equipment available, and funds to available. Plan for the day to day, create and update workflows, worksheets, database entries, most importantly…be flexible. Not everything will go according to plan.

Linda Smith, HSN Project Manager, presenting at SEMC

With regards to Photography…

Understanding the triangle of exposure consists of aperture, ISO, and shutter speed is key to good photography. Aperture settings control the amount of light reaching the sensor which also affects the depth of field in the photo. An aperture setting of f11 or f16 results in a wide or deep depth of field and allows most everything in the photo to be in focus.  Shutter speed is the length of time the light will be exposed to the sensor and it is measured in fractions of a second. The shutter speed setting of 1/100 is what we are using on this project. ISO determines image sensitivity to available light (the lowers the # the better for overall image quality). We are utilizing an ISO of 100-200.

For future reference!

Plan ahead when working offsite or with oversized objects. The South Carolina State Museum has the most experience in digitizing oversized objects. They have made use of alternative spaces to photograph their art pieces. In fact, they have converted a storage space into a photography studio by utilizing space and equipment on site. This might be a good solution for your site.

Storage room converted to photo studio at the South Carolina State Museum

Be sure the camera battery is charged or invest in an EXTRA BATTERY (yes, there’s a story there).

Work in small batches and process as you go. Tether your camera to your computer if your software and components allow. It is a big time and frustration saver.

Before/After – Processing photos

While there are many software programs for photo processing available in “pay to play” and open source options, McKissick has chosen to use Adobe Lightroom because of its ability to process in batches. Rather than processing to achieve a pretty photo, we only adjust light and exposure in order to produce an accurate representative of the object. The photographer’s color target in our images allows for color correction using the squares as reference for white balance. The South Carolina State Museum uses Capture 1 for processing. Features are similar to Adobe Lightroom, though Capture 1 is available on a disc installation format, rather than the monthly fee format of Adobe products.  

Getting by with a little help from our friends at the South Carolina State Museum and The Charleston Museum

Our friends at SCSM provided much needed insight on 2D digitization. Photographing large pieces of artwork comes with different challenges than working with smaller 3D objects. For instance, #DYK white photography paper and cheese cloth can help diffuse light reflections on artworks that are varnished or framed behind glass?

The Charleston Museum blew everyone away when describing the process of using photogrammetry and laser scanning. They utilize this technology to create 3D images of natural history specimens, like fossils, minerals, and skeletons, and can even use 3D printers to create replicas. SketchFab and Meshlab software are two open source programs they have used to stitch photos together.

The Charleston Museum creates scans of 3D objects, which then can be used to create 3D printed replicas of rare or delicate objects

Want more help? Here’s a bunch of resources!

Funding resources

Institute of Museum and Library Studies – https://www.imls.gov/

Council on Library and Information Resources – https://www.clir.org/hiddencollections/

Metadata Resources

South Carolina Digital Library Metadata Schema and Guidelines – https://scmemory.org/wp-content/uploads/2018/05/SCDLMetadataSchema_2018.pdf

Digitization Resources

iDigBio –https://www.idigbio.org/wiki/index.php/Digitization_Resources

South Carolina State Library/Digitization in a Box – https://guides.statelibrary.sc.gov/digital-collections/diab

Federal Agencies Digitization Guideline Initiative – http://www.digitizationguidelines.gov/

Connecting to Collections Care (Free Webinars) – https://www.connectingtocollections.org/resources/

Lyrasis (Fee based services) – https://www.lyrasis.org/membership/Pages/Museums.aspx

Other Cool Resources:

The Getty Research Institute – http://www.getty.edu/research/tools/

Biodiversity Heritage Library – https://www.biodiversitylibrary.org/

Digital Public Library – https://dp.la/

Adobe Lightroom – https://lightroom.adobe.com/#

Nomenclature – https://www.nomenclature.info/

Rights Statements – https://rightsstatements.org/en/

Rights and Reproductions: The Handbook for Cultural Institutions by Anne M. Young

As always we want to give a big, special thanks to UofSC, SC State Museum, The Charleston Museum and IMLS for the funding provided to make the Historic Southern Naturalist project possible.

It’s been a ‘WHORL’ wind of a year…

Get it?

Unless you happen to be a ‘sheller’ (or a student working on this project) you may not get the pun. But the truth is we have spent the better part of the project year counting whorls. Seriously!

You see to get Lewis Reeve Gibbes’ shell collection ready for digitization, many hours of painstaking behind-the-scenes work was necessary. Though packaged carefully at the time, we spent countless hours unpacking and rehousing the shells in modern, archive friendly housing. Whether suspending a tiny specimen in a capsule or cushioning the bigger ones with ethafoam, each shell has now been safely secured in its new home.

Katy (one of our digitization assistants) places Neritina virginea, 21-374A.2 in a capsule for safe storage.

After rehousing, we then had to number the shells individually. Some were so small we devised alternative ways to mark them.

Then came measuring, counting, and the describing the shells. Have you ever tried to describe a shell? This is where the term ‘counting whorls’ entered our vocabulary.

Whorls, sutures, and striae have become common terms in our vocabulary these days, take a look at the different parts of the anatomy.

What came next? Well, research… and more research… oh, and did I mention research? You see we had to research the name of the shell from multiple historic labels, often noting different scientific names. Before the internet search engine, scientists relied on their own collections or books to identify a specimen. Multiple scientists active in the field resulted in multiple books and numerous names for the same specimen. The International Commission on Zoological Nomenclature has standardized these names, so our task was to figure out the synonymy for each accepted scientific name. Just to give you an idea, we had one shell that had been mis-identified as a new species by scientists over 120 times.

Once we have a name then we move on to researching the collectors and the places of origin. Names and spellings of countries and islands have changed since the 1800’s when these shells were collected. For instance, we recently learned, thanks to your help, that Fiji was once known as Feejee island. And did you know that Demarara is a river in Guyana, or that New Holland is the continent we now know as Australia? Just being able to read the historic labels, written in 19th century English script, often using shorthand, and most times in pencil is difficult enough.

These labels are examples that show the collectors used any scrap of paper they had available to document a specimen.

This label is an example of the challenge encountered when transcribing handwritten 18th century labels. Can you read it?

Then on to photography, this has to be the easy part, right? Well ask our students how difficult and tedious this process can be. It can take numerous takes to get the correct angle and lighting. Not to mention, most of the shells aren’t flat and tend to roll around! But despite the challenges we have generated approximately 657 RAW photos of shells, 702 TIFF images of labels, with over 2200 final JPG photos.

Katy carefully places the specimen in our lightbox for photography.

And aren’t they gorgeous?

Thanks, we agree!

So, as we draw this project year to a close and are seeing the light at the end of the tunnel (or hearing the ocean in our last conch)… we will soon be looking to the skies for our next phase of the project. See you soon!

Why Don’t You Take a Picture, It’ll Last Longer! The Digitization Process for a Historic Herbarium

Today’s blog entry by Jessie Peragine, Natural History Curatorial Assistant at The Charleston Museum.

The Charleston Museum’s first naturalist collection to digitize for the Historic Southern Naturalists Project is the Lewis Reeves Gibbes (1810 – 1894) Collection. A math and natural history professor at the College of Charleston, Gibbes had an interest in botany and marine algae, accumulating an active collection over fifty years. He had a particular interest in advancing the natural sciences in his home state of [Charleston,] South Carolina and had a very active role in the Elliott Society of Natural History in Charleston. One publication from 1835, Catalogue of the Phoenogamous Plants of Columbia, S.C., and Its Vicinity, listed around 775 species of plants. Most of his plant specimens were collected from South Carolina and most algae came specifically from the Charleston area.

The Historic Southern Naturalist Project will include the digitizing of Gibbes’s personal herbarium specimens and documents that were donated to the Charleston Museum. The endless possibilities of today’s technology are actively being used by museums to preserve yesterday’s breakthrough scientific work. If Gibbes were here today and someone explained what a digital photograph and the internet was, it would most likely boggle his mind. But once he saw his herbarium (collection of dried plant specimens) preserved in this way for the world to see he would surely be enthusiastic and happy to know that new generations will continue to learn from what he taught and loved in his time.

In order to get the Gibbes herbarium digitized, we had to create metadata and photographs for each pressed specimen. We needed accurate numbers attributed to L. R. Gibbes’s herbarium, so I searched our worksheets, catalog cards, and cataloging software, PastPerfect – Network Version 5.0E2. Personally, I like collecting data and doing research, so this part was interesting to me #nerdlife. Each specimen was entered or updated in PastPerfect to then be converted into an excel sheet of metadata. The metadata is basically a detailed compilation of particular stats for each specimen. Being that this collection is so old and plant names keep changing, research was done to ensure that all the taxonomic names were up to date. Fun facts on some of the plants were learned along the way; well, at least I thought they were neat.

Screenshot of computer desktop featuring PastPerfect software and internet browser window.
All the windows! Collecting data and doing research can be a messy process.

After data is completed, we go up to the museum’s storeroom to locate each specimen for photographing. All our plant specimens are over 100 years old and much care is taken in the handling of each plant sheet so we wear gloves. Each plant was dried, pressed and attached to a herbarium sheet with an identification label. Our herbarium is located in our temperature-controlled storeroom in individual cabinets made specifically for housing herbarium sheets. These cabinets are controlled environments made to keep out pests, dust, and light, which can all become major problems for an herbarium. Sometimes mold or insects have gotten to a specimen, especially very old ones, and they need to be handled very carefully. Unwanted black mold, as in it wasn’t collected for the herbarium but got there on its own, can be particularly bad for specimens and can be deadly to humans, (quick, turn the sheet and don’t breathe!). Gloves, not just a sciencey fashion statement, are always used to protect the curator as well as the plants from possible cross contamination between specimen sheets. Preservation is always the number one concern, so if a specimen has deteriorating paper or came lose, it was carefully transferred to a new herbarium sheet to prolong the specimens usefulness to the collection. OK, I said preservation is number one, then I guess organization is almost a tie for me. Each specimen is stored in a folder with [20] other plants. The plants are cataloged in numerical order [according to the museum’s catalog number system] within a folder for their respective taxonomic Family, and each folder is then cataloged in alphabetical order. In specific situations such as a historic collection like L. R. Gibbes, they are kept and organized separately from the general museum herbarium. This makes locating specific collections much easier for curators, such as this collection which has around 150 plant specimens.

Lighting setup featuring nikon camera on stand and lit umbrella light with herbarium specimen sat on the table.
We weren’t able to use the lightbox, so we had to come up with something new!

Once all the specimens have been located, we removed one folder at a time and handled one specimen at a time. A lightbox or light stand is set-up along with a white surface and background for each sheet to be placed upon. LED lights are used instead of traditional lightbulbs which have UV rays that can damage the pigmentation of the photosensitive material. Unfortunately, our lightbox was a little too compact for what we needed and the hole for taking photos through would get in the way of the camera lens, causing a blurred, rounded edge. To fix this, we resorted to using a soft white photography umbrella lighting kit to photograph each specimen on a white background which worked much better. A scale bar is placed into the top of the frame for each photo which allows us to see the size of each plant. We have been using a fancy and heavy, D610 Nikon camera that Matt programmed to save each photo as a RAW file and a JPEG file. The RAW file is used for metadata and the JPEG for the Southern Naturalist Project website image and our museum’s catalog in PastPerfect. Once uploaded into the computer we touch-up each photograph with the freeware GIMP 2. And when all our photos look good we upload them along with the metadata to a share site for the McKissick team to finalize the digitization of each specimen into the Historic Southern Naturalist website. For a sort of sneak-peek, The Charleston Museum also has an online catalog for digitized specimens which is located on the museum’s main website.