For our seed addition experiment, we want to know exactly how many seeds we planted in each 1 m transect. Each transect got seeds from one envelope. Before planting, we took xrays of the fruits in the paper envelopes. With minimal processing, the radiographs look good! We have a batch of 251 images to classify. This sounds like a job for Allen Wagner aka “the Count” (of Achene County).
Radiograph of Echinacea fruits in envelope 105.3a /230. Other partial envelopes are visible on the margins.
We used the column blower and other techniques to remove empty fruits. We aimed for about 50 seeds per envelope. How many do you count?
It’s been a busy spring at the lab: 11 volunteers and 6 students from Northwestern and Lake Forest College contributed to the Echinacea Project. We are currently wrapping up before field season starts, and we want to celebrate everything they accomplished in the last few months! Since January, volunteers and students:
On Friday, volunteers Marty and Mike finished cleaning the last batch of heads from the 2018 common garden experiment. Huzzah! The volunteers had been working on the 2018 heads back before the pandemic started, and after a long break, 2018 is finally done. Many thanks to all the volunteers who made this possible, especially the 2021-2022 crew: Allen, Char, Elif, Laura, Luk, Marty, Mike, and Suzanne! Now, we have a lot of rechecking to do.
So far this year, we have sadly not been able to have volunteers in the lab due to the continuing threat of COVID-19. However, over the last few months, we made quite a bit of progress on the remnant Echinacea harvests from 2020 and 2021. In the fall, we had help from volunteers, students from Lake Forest College, and externs from Carleton College. Thanks for your help! In January, Sophia finished cleaning the last head from 2021, which was an exciting accomplishment.
To track our progress in the lab, I created an R script to visualize the various steps of the ACE process for each batch of Echinacea. The figures for rem2020 and rem2021 are included here. Hopefully, this method will work for the cg harvests as well.
Click on the figures to enlarge
The ACE stages are listed along the x-axis, and the number of Echinacea heads are on the y-axis. The light blue shows how much we have completed, and the dark blue shows what remains to be done. The small numbers on each bar indicate the corresponding number of heads, and the width of the bars is roughly proportional to the amount of time each step takes. Along the top, the dates indicate the last day that the totals for each stage were updated.
The script to create these graphs can be found here: echinaceasandbox/oop/trackAceProgressTest.R
Today, the Lake Forest College students returned for their second day at the lab. After cleaning heads last week, they moved on to the next steps of the ACE process today: quality control and scanning. They worked in teams of two, so one group rechecked cleaned heads from rem2020 and rem2021 while the other group scanned the achenes that had passed the quality control step. The students will have a dataset of 40 echinacea heads from 2021, 20 burned and 20 unburned, as well as 40 heads from 2020. They wondered whether the drought this summer affected seed production in echinacea or whether controlled burns influence achene count, and they developed hypotheses to test these questions.
Alondra and Marina do quality control while Maeve and Connor scan achenes
The new x-ray machine also arrived this week! It showed up in an enormous wooden crate, but fortunately the machine itself is not that large. Today, the company representatives gave us a tutorial of how to operate the x-ray. We will need to do some trials to find the best settings and adjust our protocol to the new machine. For example, we will need smaller sheets of paper to fit in the x-ray. Based on today’s test run, it seems that the x-ray can only hold 15 bags of achenes (3 rows of 5) at a time instead of 20 bags (4 rows of 5). However, each image takes only 45 seconds, so hopefully it won’t slow down the process too much. According to the Kubtec website, this model is also good at x-raying explosives, art, and gems, so I guess that might come in handy, too.
Visiting Minnesota to plant seeds last week was a welcome break from sitting at a desk all day. However, we were glad to be back in the lab this week. On Thursday, I finished the inventory of the remnant 2021 heads, so they are now ready to be cleaned by volunteers.
We have a great crew of volunteers this fall. Suzanne wins the award for the longest volunteer record; she has been helping the Echinacea Project since 1999! In contrast, Elif joined the lab in 2019 and is our newest volunteer. So far, all of the volunteers have been cleaning seed heads, an important early step in the ACE workflow. However, many of them specialize in other steps of the process such as quality control, scanning, randomization, weighing, x-raying, counting, or classifying. Once we have made a dent in the backlog of seed heads, the volunteers will be able to diversify and find the steps that they enjoy most.
Marty is an expert at the scanner and x-ray machine
Elif started in 2019 has only cleaned heads so far
Mike has pinned all the bees for the Yellow Pan Trap project
We have yet to discover Luk’s favorite job!
Suzanne specializes at inventory and randomization
Allen is a pro at counting and classifying achenes
Our other project this week was to clean out the freezer in the lab. The freezer mainly contained coolers of empty vials that were used to collect bees for the Yellow Pan Trap (YPT) project. As Mia and I sorted through the vials, we also discovered one cooler that still contained bees! Why were these bees collected? To what project do they belong? Why haven’t they been pinned like all the other bees? According to Detective Stuart, “We have a mystery to solve. First stage is to gather evidence. (Don’t disturb the scene of the crime.)” I followed Stuart’s instructions and returned the cooler to the freezer. After doing some sleuthing, I now suspect that vial GQ-9417 contains YPT specimens that were collected on 31 July 2019. The other vials, however, remain a mystery. If anyone can identify the suspects or has information about the day of the crime, 16 July 2019, please let me know.
Mia, Marty, Allen, and Stuart hard at work in the lab
On Monday, we welcomed back our second volunteer of the season, Marty. Marty is an expert on the scanner and x-ray, but since the new x-ray machine hasn’t arrived yet, she and Allen have been our rockstar head cleaners. So far, it has taken 22 person hours to clean 85 echinacea heads. Based on these numbers, it will take an additional 56 hours to finish cleaning the 216 remaining heads in the 2020 burn rem batch that we’re currently working on. If the volunteers continue to work at this rate, cleaning this batch would be completed by next Tuesday, October 26. In preparation for future head cleaning, we emptied out the seed dryer and refilled it with gbags from the 2021 harvest.
To celebrate several birthdays this month, Mia baked cupcakes for us! They were very chocolatey and delicious. We even made some new friends in the Plant Conservation Science Building by offering them cupcakes.
Tate is interning with us in November with his classmates from Lake Forest College. We’re excited to have his help around lab!
Tate, happy to see a scan with barely any chaff! Nice work, cleaners!
Hi FLOG!
I’m Tate Rosenhagen, a junior biology major at Lake Forest College doing a four week mini internship at the Chicago Botanical Garden for a Plant Biology course. It’s my second week in the Echinacea lab, coming in once a week for four hours, and this week I’m learning how to count achenes and randomize samples! Last week I learned a lot of the background of the Echinacea project; what an achene is, how to remove the achenes from the flower head, and a little bit about Echinacea and their pollinators. One of the questions I hope to answer while I’m here is if there is a relationship between seed number and average seed weight in Echinacea. I hypothesized that in heads with fewer seeds, the average seed weight should be higher as all of the plants are in the same experimental plot and thus are subject to the same conditions and nutrients. If the plants have roughly the same amount of nutrients and conditions, theoretically plants should use the same amount of energy as their neighbors. Therefore, I hypothesized that if one plant has created fewer achenes than another plant, their achenes may have more nutrients in their endosperm thus leading to a higher weight. However, a number of factors could cause plants to use their energy in places other than their seeds, such as damage repair on the plant itself or stem growth. I hope that some of the data I find while I’m here will begin to answer this question, however, only being here once a week for four weeks limits how much data I am able to collect.
Since Stuart and Team Echinacea have started summer field work in Minnesota, you might guess the lab at CBG slowed down- but you would be wrong! Last week we finished cleaning another bag of Echinacea heads, and this week we’ve gone through over half of the next bag! People counting achenes and classifying x-rays have also been super productive, and some of the newer volunteers finally got their official CBG badges. So even though there’s a lot going on in Minnesota, we’re still busy back in Chicago. Stay tuned for more lab updates throughout the summer.
From right to left, Char is cleaning, Aldo and Alan are counting, Tessa is cleaning, and Art is chatting because he was actually working outside this morning!
