I am making this post to share my project with the hopes of reaching out and connecting with others, that have similar ambitions, so that we can exchange ideas and experiences.
Throughout the forum I find a lot of cool and interesting projects and applications using the OF microscope, and I try my best to stay up-to-date seeing if anyone is pursuing similar applications as I. (Is there maybe somewhere a post i missed where members can present what they are working on? similar to the “Where are you? (OFM location survey)”-post.)
I’ve had the great pleasure of playing around with the OF microscope for a few years, slowly developing my project. I use the OF microscope for mass automated photography of aquatic samples for the purpose of environmental monitoring. The goal is to work out and provide a user-friendly workflow that can be adopted in basic education (as well as citizen science) while simultaneously generating basic data for environmental research. Throughout the last couple of years I’ve been lobbying academia and other environmental data collecting institutions to consider and look towards implementing open-source platforms such as the genius OpenFlexure microscope for the dual purpose of education and data collection. I recently got employed at a research company (https://www.swedenwaterresearch.se/) dedicated towards sustainable water use. Through this it looks like I might be able to organize local workshops sometime next year. I am therefore very much interest in other peoples experience organizing OF-workshops coming out of the “Have you run an OFM workshop? Share your experience”-post.
I currently have a webpage/blog under construction https://pkiw.github.io/. It is very much a work in progress, using my limited skills, but it contains a little more info and images about the project.
If anyone has any questions, suggestions or ideas regarding this project and my application of the OF microscope, please drop me a message!
Hi Per,
Thanks for the post it looks like an interesting project!
One part I’m curious about is that you are scanning quite a large area (4cm^2). Have you had any issue with the limits of the actuators? How about focus shifting out of range during the scan? Last time I tried making such a large scan the foot on the Y actuator snapped!
What is the step size and number of steps you have setup in the stack and scan?
Thanks
Al
thanks a lot, I am very glad that you are interested!
You are right, the area is not scanned in one go but 4x 1cm^2 scans. I have designed a dish stage that when the microscope is centered it is beneath the center of a 1cm^2-area. Then, I can easily rotate the petri-dish 90 degrees, reaching the center of the next 1cm^2, and scan again. So after ~50 min I have to spin all the dishes 90 degrees and restart the scan procedures. For each 1cm^2 I usually scan from ~ +45K → -45K in both x and y, 14 steps x and 19 steps y. I am happy to share the stl/cad-files if you are interested.
Thanks so much @Pelle for posting this, and for doing such a great job of documenting this on GitHub. I’m not sure there is one obvious thread for introducing what you’re doing - there’s a “build reports” category but not an “applications” category. I should really fix that! I think I started many bits of this project in a “people want to build a microscope” mindset, and never really made the jump to “people want to use it”. I think I will make an “applications” category and move this topic over as the first one
Thanks to you @r.w.bowman! You and everyone involved have indeed set something with unimaginable potential in motion, so I am really looking forward to following the “Applications” category!
hi @Pelle nice work!
We did something similar for soil… at least on the educational side
Image analysis sounds good! maybe we can learn from your experience
Thank you @nanocastro. Yeah, your post on DIY soil microscopy workshop is inspirational. When I manage to work out a nice image analysis pipeline it should not require to much modifications to use and train on pollen imagery.
I just wanted to share (somewhat) recent (somewhat) OFM related material developed within the framework of my aquatic environmental monitoring application.
OFM image species lists I’ve had the great opportunity of working with students, teachers and researchers exploring the use of OFM in aquatic environmental monitoring and education. This has resulted in a semi-annotated species list, compiled of OFM images taken by participating students and teachers (more images can be found at Nordic Microalgae).
Pdf version here. Long term goal is to continue expanding the species list.
Cheat sheets for using the OFM I’ve also had the great opportunity of building OFMs with school teachers. Though official OFM instructions and the forum is a great resource, with all the help needed, I felt I had to make instructional cheat-sheet (lathund) saving the teachers some time recalling what they heard during the workshop. Hopefully they can be of use or inspiration. One for when using software version 2 and version 3.
Unfortunately, at the moment, non of the material is their own git project, so contributing to the material is not really possible at the moment. Feel free to make use of the material and contact me if you have any questions, suggestions or ideas (info@pkiutv.se).
It turns out that some 28BYJ-48 motors steps the opposite way from others . The v3 software assumes that increasingz will lift the camera. It was set up with different motors to yours.
In a couple of weeks we will release beta 1. This will solve the problem for z with this new first use calibration question:
Currently there is still nothing fixing which way X/Y move. The plan is that we build this into camera stage mapping. This has missed the merge window for beta1 but will come soon.
thanks for your reply and sharing what’s to come. Really nice calibrations step to get around that some motors are stepping the opposite way from others!
This looks great Per. It’s really useful to understand how teachers are using it and how we can help them. The images in the species list look amazing as well!
. The v3 software assumes that increasing z will lift the camera. It was set up with different motors to yours.