Digitization Proceeds

The last two weeks, I began working on the process of digitizing the Herbarium's 25,000 specimens. During digitization, the photos begin as raw images associated with barcodes, and they must be converted to JPEG form before they are browser-friendly. This conversion can take hours, depending on how many photographs you have taken that day. For this reason, it has become taboo to ever shut down the digitization computer, in case the program is still working on batching out images from the previous session. I had a bit of a scare after my first session, when the digitization computer insisted that it needed to shut down for updates. So, I finished batching out the 165 photographs that I had just taken and restarted the computer manually, so that it would not turn itself off in the middle of the program while I was not there.

Unfortunately, when I logged back on, the programs were not there, and neither were my photographs. I will not lie to you: I was a bit stricken with terror at that. Luckily, the problem was a simple one: the programs were only accessible through a specific username and password for the computer. Our amazing Biology department technology staff helped me out, and this week I was up and running again.

Now that we have ironed the process out, it is incredibly easy and fast. First, I go through the cabinet and I barcode every specimen (preferably in the same order in which they are stored, so that the barcodes are sequential...this helps to keep track of them once photographing begins). I also double-check the organization and make sure that all specimens have been annotated and accessioned. I do this during a work shift ahead of time, so that photographing runs smoothly.

After prep, the actually photographing is easy. I turn on the camera and the lights, open the imaging programs, log in, and open the correct project. I remove an entire shelf of specimens from the cabinet, and I organize them so that there are separate piles for folders whose specimens have been taken, are about to be taken, or are being taken.

 I simply place a specimen on the photographing deck:

Then, I make sure that within the SilverImage program, the cursor is within the green barcoding space:

Then, I use the hand remote to take a photograph.

 

Next, I run the barcode of the specimen that I just photographed under the scanner:

And that's it! That specimen is now a high-resolution raw image, and is now associated with its very own barcode. After I am done photographing for the day, there is a protocol for editing and "batching out" the images, which converts them from raw data to JPEG format and transfers them to their final home on the hard drive. This process is easy, though, once you get the hang of it. The programs are pretty intuitive, and I do not usually have to even look at my protocol to remind myself. I have only done a few short photography sessions so far, and yet I have photographed nearly 400 specimens. Plus, that was before I had really gotten the hang of it. I am sure that from now on, barring any mistakes on my part, I should be flying through the cabinets!

Until next time,

Abigail

 

Where do the plants come from?

Where do the plant specimens come from?

This blog is all about the Herbarium, but how does the Herbarium come across all these fascinating plants to share with the world? That is where we come in:

Figure 1. Hillary and Rachel, prairie fen fanatics and student researchers.

Specimens are usually contributed to the CMC Herbarium by students who take plant-related classes, student researchers, and professors, but anyone can collect given they know and follow State and Federal laws and acquire the proper permits. This summer Hillary, a junior at CMU, and I, a graduate researcher, set out to study the wide diversity of the plants of prairie fens.

We visited ten different prairie fens in south-central Michigan and collected over 800 voucher specimens. These specimens will support our field identification of the plant species for our theses and papers. A great specimen must have all the plant parts, including the roots (a tough job with some Carex and wetland species). These specimens must be pressed and dried for at least two weeks and frozen in a no-frost freezer to prevent insect and mold contamination of the Herbarium collection. For more information on collecting see the CMC Herbarium website (http://cmcherbarium.bio.cmich.edu/collections.html). After confirmation of species identity and properly mounted and labeled, they will be submitted to the Herbarium as specimens.

Figure 2. On the top is the specimen of Scirpus atrovirens in the field. It was pressed, dried, and frozen (bottom left). After a confirmation of its identity, an herbarium label will be printed and the specimen will be mounted and catalogued in the CMC Herbarium (bottom right).

 

Figure 3. The common elderberry (Sambucus canadensis) was collected (top), pressed (bottom left), and will be labeled and mounted (bottom right). When pressing, it is important to make sure that all leave surfaces and many different angles of flowers and fruits are showing, because once a specimen is dried, it is very delicate and breaks easily.

Traveling to all of the different prairie fens and watching the plants come into bloom was amazing. Hillary and I learned to identify so many new wetland and prairie species. With the Herbarium, we can share all of our beautiful plants with others.

Rachel

Photos by Rachel Hackett and Hillary Karbowski.

A fresh start and a familiar task

Wow, is it good to be back at school and starting work again in the herbarium. It really feels like a whole new place (thanks to all of the hard work Dr. Monfils, Emilie and Abigail put in over the summer). I’m on board and ready to make some changes to the ways in which I am used to doing herbarium tasks however, I am happy to begin my work with the familiar task of mounting specimens.

I’m picking up right where I left off, mounting specimens from Dr. Monfils’ wetland plants course that is usually taught once per year. One of the many things that the students in wetland plants learn is the process of collecting and identifying specimens. The students travel to many places around Michigan to collect. Once the specimens have been collected, they should be pressed and all of the necessary information (e.g. locality, family name, species, collector and collection number) should be included before handing them over to be mounted. This should be done ASAP before all of the information is forgotten!

One of the most interesting parts about mounting specimens is trying to get the pressed specimens to fit just perfectly on the special herbarium mounting paper. It is very amusing to find that a collector’s point of view on a properly pressed specimen is quite different than that of the one mounting the specimens. When mounting, I am hopeful that a collector will have deposited a specimen to the herbarium that has the most information in the least amount of space. It is a challenging task to fit a specimen (with as many identifying characteristics as possible), label, herbarium stamp, accession number, and envelope all on to one sheet! Here are some of the photos from the mounting process.

As I was mounting, I captured some of the steps and the equiptment:

Here is a collage of my favorites that I mounted today:

Thanks for reading!

My Best,

Adriane Shorkey

A place for research

Around two years ago I had little comprehension of herbaria, let alone appreciation and respect for their value. I’ve grown up collecting things and have loved observing different species of plants and animals, but working in a place that is home to a diverse collection of plants never crossed my mind as I imagined myself as a scientist. My name is Derek; I am not a CMC herbarium employee like Emilie, rather, I am a user of the herbarium. My use of the herbarium as a graduate student will be the primary subject of my blog entries.

I was approached over a year ago by a professor (who teachers an introductory biology class over the summer) who asked if I would give a short presentation to his class about the herbarium. I agreed, but never wrote any reminder down. Two summer’s in a row now, while working in the herbarium, here comes his class filing in—ready to listen to my spiel. I’ve been amazed each time by how excited I have been about the herbarium and dry, dead plants in my off-the-cuff expose. Herbaria have become for me a great research tool and I love research. I have discovered that the dead plants come alive with facts and data about a species, a region of the state, country or world, a collector or a time period.  I just counted again to be sure—I have loans of herbarium specimens from 16 different herbaria! Now, when I say “I” what I actually mean is Dr. Monfils—CMC Director— has requested specimens on my behalf for my research and the lab’s biodiversity research on Schoenoplectus and Schoenoplectiella. Herbaria from all over the world will loan specimens for research to other herbaria, but these loans must take place between a dedicated curator who can be responsible for their safe keeping. Some of the specimens we have from the New York Botanical Garden and the Missouri Botanical Garden were collected from countries scattered across the globe. I need to spend more time with these specimens and I will write about that next time.

-Derek

New working peers at the Herbarium!

Hello all,

The fall semester started some weeks ago and it has been very busy already! I am taking 14 credits this semester, doing an undergraduate research and keeping up with work at the Herbarium!


Luckily, two new women were hired to work at the Herbarium which makes it more pleasant to work in! I worked pretty much by myself all summer and it is refreshing to have people to talk to and to share the work with!

The new workers are Abigail (Abbie) and Adriane and both of them have good work ethics and are organized. They are also always willing to help me, which is great.

One week before school started, I introduced Abbie to the Herbarium and taught her how to database the cabinets we had left (take note of the numbers of specimens of each species we have). Remember, Ashli was working on that earlier in the summer? She was able to database cabinets 4 to 9, and Abbie is continuing this work (we have 14 cabinets full of specimens)! I also taught her how to annotate specimens!

Just a reminder on why this step is necessary

I need to know how many specimens of each species we have, so then I can name verify each species (see if the scientific name was changed, or if a certain genus changed families or if a family name changed) to then produce annotation labels and annotate the specimens!

Here it is a small summary of the process:

(1) Database Cabinets
(2) Name verify species for name changes

(3) Produce the right amount of annotation labels
(4) Annotate specimens or correct the names

(5) Organize cabinets according to Edward G. Voss’ Michigan Flora 2nd edition which contains 3 volumes

(6) Re-folder specimens
(7) Produce Genus and Specimens labels for the folders using a label maker
(8) DIGITIZE!!

I have posts written in each of these topics, so you can always go back and check them in more detail!

Adriane has worked at the Herbarium before for a long time! So, she already knew many details about the Herbarium. She is our mounting specialist and she is working on mounting specimens from classes taught by Anna. She also helps me with annotating specimens when our working times overlap!

Lately, I have been working on annotating specimens from Cabinet 3 (YEAA, Cabinets 1 and 2 are fully annotated and organized!!) and name verifying some other cabinets! I am leaving in December, when I graduate, and I have to finish name verifying all cabinets before that because it was a hard and very time consuming process to learn!

Overall, it has been a pleasure working in group. I feel that the 3 of us are doing a good job on communicating where we are at and what our next steps will be.

Thanks for reading!

Emilie

Digitization

Last week was mostly spent databasing our tenth and eleventh cabinets and returning newly accessioned specimens to their proper homes. On Friday, however, our humble (but worthy) Herbarium reached a new stepping stone in the digitization process. Dr. Monfils and I had a video conference with Michael Giddens, who was kind enough to give us a detailed walkthrough of how to go about barcoding, photographing, and digitizing our specimens using our new SilverImage software. It seems like it will be a very efficient and easy process once we get in the swing of things. The high resolution photos that we have taken so far are looking gorgeous!

In layman's terms, we are giving each specimen in our Herbarium a sequential barcode (much like each specimen has an accession number); we photograph each specimen and then immediately scan its barcode. This barcode will then be associated with that image within the database. The photos begin as raw images and at the end of each day, we easily edit the pictures in bulk and then we "Batch out," converting the images to browser-friendly JPegs that can then be uploaded to online databases. For now, the online database will just have the image and the barcode of each specimen. Later, the high-resolution photos will allow us to add detailed information about each specimen to its entry within the database without having to actually pull the specimen from the cabinets.

I have just finished writing up the protocol for the process, and I will spend this week preparing specimens by double-checking organization and adding barcodes to the specimens in Cabinet 1. This Thursday, I will begin imaging in earnest. I am honored to be a part of pioneering this process, and I cannot wait to get started!

Again, my thanks go out to Michael Giddens, for his awesome tech support and his patient teaching as our Herbarium enters into this modern age. For a closer look at the equipment that we will be using for this process, see Mr. Giddens' website at SilverBiology: http://www.silverbiology.com/.

Until next week,

Abigail H.

Preservation in the face of Radicans

As I delved back into the cabinets this week, I found some stunning specimens. Some impressed me because they were so well pressed, such as this Parnassia glauca, or the American grass of Parnassus (family Saxifragaceae).

Other specimens impressed me because they had maintained their coloration so beautifully despite their age. For instance, take this Polygala paucifolia, or Fringed polygala (Family Polygalaceae) pressed in 1986. Look how its purplish hue has remained intact!

My most exciting finds of the week, however, were specimens from Central Michigan University's original Herbarium. Some even had the original labels, written by hand with an ink pen!

Saxifraga pennsylvanica, or Swamp Saxifrage (Family Saxifragaceae)

This Swamp Saxifrage was collected May 28, 1927!

 

 

I was impressed with this specimen, but even more impressed when I found these two samples, pressed in 1906:

Euphorbia cyparissias, or Cypress spurge (Family Euphorbiaceae)

 

 

Euphorbia polygonifolia, or Seaside spurge (Family Euphorbiaceae)

 

I hope to continue finding fascinating pieces of history like this...and I hope I look that good when I am over 100 years old.

 

 

And, finally, I worked a lot this week within the family Anacardiaceae. This family includes more innocuous species, like Staghorn sumac (Rhus typhina), but it also contains Poison ivy (Toxicodendron radicans), Poison oak (Toxicodendron diversilobum ), and Poison sumac (Toxicodendron vernix ). Thus, my hat goes off to whomever collected those fine specimens. I hope you did not suffer afterwards.

 

Toxicodendron radicans (Poison Ivy)

 





 

 Until next time,

Abigail H.