Portability & Visitors

I took a portable version of the scanning setup to the beaches of Lake Michigan last week. It was interesting, not as successful as I would have liked it to be but I did learn a bit, took some notes, and have a better idea of where things can be improved.

The home setup continued to work fine while I was gone. The biggest issue I have to resolve is storage, switching to a portable USB drive should resolve that, but I'll miss the joy of uploading everything to a remote server, crunching all the images into a video and uploading to youtube / wherever at high speed. It doesn't make sense at this point to justify spending $50 / month when a 1TB drive can be purchased for $70.

I

Aside from technical fun, it looks like we've had a creature of some sort dig a hole in front of the scanner! No good images of the animal itself, the limited depth of field only gives us blurry images of anything more than 1 or 2 mm away from the scanner.

Documentation Progress + Battery Power

Brief updates

 - Incomplete process notes for Raspberry Pi setup

 - Rough draft of Scanner Prep

 - Rough draft of Burial Process

Lots of work still needed on the Pi setup process.

 - Still trying to decide how much information to include here

 - - Is it necessary to discuss initial image / OS installation, network setup, 

 - - This version assumes everything happens on the Pi - lots of pros & cons with this : )

 - Still need to compile a section on device setup (hub/scanner/wifi) along with pros & cons of different device choices.

I would love to spend more time with someone discussing and either building or linking to information that helps myself and others understand what can be seen in the images.

 - Root Growth

 - Insect life / processes that we're able to see

 - Soil type

 - Seasonal differences

Last, another objective has been to get battery powered version running. I spent a couple hours today setting up a battery (on loan from the wonderful AADL). At roughly 500mA idle and 900mA scanning (figuring 1 min/scan) should provide plenty excess energy to document for a solid day. (27,000mAh Battery).

Though my current understanding is that I can not charge the battery AND power the setup at the same time. The specs for the battery specify a max of 1 Amp output. With a WiFi dongle power hitting 1007mAmps for roughly 30 seconds at a time. It was recommended I avoid exceed the max amperage, even if just a little.

Documentation

Slowly documenting things! I'm aiming for minimal documentation that communicates as much as possible. This is proving to be difficult : ) This also meant burying another scanner : )

I currently plan on breaking documentation into three sections:
1. Setting up the Raspberry Pi to automate scans
 - Process documented, needs testing and significant clean up before starting rough draft

2. Preparing a scanner for burial
 - Photos taken and rough draft done, needs review

3. Burying the scanner
 - Photos taken and rough draft done, needs review

The last two sections are pretty straightforward. The first section needs a couple dedicated afternoons cleaning up the existing documentation, testing from scratch, and finding a balance of what+how much to communicate. I would love to see if the entire project could be done by a group of young students, and that brings up a number of questions.

What and how much to communicate really depends on the goal of whoever's perusing it. It's somewhat amusing that the easiest way to document is to document everything in excruciating detail. Which is probably a buzz kill for most...  Trying to take into account things like:
 - Would it help to include automated publishing of images + videos.
 - - Do we cover rsync, backing up, ssh, etc.? Or discuss GoogleCL?
 - Is local access to images and videos preferred, and then they can decide what to do with it?
 - - Do we discuss methods on Windows & Apple to process images and video?
 - What's a good price point to assume? Minimal: ~$100. Ideal: ~$150.
 - - This changes how much data can be recorded and methods of storage.
 - Do we keep it to the command line environment?
 - - Aside from viewing videos it's all been SSH. This can be a huge barrier for some.
 - Do we discuss open source software, hardware?
 - - This whole project would likely not have happened without it.

Mmmmm, food for thought! Sounds like I need to spend some time communicating with people who might want to use it, and what their goals and desires might be.

Scanner Unresponsive - What Next : ) ?

For the past 24 hours the scanner has not been functioning. Initially the top half of the image displayed the same repeating line of pixels, and a power cycle resulted in the device no longer appearing (lsusb) on the Pi

Both problems have separately occurred before. The former problem happened when the scanner was first buried. Dirt compacted too forcefully against the scanner meant the sensor was unable to complete a full pass, resulting in a similar image. The latter happened with the device reappearing after a day or two and several power cycles un/replugs, cause unknown.

So far the scanner has:
 - Spent ~6 months below ground
 - Captured ~17,000 images
 - Survived above-ground temps well below freezing

I'll wait a day or two more before going beyond power cycle and un/replugging the device : )

Meanwhile:
 - Automated uploading images to a remote server (Linode) and building daily videos.
 - - Next Step: Automate compilation of weekly and monthly videos, post online.

- Automated backup of the original images to Amazon S3 + file cleanup.
- - Next Step: Set it up to run regularly (right now I'm running the script instead of setting it up as a Cron job)

- Documentation / Build Guide.
- - Next step: Use the backup Canon Lide 20 to assemble the physical build guide
- - Next step: Review notes on existing process and create:
- - - Simple Pi guide (Just to view images as you like from the scanner)
- - - Timelapse Pi Guide (Include automation for creating timelapse video)

Beyond the above, there are two variations on this project that I would like to pursue:
1) Building a cylindrical scanner. Scrap the frame/body of an existing scanner, mount it to a glass cylinder and have it scan 360 degrees. I think it would be easier (physical constraints) to get it to scan from the outside in, but I think it might be more interesting to get it to scan from the inside out (buried in the ground). Similar to existing Mini-Rhizitrons, but with a 360 degree view.

2) Building a webcam version. Similar to existing Mini Rhizotrons, but significantly cheaper. This is how this project originally started. The image quality and viewing area will be reduced, but we'll have a significantly higher frame rate and nearly real time (ms delay) viewing. Taking an image once a day seems fine for tracking root growth, but tracking the path of certain bugs below ground seems like a 1 frame / minute frequency.

It would be wonderful to include additional data for both build options, ie:
 - Moisture
 - Humidity
 - Temperature

5 Months, Secondary Root Growth, and Things Moving Up

Compiled video for the last five months (see below). Brief notes of interest:

1. Secondary Root Growth. Around Sept. 21st there is a burst of root growth extending out from many of the existing roots. This lasts for about two weeks before settling down. Nearly all of the easily visible roots exhibit the same behavior at the same time. Neat! I'm assuming they are all coming from the same plant. What changed took place that enabled this process to happen? Temperature, sunlight change, moisture?

2. Underground Plant Growth. Plants generally start their life below ground, running their roots/radicles down, and their shoots/hypocotyl towards the sky. It's strange for me to see the upward growth below ground. At the 43s mark of this video you can see this happening. That behavior isn't abnormal, but it's growth I'm normally used to seeing only when a plant emerges above the earth. I mistakenly assume everything below ground is a root : )

43 seconds in the linked video puts us at late October with the growth continuing through November. With an average temperature of 34°F / 1°C, I have a hard time believing whatever sprouts above ground will survive long?

If this setup continues to survive, what other growth will we see as the temperature stays below freezing? It's about time I started measuring the soil temp!

~5 Months played back at ~10 seconds/month. 

See below for playback of 1 second/month.

~5 Months played back at ~1 second/month.  

After These Messages

Spent the past two months out of the country. Automation was only partially functioning. In short, images from the scanner were not automatically offloading to a remote server, so I had to SSH in from Cambodia, Thailand, and New Zealand every few days to do this manually. A few days of data was lost, but beyond silly user error problems the setup has continued to function. The past week has seen an average temperature below freezing. Neat! Hoping to recompile some new timelapse videos over the next week. Will update soon.

10 Weeks in 10 Seconds

The project has been running for approximately ten weeks. Geologists probably know this better than almost anyone: Ten weeks is a terribly short period. I think if this project lasts a year I will find myself only partially satisfied. Seeing things change (roots grow, leaves decompose, roots get eaten, water saturating the soil in a storm, etc.) is fascinating, but I still have no idea what the changes in seasons or significant temperature change will have on the appearance of the soil. Things to look forward to : )