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.
Monday, September 10, 2012
Tuesday, September 4, 2012
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!
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.
Abigail H.
Sunday, August 26, 2012
An Air of Mystery
As the newest undergraduate addition to the Herbarium, I have many things to learn: not only the many rules involved in the process of databasing, name-checking, annotating, accessioning, and foldering specimens, but also the many exceptions to the rules. Emilie has been a wonderful teacher, and so far I have learned the basics of our assembly line of organization. I now know how not to handle the specimens, how to database in such a way that anyone could pick up and continue where I left off, and what to do with mystery specimens that have no species name, no accession number, multiple species on one mounting, or no mounting at all.I have learned the importance of everyone in the Herbarium working in the same order and with the same process.
And, I have also learned things that no one tells you, like that when you have been annotating the same species for three hours, your vision tends to begin to split in two. Now I understand why shorter shifts are important. Forgetting to set aside a non-accessioned species, or forgetting to annotate a species whose scientific name and phylogeny has altered sometimes two or three times since its collection, will only lead to confusion and headaches later.
Thus far, despite the occasional split vision, working here at the Herbarium has been a very rewarding experience. At the end of each shift, I feel accomplished at the progress that I have made, even if that just means weeding out non-accessioned or unidentified specimens, or giving multiple species within the same folder a new home. I take satisfaction in knowing that everything that I do will make it all the more easier for the next person at the next step in this massive project. And, it feels good to know that when this is all finished, the whole scientific community, not just Brooks hall, will benefit from what we do here, and from what our predecessors started.
That is another thing that I love about the Herbarium. It has an air of quiet, peaceful mystery. I am fascinated by the history involved. Having grown up in the era of cold, clinical internet text, it is novel to directly handle specimens that have such history to them. Some of the specimens were collected over fifty years ago. I have seen the handwritten annotations of E.G. Voss, the author of the textbook that we are using as a guide to our phylogenic organization of the Herbarium. I feel a sort of excitement working with them, the special brand of feeling I usually only get when I hold the 100-year-old books that my great grandfather collected, or when I buy a used book that has a handwritten message to a loved, previous owner inside.
Furthermore, seeing multiple annotations on each specimen makes me realize how far we in the scientific community have come, and how much the field of botany has changed and will continue to change. I have to wonder if twenty years from now,a new set of students and professors will be shaking their heads at our out-of-date organization and our incorrect family names. Somehow, however, I doubt that Dr. Monfils will let that happen.
Until next week!
Abigail
And, I have also learned things that no one tells you, like that when you have been annotating the same species for three hours, your vision tends to begin to split in two. Now I understand why shorter shifts are important. Forgetting to set aside a non-accessioned species, or forgetting to annotate a species whose scientific name and phylogeny has altered sometimes two or three times since its collection, will only lead to confusion and headaches later.
Thus far, despite the occasional split vision, working here at the Herbarium has been a very rewarding experience. At the end of each shift, I feel accomplished at the progress that I have made, even if that just means weeding out non-accessioned or unidentified specimens, or giving multiple species within the same folder a new home. I take satisfaction in knowing that everything that I do will make it all the more easier for the next person at the next step in this massive project. And, it feels good to know that when this is all finished, the whole scientific community, not just Brooks hall, will benefit from what we do here, and from what our predecessors started.
That is another thing that I love about the Herbarium. It has an air of quiet, peaceful mystery. I am fascinated by the history involved. Having grown up in the era of cold, clinical internet text, it is novel to directly handle specimens that have such history to them. Some of the specimens were collected over fifty years ago. I have seen the handwritten annotations of E.G. Voss, the author of the textbook that we are using as a guide to our phylogenic organization of the Herbarium. I feel a sort of excitement working with them, the special brand of feeling I usually only get when I hold the 100-year-old books that my great grandfather collected, or when I buy a used book that has a handwritten message to a loved, previous owner inside.
Furthermore, seeing multiple annotations on each specimen makes me realize how far we in the scientific community have come, and how much the field of botany has changed and will continue to change. I have to wonder if twenty years from now,a new set of students and professors will be shaking their heads at our out-of-date organization and our incorrect family names. Somehow, however, I doubt that Dr. Monfils will let that happen.
Until next week!
Abigail
Friday, August 3, 2012
Keep Calm and Organize the Herbarium
It's been very eventful couple of weeks around here! Since the Botany 2012 conference our main goals are: organize, organize and organize!
Here at the CMC Herbarium we have a total of 20 cabinets that are reserved for our collection and 12 that are reserved for research. However, we had many research specimens that were in our collection cabinets and vice-versa. So, this week we worked on putting the research specimens and in the research cabinets and we did the same for the collection specimens.
Note that after a research is completed, the specimens will be returned to the collection and the loan specimens will be returned to their respective Herbaria.
However, before filling back the collection specimens we have to figure out in which cabinet they have to go in. So, we temporaly store them into a "Need to Filed" cabinet in which each cubbie represents a collection cabinet.
Ashli and I are also working on accessioning many specimens there were left unaccessioned. Accessioning means assigning a number to each specimen of an herbarium. This provides a permanent reference for each specimen of the collection. Often times when a specimen is used on a research, the accession number has to be cited in the publication. Therefore, it is crucial that all herbarium specimens have a accession number and that there are never 2 specimens with the same number.
First we stamp the specimen (preferentially on the upper right corner of the sheet) with our CMC stamper, and then we stamp the number with a automatic numbering stamper.
After we are done accessioning for the day, we enter the first and last accessioning numbers on acession book, so we keep track of the numbers used and how many specimens were accessioned in a day.
Here at the CMC Herbarium we have a total of 20 cabinets that are reserved for our collection and 12 that are reserved for research. However, we had many research specimens that were in our collection cabinets and vice-versa. So, this week we worked on putting the research specimens and in the research cabinets and we did the same for the collection specimens.
Note that after a research is completed, the specimens will be returned to the collection and the loan specimens will be returned to their respective Herbaria.
However, before filling back the collection specimens we have to figure out in which cabinet they have to go in. So, we temporaly store them into a "Need to Filed" cabinet in which each cubbie represents a collection cabinet.
 |
| To be filled cabinet |
 |
| Cubbie reserved for specimens that belong in Cabinet 11 |
This way we can separate all the specimens that need to be filled first and then we work on filling them into the main collection by individual cabinet!
Ashli and I are also working on accessioning many specimens there were left unaccessioned. Accessioning means assigning a number to each specimen of an herbarium. This provides a permanent reference for each specimen of the collection. Often times when a specimen is used on a research, the accession number has to be cited in the publication. Therefore, it is crucial that all herbarium specimens have a accession number and that there are never 2 specimens with the same number.
First we stamp the specimen (preferentially on the upper right corner of the sheet) with our CMC stamper, and then we stamp the number with a automatic numbering stamper.
CMC Herbarium Stamper (left) & Automatic Numbering Stamper (right)
Acession Book
Ashli has been working extensively on acessioning, while I figure out plant families for specimens that lack that information on their labels so she can accession them later!
Ashli working on accessioning specimens!
Myself helping out Ashli!
There is a lot to do in here and so in order not to get overhelmed, I have an advice for everyone that is currently working on planning on working in here :)
Thanks for reading!
Emilie
Emilie
Thursday, July 19, 2012
Workshop and CMC Progess
Hi guys,
Last week I got the privilege of attending a workshop sponsored by iDigBio on Digitization and Databasing Natural Collection. Before I tell you more about the meeting, let me first tell you a little bit about iDigBio.
iDigBio stands for Integrated Digitized Biocollections and it is a program funded by the National Science Foundation (NSF). It's purpose is to serve as a resource for advancing digitization of biological collections. If you want to learn more about their workshops or the program itself, here is the link to their website - https://www.idigbio.org/
Now, a lot of people don't understand the importance of initiatives like this, so let me try to give you some insight. The digitization effort makes data and images for millions of biological specimens available electronically for everyone. Basically, it takes the wealth of data that can be found in museums or herbaria and puts it out on the internet so that it can be used for anything from simple curiosity to answering pivotal research questions.
So at this workshop, I got to hear stories from several important people and organizations in the realm of natural collections. Some organizations that had representatives at the meeting include the New York Botanical Garden, the Smithsonian Institue, Specify, iPlant, MorphBank, and a wide variety of smaller herbaria and collections across the United States. These representatives shared stories of their personal digitization efforts as well as some useful workflow tips and software to make the digitization process quicker and more efficient.
One thing I learned was that there is a program available for easing the burden of verifying specimen names (verifying that the name on the specimen is the most current and legitimate name for the species). This program comes from the iPlant collaborative and it is called Taxonomic Name Recognition Service. It allows you to upload a list of names that you want to verify and it runs all of the names through reputable sources and gives you the accepted name and a score for the name accuracy. This allowed us here at CMC to complete a task that used to take several hours, if not days, to about half an hour. Here's the link http://tnrs.iplantcollaborative.org/.
Next I want to show you the progress of organization here at CMC.
And we are making some progress in the cabinets as well.
Well, that is all I have for you this time. Thanks for reading.
-Taylor
Last week I got the privilege of attending a workshop sponsored by iDigBio on Digitization and Databasing Natural Collection. Before I tell you more about the meeting, let me first tell you a little bit about iDigBio.
iDigBio stands for Integrated Digitized Biocollections and it is a program funded by the National Science Foundation (NSF). It's purpose is to serve as a resource for advancing digitization of biological collections. If you want to learn more about their workshops or the program itself, here is the link to their website - https://www.idigbio.org/
Now, a lot of people don't understand the importance of initiatives like this, so let me try to give you some insight. The digitization effort makes data and images for millions of biological specimens available electronically for everyone. Basically, it takes the wealth of data that can be found in museums or herbaria and puts it out on the internet so that it can be used for anything from simple curiosity to answering pivotal research questions.
So at this workshop, I got to hear stories from several important people and organizations in the realm of natural collections. Some organizations that had representatives at the meeting include the New York Botanical Garden, the Smithsonian Institue, Specify, iPlant, MorphBank, and a wide variety of smaller herbaria and collections across the United States. These representatives shared stories of their personal digitization efforts as well as some useful workflow tips and software to make the digitization process quicker and more efficient.
One thing I learned was that there is a program available for easing the burden of verifying specimen names (verifying that the name on the specimen is the most current and legitimate name for the species). This program comes from the iPlant collaborative and it is called Taxonomic Name Recognition Service. It allows you to upload a list of names that you want to verify and it runs all of the names through reputable sources and gives you the accepted name and a score for the name accuracy. This allowed us here at CMC to complete a task that used to take several hours, if not days, to about half an hour. Here's the link http://tnrs.iplantcollaborative.org/.
Next I want to show you the progress of organization here at CMC.
 |
| We got all the tables set up |
 |
| File cabinets set up and dissecting microscopes out and available for use |
 |
| Cabinets organized and appropriately labelled |
And we are making some progress in the cabinets as well.
 |
| Example Specimen |
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| Example Annotation |
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| Example Species Folder Label |
 |
| Example Genus Cover label |
-Taylor
Friday, July 13, 2012
Botany 2012 - Columbus, Ohio.
This week Rachel, Derek, Lisi, Hillary (students that work at Anna's lab) and I went to the Botany 2012 conference in Columbus, OH!
We arrived in Columbus on Sunday and I rushed to the workshop: " Successful Manuscript Preparation and Publication." The workshop explained, in details, the process of getting an article published from its submission to its denial/acceptance. I found this workshop VERY helpful as I intend to publish an article out of my undergraduate research this year. I was also very happy to find that many international students attended the workshop! Luckily, I had the chance to meet a Brazilian lady and it felt really great to finally speak Portuguese after months without doing so(I don't know if I mentioned before, but I am an international student from Brazil at CMU)!
That night we went to the key note speech "Respecting the Past and Embracing the Future: Envisioning Botany in the Next Generation" by Sir Pete Crane from the School of Forestry and Environmental Studies of Yale University! It was quite an inspiring speech in a great atmosphere.
On Monday, I attended student presentations in the morning and the "Student Involvement in Botany Luncheon and Interactive Career Panel" in the afternoon. Lunch was served while their main speaker gave a talk on choosing a career path. After this, we briefly talked with a professional that was sitting in our table and to all the other that were sitting in different tables. There were professionals there from various backgrounds: research institution, academia, liberal arts institution, government, NGO, industry and private sector/consulting. The luncheon was, without a doubt, one of the most important events I attended at this conference! I was able to talk to people about research, graduate school and learn more about the employment possibilities for internationals at the U.S.
I also presented my poster on Monday night! I have been doing research with the Biology faculty Dr. Dannenhoffer since 2010. I research the growth patterns of aspen trees in a rare environment of the Great Lakes called "Alvar." Basically the aspen trees that grow on the alvar look very weird and stunted and we are looking for the diferences in between then and the "regular" aspens that grow on the forests nearby! That's what my poster is about!
On Tuesday, I went to more speeches and I started volunteering at the venders stands so I could cover my registration costs! The Botanical Society of America (BSA) was quite awesome and offered volunteering opportunities for students so they could cover the costs of the registration. Also, they offered scholarships for field trips!
I also went to the student social at night at the Barley's Brewing Company! It was very fun getting to know botanists from all around the world! I personally love talking about plants and let's say people don't talk about it too frequently hahaha. So, it felt every refreshing and encouraging to be in an environment where I could discuss my ideas and talk about what I do and actually be understood!
Usually when I am back at Central Michigan University, people ask where I work and the conversation never gets too far because not many people heard about Herbaria before in their lives! So, I am usually the one that introduce them to the subject, heheh!
Wednesday morning, I attended the Michigan Consortium of Botanists breakfast! It was great to see some familiar faces (most people there were at the Michigan Consortium of Botanists meeting previously that summer) and make some more connections!
I took the afternoon to walk around the Short North District which was just a 15 min walk away from the conference! There, I could see lots of street art (which I love!!) and visit art galleries, patisseries,eat at yummy restaurants and buy some gifts!
On Wednesday night, Anna, Anna's students and I went to the all Society's banquet! It was a huge event with great food and talks! I got to stand up when they congratulated the students that got a BSA award this year!
I didn't mention it before, but I got the "Young Botanist Award" this year due to my work in the Botanical area! Also, it was only possible thanks to my research, Dr. Dannenhofer, that nominated me!
On Thursday, the girls, Derek and I participated in the Prairie Fens of Ohio field trip! We went to 3 different sites and had a day full of "botanizing"! Lots of beautiful plants and interested conversations, the things I like the most!
After nearly 5 hours of botanizing we drove back to Mt. Pleasant and our Botany adventure came to an end!
Overall, I had an AMAZING time at the conference and I thank everyone that made this trip a reality for me!
Thanks for reading this giant post :D
Emilie
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| Botany 2012 Logo. Source:http://www.botanyconference.org/ |
That night we went to the key note speech "Respecting the Past and Embracing the Future: Envisioning Botany in the Next Generation" by Sir Pete Crane from the School of Forestry and Environmental Studies of Yale University! It was quite an inspiring speech in a great atmosphere.
On Monday, I attended student presentations in the morning and the "Student Involvement in Botany Luncheon and Interactive Career Panel" in the afternoon. Lunch was served while their main speaker gave a talk on choosing a career path. After this, we briefly talked with a professional that was sitting in our table and to all the other that were sitting in different tables. There were professionals there from various backgrounds: research institution, academia, liberal arts institution, government, NGO, industry and private sector/consulting. The luncheon was, without a doubt, one of the most important events I attended at this conference! I was able to talk to people about research, graduate school and learn more about the employment possibilities for internationals at the U.S.
I also presented my poster on Monday night! I have been doing research with the Biology faculty Dr. Dannenhoffer since 2010. I research the growth patterns of aspen trees in a rare environment of the Great Lakes called "Alvar." Basically the aspen trees that grow on the alvar look very weird and stunted and we are looking for the diferences in between then and the "regular" aspens that grow on the forests nearby! That's what my poster is about!
 | ||||||||
| My poster at the BOTANY 2012 Conference |
On Tuesday, I went to more speeches and I started volunteering at the venders stands so I could cover my registration costs! The Botanical Society of America (BSA) was quite awesome and offered volunteering opportunities for students so they could cover the costs of the registration. Also, they offered scholarships for field trips!
 | ||
| I volunteered selling books at the vendors stands |
I also went to the student social at night at the Barley's Brewing Company! It was very fun getting to know botanists from all around the world! I personally love talking about plants and let's say people don't talk about it too frequently hahaha. So, it felt every refreshing and encouraging to be in an environment where I could discuss my ideas and talk about what I do and actually be understood!
Usually when I am back at Central Michigan University, people ask where I work and the conversation never gets too far because not many people heard about Herbaria before in their lives! So, I am usually the one that introduce them to the subject, heheh!
Wednesday morning, I attended the Michigan Consortium of Botanists breakfast! It was great to see some familiar faces (most people there were at the Michigan Consortium of Botanists meeting previously that summer) and make some more connections!
I took the afternoon to walk around the Short North District which was just a 15 min walk away from the conference! There, I could see lots of street art (which I love!!) and visit art galleries, patisseries,eat at yummy restaurants and buy some gifts!
 |
| The Cliff Dwellers Mural |
 |
| The American Gothic Mural |
 |
| The Monalisa Mural |
 |
| The City of Archs! |
On Wednesday night, Anna, Anna's students and I went to the all Society's banquet! It was a huge event with great food and talks! I got to stand up when they congratulated the students that got a BSA award this year!
I didn't mention it before, but I got the "Young Botanist Award" this year due to my work in the Botanical area! Also, it was only possible thanks to my research, Dr. Dannenhofer, that nominated me!
 |
| BSA Young Botanist Award |
On Thursday, the girls, Derek and I participated in the Prairie Fens of Ohio field trip! We went to 3 different sites and had a day full of "botanizing"! Lots of beautiful plants and interested conversations, the things I like the most!
 |
| Botanists at the Field Trip |
 |
| Rachel (on the back) and I hanging around the Fen! |
After nearly 5 hours of botanizing we drove back to Mt. Pleasant and our Botany adventure came to an end!
Overall, I had an AMAZING time at the conference and I thank everyone that made this trip a reality for me!
Thanks for reading this giant post :D
Emilie
Tuesday, July 3, 2012
Week 1: Arrival and Exploration
Hey guys,
My name is Taylor. I am the newest graduate student to start in the Monfils Lab. I have been given the pleasure of helping Emilee and Dr. Monfils digitize and re-organize the Central Michigan Herbarium.
While we were cleaning out one of the cabinets near the front of the herbarium, we found some very incredible books!
> >I look forward to sharing the continued progress of the Central Michigan Herbarium, as well as the continued progress of the digitization progress with Emilee and Dr. Monfils.
Thanks for reading
-Taylor
CMU Research Assistant
My name is Taylor. I am the newest graduate student to start in the Monfils Lab. I have been given the pleasure of helping Emilee and Dr. Monfils digitize and re-organize the Central Michigan Herbarium.
The first task I was given was to address workflow issues by re-organizing the herbarium for digitization. The following pictures will serve as our "before" shots.
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| A collection of hand drawn and hand painted floral drawings |
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| Book 1 of a 5 book set of North American Wild Flowers issued by the Smithsonian Institute |
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| A book of hand drawn and hand painted flowers found in Hawaii |
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| A book of pressed plant specimens from the late 1800s |
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| A book of pressed New Zealand ferns arranged in artistic combinations. The cover is made of real wood! |
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| A book of prepared algae specimens, most colored artistically |
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| Some impressive specimens from "Algae" |
> >I look forward to sharing the continued progress of the Central Michigan Herbarium, as well as the continued progress of the digitization progress with Emilee and Dr. Monfils.
Thanks for reading
-Taylor
CMU Research Assistant
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