Category Archives: DDW5

DDW5: Water Day 25 (Delayed)

I took these pictures on Day 25, but haven’t had time to post them because of all the SDM work. So here they are:

One more set of pictures to take.

DDW5: Water Day 20 (Day 21)

DDW5: Taking pictures and manipulating them in bulk

A lot of this project is managing how I take pictures of the plants. I’ve talked a lot about my setup and I’ve talked some about how I take pictures and the software I use. Well I’ve had to make some changes to the process and now I’m letting you know so I can continue to be a good open notebook scientist.

camera setup

Above is a picture of my current setup. I noticed that some seedlings will float in the sample and I couldn’t fit the entire cell in the frame of the camera so I had to find an alternative to my previous method. My solution? Rotate the camera! Simple!

I just found another optical post (4″ in this case) and a 90 degrees post holder. I put the two together and used the post holder from the previous setup (2″ long) to get the current setup. All equipment used in the photo above can be purchased from ThorLabs (and if you buy a bunch you get some lab snacks with your order!).

Also since last time, I added a black backdrop (the one I’m using is a big piece of thick paper). The black provides excellent contrast to the white root hairs.

Finally I’d like to talk about the software that I use. In the previous trial of the DDW experiment (Category: DDW4) I used some software called JPEGCrops to crop the photos in bulk, and I used a program named Rename Master (both open source software) to rename the photos in bulk for organizational purposes.

With this new camera setup, rotating the frame actually allows me to minimize the amount of the other samples in the frame. But I do need to rotate the images in bulk. Windows actually does something right in this regard. If you select a bunch of images and right click, there is an option to rotate the images either clockwise or counter-clockwise in bulk. Using this handy feature saved me a ton of time. Then I can use Rename Master to rename the images in bulk as well.

And that is my whole process, well up until I upload them to my notebook. But from there you can add captions and do some other minor editing features (that I almost never use). Hope this helps someone somehow.

DDW5: Water Day 20 (pics postponed)

I was supposed to have the day 20 pics today, but I took one picture and the camera battery died so I’ll have to get them up tomorrow. In the meantime I have another day to build a camera holder that can hold the camera vertically so I can fit the entire cell in the frame.

DDW5: Water Day 15

DDW5: Water Day 10

DDW5: Water Day 5