Science and Trouble-shooting

The last few weeks have found me working on a variety of projects in the Herbarium. I have been helping Emilie organize the cabinets prior to annotation, instead of during/after, and we have found that it is a far more efficient process. I am sure that all Herbariums, or libraries, for that matter, have the issues that we came face-to-face with these last few weeks. It was alarming to me to discover that within our Juncaceae shelves, (in fact, within most of the families) nothing was organized alphabetically or even by species. Specimens had been placed randomly back in the correct family, but not in the correct genus or species folders. Emilie had discovered this same problem within Cabinet 3 and 4, which is why it took so long to organize and annotate the monocots, especially since she was working alone then.

So, Adriane and I have begun dedicating part of our week to organizing the cabinets prior to Emilie's name-checks and annotations. Even though it means handling the specimens slightly more, it makes the entire process go by faster and more smoothly. This is especially because we encountered huge stacks of specimens that were completely unaccessioned. Without accession numbers, the specimens cannot be placed in our database, nor can they be tracked in any way. In the last two weeks, I must have accessioned at least three hundred specimens, just within Cabinet 5!

I also spent the last two weeks learning more of the ups and downs of the digitization process. We had some trouble with the software, but Michael Giddens was an invaluable help, and now I can proceed with my photographing. I was not bothered by the early software glitches, since it is a brand new program, and we are some of the first guinea pigs to use it. I am gaining more confidence with the software as I realize that it is actually fairly difficult to make a mistake with the photographing itself. The software warns me if I take two photographs without scanning a barcode, or if I scan the same barcode twice. I found the overwrite feature of the software particularly helpful last week, because I had to rephotograph multiple specimens, and I was petrified that I might have to wade through the computer's hard-drive, trying to delete the correct photos before I could retake them. With Michael's help, however, I discovered that the overwrite is extremely easy. You simply rephotograph the specimen, rescan it, and a box pops up letting you know that the barcode is already in the database and associated with a photo. You tell it to overwrite the previous photo, and the deed is done.

I can see such a feature coming in very  handy in the future. I am learning that science, and especially systematics, is an extremely recursive, dynamic process. The phylogenies of plants and their organization--even their names--are constantly evolving.This is especially true because of the recent advances in genetics and technology. The easy overwrite feature will make it simple to rephotograph specimens in the future if they have had to be annotated or re-accessioned for any reason.

Although the last two weeks have been full of trouble-shooting, they have also been very informative, and I have confidence that Emilie, Adriane, and I will continue to discover more efficient ways of completing our mission: the complete reorganization and digitization of 25,000 specimens.

Until next time,

Abigail H.

Organizing and Annotating the Monocots!

Hello Everyone,

Thanks for visiting out Blog!

During the past couple of weeks, I have been working heavily on organizing and annotating the Monocots we have here at the Herbarium!

Our Monocots take up 3 cabinets here at CMC and they are the most challenging group to organize for some reasons:

1. Within the Monocots we have the families Cyperaceae, Poaceae and Juncaceae. These 3 families are very big, meaning they have looooots of genera and species!
2. A lot of name changes happened recently (Scirpus is one good example. Many species of this genus were transfered to Schoenoplectus and other genera!) in such families.
3. At last, our 3 monocots cabinets were a bit unorganized, in a way that we had many specimens of different species in the same folders and everywhere in the cabinet.

I also found many specimens that needed to be accessioned already filled in the collection.

All of these things slow down our organizing process a lot, but I am happy to tell the world that two of these cabinets are down and we "only" have one more to go!

A big thank to Adriane and Abbie that helped during many steps of the organization process!

Until next post,

Emilie

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