pre-GOSH: Open Soil Research

for my citizen science attempts with micronuclei and comet assays this is also an impt problem. almost no one manages to count the 1000 cells to know whether the few micronuclei they see are significant, for instance. for the comet analyses, the epifluor micrographs have to be segmented to get each comet in the good orientation to analyse ratios of fluorescence (in ‘tail’ vs nucleoid) in addition to tail lengths, relative to controls. does that sort of image analysis count for your ‘signal’ definition? :slight_smile: Making an ‘app’ for the micronuclei, was what one student has already started coding for, but this is entirely out of my expertise!

we can find space. the days before the main GOSH is starting we already have access for example to the openFIESTA lab. it’s big.

1 Like

yes, as Vanessa couldn’t come, maybe Urs’ recent plastic experiences will also be of interest… but including the bio-pigments as V worked with, is extra special…

Yes, it definitely does fall under the definition of signal, and pretty well too.
But this is an instance segmentation problem, and the most painful of this is usually to have enough training data.

But if you have some training data with you at GOSH, it could be a good use case of how you can spend maybe an hour or two to create a small annotated set yourself with a small bit of effort, and see if the model can actually learn from these small number of annotations and can predict other similar segmentations in the dataset (and then humans have to just correct the segmentations). And its practical to even cover what tools to use, what hardware you would need, and what timeframes are we talking about (after 1-2 hours of small annotations, a single training can take upto a day; so good GOSH is a multiday event)
Lets catch up at GOSH :smiley:

PS : @gbathree: Sorry for hijacking the thread :’)) Lets get back to the soil discussion !

hi all
I think we can make more than one run of chromatographies while we share some other soil geeking. Hope you can join us @saibhaskar .
I’m going to be at Shenzhen on the 5th so we can try to do an early first run 5 - 6. What do you think @Rachel @vektor? I was thinking on 20 soil samples for each run. We need to collect samples before do…
We can repeat againg before (7-9) and during gosh for the ones arriving later
The “code” of Restrepo travels with me.
In this gdoc I’ve gathered some info on chromas (including a pdf of J. Restrepo book) and the list of materials, feel free to add some other resources .
Nos vemos pronto


I will be in shenzhen on the 5th too! But I also wanted to start working on the MiPi extension but I guess I can combine both!

This threads gone banana’s, so I’ll just throw more stuff in :slight_smile:
I have about 150 soil samples which have the following information:

  • total carbon
  • soil respiration (using the 24 hour burst test, tells you about biological activity, google it)
  • minerals (from Na --> U)

I think I get into big trouble if I bring soil samples over the border, but if we agreed on a method and process, and we had someone to help with the prediction part, I could certainly run those samples here when I get back. Would make a nice starting test set.

1 Like

doing a session now here in Stuttgart!
Really looking forward to all this interests in soil of the pre-GOSH activities.

please also look into all our activities within HUMUS Sapiens and the hackteria forum, where we just did maaaany activities through-out this year.

and the wiki:


just love these… should I make a new topic to talk about the latest ‘urban gardening’ project at Hackuarium? btw, the wrap up party will be 31oct - to which all are invited!!
(costume wearers get special surprises!)

1 Like

i think we should start these Open Soil Research Actitvities on Monday 8th already using our lab/hack space available at openFIESTA. @Rachel when are you arriving?

we just recently did some chromatography and had earlier activities documented on the hackteria wiki:

now fixing the cable of the soil respiration chamber, but happy to share and demo when we meet. @gbathree

until then we had already actively shared some experiences on Collaborative Fabrication and ordered PCBs. see other thread if you wanna join. actively coordinating the meeting on our wechat group.

1 Like

Congratulations on the work you!

I was really happy to hear that you’re doing soil chromatography around here too. Here in Porto Alegre / Brazil we are just beginning to make some chromatograms, we learn the technique with the great master Sebatião Pinheiro.

It will be very gratifying to talk more with you about this incredible ancestral technique.

I have great desire to make a global map with people who go up their chromatograms, with date and locality, it would be incredible and we could exchange knowledge about rock dust, primary metabolism (protein) and tertiary (enzymatic) metabolism of microorganisms that exist in different biomes around the world.

Have you thought to use this map allied to a blockchain to traceability the nutritional quality of food?

Here is an image of a chromatogram that Sebatião Pinheiro took us last week from a sample of the “Terra preta de índio!” in the Amazon rainforest.


Sorry for writing errors, my English is not very good.

In the wiki of the automated vertical vegetable garden project I did a documentation of a crazy idea. It will be very cool to share it with you!

I translated the excerpt that is contained in “Principais caracteristicas” more specifically in "Rastreabilidade.

"Traceability: By using Blockchain technology in conjunction with sensors and actuators integrated with communication systems (IoT), the still manual collaboration of small rural and urban farmers is making it possible to track the entire history of a food, all this data will be sent to the In order to show the quality of seed planted (Kirlian Photography), or what nutritional condition and chemical balance of the soil to which the seed was planted and harvested (chromatography), as well as the quality of the seed and with the implementation of the Modular Metereological Station in this project we were able to record the environmental conditions of the microclimate in the food being produced, such as temperature, atmospheric pressure, altitude, relative air humidity, rainfall and wind speed. was generator until arriving at your plate, is accessible through QR code of the history of the food. "

both the automated vertical gardens project and the chromatograms are kind of stopped here, I hope that by sharing some knowledge we can continue.