Overview issue [Loes Ettema]

lettema1 commented 7 months ago

Introduction

Hello everyone, my name is Loes and I'm a PhD student at the department of Imaging Physics.

Describe your research in 2-3 sentences to someone that is not from your field (please avoid abbreviations)

In our group, we work on a new imaging technique called Computational Scattered Light Imaging. With this technique, we can retrieve the direction of fibers or fiber bundles within biological samples (e.g. nerve fibers in a brain section). This is done by illuminating a sample from multiple angles with an LED light source, capturing the scattered light under normal incidence with a camera, and subsequently analyzing the change in intensity for each image pixel.

My research entails the following aspects:

Research Aspect	Answer
Use/collect personal data (health data, interviews, surveys)	No
Use/collect experimental data (lab experiments, measurements with instruments)	Yes
Collaborate with industry	No
Write/develop software as the main output of the project	No
Use code (as in programming) for data analysis	Yes
Work with large data (images, simulation models)	Yes
Other:	N/A

Reflections on the importance of RDM videos

The video shows good reasons of why RDM is important. I fortunately never lost my data, so I don't have a horror story. However, I do sometimes encounter problems when trying to remember how I performed my analysis some time ago. I therefore agree that it's important to work reproducibly.

What would you like to learn during this course?

During this course, I would like to learn how to save my data in a reproducible and save way and how the version control with Git works.

Checklist assignments

[x] Assignment 1: creating a GitHub issue (the overview issue) (before 15 February, 10:00)
[x] Respond to the GitHub issue #101
[x] Assignment 2: Data Flow Map 1 (share a link in this issue before 22 February 13:00). Link: https://surfdrive.surf.nl/files/index.php/s/2T0ISz9CZiHl2Jh
[x] Provide feedback to at least one Assignment 2 from another participant
[x] Respond to the GitHub discussion #103
[x] Respond to the GitHub discussion #102
[x] Assignment 3: Data Flow Map 2 (share a link in this issue before 5 March 13:00). Link: https://surfdrive.surf.nl/files/index.php/s/ZZ9xP0FmJvgEpRW
[x] Provide feedback to at least one Assignment 3 from another participant
[x] Assignment 4: Data Management Plan (before 8 March, 13:00)
[x] Respond to the GitHub discussion #104 if you have any questions (optional)
[x] Assignment 5: Data Flow Map 3: submit your slide (before 11 March, 17:00)

ignasisg commented 7 months ago

I do feel the Data Flow Map 1 is very clear! It feels like you are dealing with more codes and images than me, which is interesting. Might need to consider some of your methods in the future.

EstherPlomp commented 7 months ago

Thanks for sharing assignment 2 @lettema1! And thanks for the feedback @ignasisg!

It looks very clear - well done! I only have a couple of pointers:

Some of the file formats are not super clear yet (I can guess from your descriptions!) - this becomes more important in Assignment 3.
Project drive is indeed a secure and backed up solution!
Great flag for the image sizes: that is indeed challenging!
Some of the other course participants have also considered datasets like presentations, figures or meeting notes - you don't have to add these but you may want to consider them for your folder structure that you'll have to share https://github.com/EstherPlomp/TNW-RDM-101/discussions/102

EstherPlomp commented 6 months ago

Thanks for sharing assignment 3 @lettema1! It again looks very clear and comprehensive - well done!

I therefore only have a comment that I also added to your DMP, but I'll also share it here for completeness:

Sharing software/code via platforms like GitHub is not sufficient to adhere to the FAIR principles, as GitHub does not assign a persistent identifier/DOI and it doesn't have a long term preservation policy unfortunately. You can share your software on GitHub/GitLab and share a snapshot/version of the code in a data repository as well. See here for more information between the GitHub/Zenodo integration, and 4TU.ResearchData can also be used for this (in a more manual fashion :)).

And a question:

Are SPSS file formats open as well?

lettema1 commented 6 months ago

Thank you for the feedback! About your question, I initially get the data from running a script in Python, after which I use that data in SPSS. In principle, I do not alter the data in SPSS, I only use some tools to visualize the data. However, it is possible to load the SPSS file in e.g. Python or R

EstherPlomp commented 6 months ago

Ah thanks for clarifying! Is there a way to do the visualisations with Python and/or R? That way even your visualisation would be reproducible!

lettema1 commented 6 months ago

Yes, that would also be possible. However, since I'm not so familiar with programming, I preferred using different software

EstherPlomp / TNW-RDM-101