August 2009 « The Echinacea Project

software for counting seeds in images

We have been very happy using ImageJ to count Echinacea seeds. ImageJ is free, open-source, public domain software. It runs on any platform.

We have also used ImageTool. This program is free and runs on Windows only.

Histogram of pollen sizes

Here’s a histogram of pollen sizes (~30 grains per species) from 3 individual plants of Coreopsis palmata, Echinacea angustifolia, and Heliopsis helianthoides.

Greg outlined the methods taking the measurements here. Greg, what software program did you use?

Mimi’s Last Day- long ago, but not forgotten!

You WISH you were eating these cakes!!!!!!

We miss you, Mimi!

You too, Greg!

pollen storage data

Here is a file with the pollen storage data (excluding Stuart’s data on the 48 hour style persistence).

pollen storage data sheet.xls

We pollinated 3 plants in the common garden that were still flowering. Each plant had 3 treatments of stored Echinacea pollen; ambient temperature, frozen, and refrigerated. The frozen and refrigerated pollen caused shriveling, the ambient temperature treatment did not.

How many do you see?

Hey All,
Long time no post, I know. Things certainly have been busy around here. As you all probably know, I finished making slides a while back – 372 slides total. WooHoo!!

Now, onto the next step, taking pictures of these slides. I took my very first pictures today, just a couple to get the hang of things, they are attached to this post. From my fiddling around today, I can see that this is going to be a lot more work than I thought. First off, the pollen is hard to find, it’s not all at the same level of view, some of them are on top of the stigma and then they’re really hard to see. Also, it’s challenging to focus in enough to where I can ID pollen grains. Stuart suggested working on a random sample of my slides for the rest of the summer, and completing them this fall at the CBG. The only issue there is the change of machinery, but hopefully we can figure something out.

As for the rest, I think I’ll be taking 1-2 shots of the entire style, and labeling them thus: stylevialID_site_date/time_A# – so A1, A2, etc. Then I’ll zoom in and proceed to take pictures at sites B through F on the style, and for each change in focus will be another number. The question is whether I should attempt to get a good sense of the exact number of pollen grains on the stigmas or try to ID the pollen types. I’d like to be able to do both, but I think for this summer at least, I’ll try to get a handle on the former rather than deal with the later.

On that note, Caroline suggested using a clicker to count the number of pollen in a picture, and that seems like an excellent suggestion. Does anyone know if we’ve got one?

Anyway, enjoy the pictures that I took so far:

-Kate Monster

Files for Gretel to make visor forms AND a reminder for Stuart

Here are two spreadsheets with information to be made into visor forms.
The first is a list of Echinacea positions we will measure from, in order to plant Stipa seeds. The relevant worksheet is the first one. In the visor form, I would like to be able to see row, position, Echinacea plant status and a column for notes. Breaking this list into multiple forms would be fine.

Complete list of Stipa positions81409.xls

The second is information for the “Next generation rescue” August seedling refind. I would like block, row, position and number of seedlings in May visible and would like number toothpicks, number toothpicks with no seedling, number new seedlings, longest leaf lengths and notes as editable fields.

Nextgenresc-For Aug 09 visor form.xlsx

And finally, Stuart, could you check out some Stipa bunches in Staffenson and decide how close we could comfortably plant seeds next to the Echinacea in the garden?

Allegra’s pollination data .csv file

Here is my dataset that I am working on analyzing in R as a .csv file.

halverson.data.091.csv

Stuart, here is my R script so far:

halverson.data.analysis1.R

I made new columns in the .csv spreadsheet for the factors and levels we discussed. I will work on a list of hypotheses to test. I think I changed the definition of “y” when I did my 24 hour analysis. Can I give “y” a different name for each analysis? Or does the code need to read a defined “y” each time?

Thanks for the help and check out the graph of 24 hours and the summary m2.

Allegra

Pollen measurements – bad and good news.

Here are the data on the three pollen types and the protocol for measuring.
I used the same plant/pollen from each plant and measured at least 30 different pollen grains from each. I didn’t use any pollen if its pole faced forward – only if it was sideways.

Bad news – the Ech. ang. and Heli. heli. are very close. Good news – maybe the pollinators and plants can’t tell them apart either.

Book1.xlsx

PS – I am in SE Minn and the Monarda Sunflower and Miss. Goldenrod are in full bloom all over.

Protocol for slide image recording and measuring.docx

Fun with the Internets!

So, for another update from the luxurious Hjelm house, which is THE place to be this summer. We recently had the wireless router in the basement stop allowing people to log on to the network wirelessly, so Stuart ordered a new wireless router, along with an 8 port switch so that we can have more than 3 computers connected at the same time. They got here yesterday, and I took them downstairs to set up.

The entire process of setting up took about 20 minutes, and everything worked like a charm. I hooked the cable modem up to the router, set up the router DHCP (Dynamic Host Configuration Protocol, used to assign IP addresses to computers on the network), and hooked the router up to the switch, after mounting them on the wall. However, I wanted to see if we could get wireless access in the Wagenius house, about 60 metres away.

Setting the router up near the window in the basement did not work, so I moved the router upstairs. After a couple hours trying various spots, it was placed in Stuart’s office, which offered easy access to an Ethernet jack, as well as a convenient window.

In order to enable both the wireless router and the wall jacks, while preserving the network, I had to disable DHCP on the new wireless router, and place the old one downstairs to act as a DHCP distributing thingy for the house. It took me a couple hours to figure this out as well, since I thought the wireless router could perform the same function through the switch.

Anyway, to cut a long boring story short, the new router upstairs fell just short of the Wagenius house computer’s range, so using the excellent resources of (Lifehack.com, I made three parabolic reflectors out of cardboard and tin foil to boost the signal. They worked like a charm! They are originally the idea of this site: http://www.freeantennas.com/projects/template/, and I got the template to build the antennas from here: http://www.freeantennas.com/projects/template2/index.html.

Some pictures of the new wireless router:

Baggie collection this week?

So sadly, it looks like I won’t be able to come back to Minnesota again this summer. It’s taking much longer than I anticipated to score slides and time is really running out (is anyone else wishing they had a few more days this summer? I sure do..).

I was hoping someone could remove my bags from the ground sometime this week. I’ve posted a file with all the individuals who should have a bag located just south of the plant. I hope this isn’t a very busy week for you guys! The bags can definitely wait if that’s the case.

dataSheetMycorrhizae_8_12_2009.xls

I think Amanda should still have a file on her computer with labels for each individual plant. Coin envelopes were the perfect size for the baggies so hopefully there are still some of those left in storage.

Also, some of the bags may rip when you pull them out of the ground. To retrieve the membranes you may have to dig so you should have a trowel ready. You won’t have to dig more than 5 cm to find the brightly colored mesh with the membranes. Thank you so much for your help!

-Andrea

Categories

Experiments