Creating a platform for open sharing of multibeam electron micoscopy data and methods

[arentkievits]

Project Lead: @arentkievits

Mentor: @EstherPlomp @martlj

Welcome to OLS-4! This issue will be used to track your project and progress during the program. Please use this checklist over the next few weeks as you start Open Life Science program :tada:.

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Week 1 (week starting 13 September 2021): Meet your mentor!

• [x] Meet mentor for 30 minutes
• [x] Create an account on GitHub
• [x] Check if you have access to the HackMD notes set up for your meetings with your mentor
• [x] Prepare to meet your mentor(s) by completing a short homework provided in your shared notes
• [x] Complete your own copy of the open leadership self-assessment and share it to your mentor If you're a group, each teammate should complete this assessment individually. This is here to help you set your own personal goals during the program. No need to share your results, but be ready to share your thoughts with your mentor.
• [x] Make sure you know when and how you'll be meeting with your mentor.

Before Week 2 (week starting 20 September 2021): Cohort Call (Welcome to Open Life Science!)

• [x] Attend call or catch up via YouTube

• [x] Create an issue on the OLS-4 GitHub repository for your OLS work and share the link to your mentor.

• [x] Draft a brief vision statement using your goals

  This lesson from the Open Leadership Training Series (OLTS) might be helpful

• [x] Leave a comment on this issue with your draft vision statement & be ready to share this on the call

  I am working with electron microscopists, computer scientists and data scientists to create new methodology for volume electron microscopy so that researchers that have no experience in volume EM can enter the field more easily and make use of existing architecture. I am working open because there are many different people from different field who want to do volume EM and we are facing common challenges such as data storage, segmentation and visualization.

• [x] Check the Syllabus for notes and connection info for all the cohort calls.

Before Week 3 (week starting 27 September 2021): Meet your mentor!

• [x] Suggest a cohort name at the bottom of the shared notes and vote on your favorite with a +1
• [x] Share a link to your Open Canvas in your GitHub issue
• [x] Meet mentor
• [x] Complete your Open Canvas (instructions, canvas)
• [x] Look up two other projects and comment on their issues with feedback on their vision statement
• [x] Start your Roadmap
• [x] Complete this compare and contrast assignment about current and desired community interactions and value exchanges
• [x] Comment on your issue with your draft Roadmap

Before Week 4: Cohort Call (Tooling and roadmapping for Open projects)

• [x] Attend call or catch up via YouTube
• [x] Look up two other projects and comment on their issues with feedback on their open canvas.

Week 5 and later

• [x] Create a GitHub repository for your project
• [x] Add the link to your repository in your issue
• [x] Use your canvas to start writing a README.md file, or landing page, for your project
• [x] Link to your README in a comment on this issue
• [x] Add an open license to your repository as a file called LICENSE.md
• [x] Meet mentor

This issue is here to help you keep track of work as you start Open Life Science program. Please refer to the OLS-4 Syllabus for more detailed weekly notes and assignments past week 4.

Week 6

• [x] Attend call or catch up via YouTube

Week 7

• [x] Add a Code of Conduct to your repository as a file called CODE_OF_CONDUCT.md
• [x] Meet mentor

Week 8

• [x] Add a contribution guideline to the project
• [x] Do the Agile project management assignment
• [x] Attend call or catch up via YouTube
• [x] Comment on issues
• [x] Process feedback into Open Canvas
• [x] Process feedback into vision statement

Week 9

• [x] Meet mentor

Week 10

• [x] Attend call or catch up via YouTube
• [x] Work on assignments
• [x] Process feedback into Github repo

Week 11

• [x] Personas and pathway assignment
• [x] Meet mentor and expert

Week 12

• [x] Attend call or catch up via YouTube

Week 13

• [x] Restructure files in demonstration repo for project
• [x] Add demo data
• [x] Add gitignore file
• [x] Meet mentor
• [ ] Add more demo data
• [ ] Add Dockerfile / instructions to setup environment
• [ ] Expand readme
• [ ] Get the Jupyter notebooks working with Dockerfile / environment
• [ ] Mountain of engagement exercise

Week 14

• [ ] Attend call or catch up via YouTube
• [ ] Include persona and pathways in contributor file
• [ ] Clean up Jupyter notebooks and add documentation
• [ ] Make MVP of interactive demo notebook
• [ ] Add progress bars
• [ ] Add Zoom function for images
• [ ] Embed html CATMAID viewer into Notebook? Don't know if it will work, if it does it would be great.
• [ ]

Week 15

• [ ] Meet mentor
• [ ] Invite new contributors to into your work!

[arentkievits]

Vision Statement I am working with electron microscopists, computer scientists and data scientists to create new methodology for volume electron microscopy so that researchers that have no experience in volume EM can enter the field more easily and make use of existing architecture. I am working open because there are many different people from different field who want to do volume EM and we are facing common challenges such as data storage, segmentation and visualization.

[arentkievits]

My Open Canvas: https://docs.google.com/presentation/d/1YzTxXuZL2jkDqhEdKVU5fgEg4IJHLL3cKopgwL-TZtY/edit?usp=sharing

[arentkievits]

Opened up a repo for the project https://github.com/arentkievits/MB-SEM

[arentkievits]

The README https://github.com/arentkievits/MB-SEM#readme

[Lisanna]

My Open Canvas: https://docs.google.com/presentation/d/1YzTxXuZL2jkDqhEdKVU5fgEg4IJHLL3cKopgwL-TZtY/edit?usp=sharing

Hi @arentkievits, I would like to share some feedback about your open canvas. I think I understand the problem that you are trying to solve, but I am not sure it is phrased clearly in your canvas. Is the usage of the multibeam electron microscope data not straightforward? Are you trying to build some sort of open documentation to make other users able to handle it, or rather you want to openly share the results of your work? Also, I am not familiar with the two acronyms you used in the user channels: could you maybe specify more in a comment?

[manulera]

Hi @arentkievits! Just catching up with the previous assignments. Nice Open Canvas and Readme, I think the goal of the project is very clear. I was thinking that it would be nice to have an example (an imaginary case study) where you describe a particular use-case. For example, what question does a researcher want to answer using this particular EM technique, how does he approach MB-SEM and what he gets out of it in terms of info, data storage, methods, etc.

You also mention a python package, is this to manage the microscope acquisition or for data processing? This was not clear to me from the readme.

[arentkievits]

My Open Canvas: https://docs.google.com/presentation/d/1YzTxXuZL2jkDqhEdKVU5fgEg4IJHLL3cKopgwL-TZtY/edit?usp=sharing

Hi @arentkievits, I would like to share some feedback about your open canvas. I think I understand the problem that you are trying to solve, but I am not sure it is phrased clearly in your canvas. Is the usage of the multibeam electron microscope data not straightforward? Are you trying to build some sort of open documentation to make other users able to handle it, or rather you want to openly share the results of your work? Also, I am not familiar with the two acronyms you used in the user channels: could you maybe specify more in a comment?

Hi @Lisanna, thank you for having a look and giving feedback! I agree that I still have to phrase it a bit more clearly, thanks for pointing that out. The use of the multibeam electron microscope brings some challenges: sample preparation is more difficult, it produces more data than a regular microscope, where to store this data, how to annotate it, how to share it with other researchers.

My primary goal is to openly share the methods and results, so that other researchers that are going to work with this technique (which will be the case in a year or later) can learn from this. I also want to encourage other researchers to contribute.

The acronyms: volume electron microscopy (Volume EM, which is kind of a new research field), correlative light and electron microscopy (CLEM, also a quickly developing research field with dedicated conferences) and Netherlands Electron Microscopy Infrastructure (NEMI). These are all opportunities for me to share my work, either via conferences or workshops.

[arentkievits]

Hi @arentkievits! Just catching up with the previous assignments. Nice Open Canvas and Readme, I think the goal of the project is very clear. I was thinking that it would be nice to have an example (an imaginary case study) where you describe a particular use-case. For example, what question does a researcher want to answer using this particular EM technique, how does he approach MB-SEM and what he gets out of it in terms of info, data storage, methods, etc.

You also mention a python package, is this to manage the microscope acquisition or for data processing? This was not clear to me from the readme.

Hi @manulera, very good suggestions! It would indeed be a good idea to add a case study. In fact, I am thinking about some at the moment. Since I am still in the early stage of my PhD and the multibeam electron microscope has just been installed, I have not had the time to work on this yet but it will soon follow.

Currently I am working on a separate repository for visualizing some data with the detection method used in the new multibeam electron microscope. The one you are referring to is still on the planning, but it will be related to data processing. We still need to figure out how to go from the raw data to a reconstructed volume. There are methods available but we should customize them to our situation. I am going to design a flexible and scalable approach such that it can be used for small but also very large data sets. The plan is to make it deployable on high performance clusters

[EstherPlomp]

Hi @arentkievits: Nice Open Canvas!

I agree with earlier feedback that your problem statement could be a bit more specific about the problem that you're trying to solve (why is producing a lot of data an issue: sounds like a fantastic problem to have if you do not have any data ;)), so perhaps you can incorporate some of your answers here into the canvas?

From your Unique Value Proposition I get the feeling that you would like to provide a space where people from different disciplines can work together? Perhaps add something in terms of 'allowing for interdisciplinary commutation/contributions' ? I suppose what would make your idea unique is that there are currently perhaps databases with shared resources but they do not necessarily include the involvement of the community to contribute to the development? Or a discussion forum? Maybe you can be a bit more specific about what sets your initiative apart from existing ones?

For resources I would also list the human resources such as the time needed to contribute or maintain your solution.

User Channels: I'm going to be annoying again and suggest Twitter? ;)

Contributor channels: Did you already have to set up your contributor.md file for the repository? This is generally a place where people would look for information on how to contribute to projects. Let me know if that needs more explanation!

Contributor profiles: a suggestion for "people who like to code": data managers or research software engineers?

Hope this is helpful! If anything is unclear, please let me know.

[EstherPlomp]

Hi @arentkievits: Well done on processing the feedback! I only have one comment on your unique proposition as it says "This would be unique compared to other data repositories". Why is this different from other data repositories? Because they only allow uploading and no discussions? Or are discussions organised more top down?

Other than that it is super clear! I also have no further comments on your Project Development Plan: the milestones look good and the time estimates are reasonable: well done!

Something else (and maybe your supervisor already mentioned this to you): The Digital Competence Center of TU Delft has a call out for support from research software engineers which might also be helpful so that you have some support in working on this? Deadline is 1 Dec. See their website for more information: https://www.tudelft.nl/en/library/library-for-researchers/library-for-researchers/setting-up-research/dcc/apply-for-support.

[arentkievits]

Hi @arentkievits: Well done on processing the feedback! I only have one comment on your unique proposition as it says "This would be unique compared to other data repositories". Why is this different from other data repositories? Because they only allow uploading and no discussions? Or are discussions organised more top down?

Other than that it is super clear! I also have no further comments on your Project Development Plan: the milestones look good and the time estimates are reasonable: well done!

Something else (and maybe your supervisor already mentioned this to you): The Digital Competence Center of TU Delft has a call out for support from research software engineers which might also be helpful so that you have some support in working on this? Deadline is 1 Dec. See their website for more information: https://www.tudelft.nl/en/library/library-for-researchers/library-for-researchers/setting-up-research/dcc/apply-for-support.

Hi Esther,

Thanks a lot! 👍 I will have a look at your suggestion.

Indeed my supervisor has informed me about the DCC call and we are actually submitting a request for help with a file converter to make our electron microscopy data more FAIR! Anyway, good suggestion to ask for support with the Open MB-SEM project, I will think about it!