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EstherPlomp / TNW-RDM-101

Self paced materials of the RDM101 course
https://estherplomp.github.io/TNW-RDM-101/
Creative Commons Attribution 4.0 International
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Assignment 1 Isabel Droste #87

Closed ieacdroste closed 10 months ago

ieacdroste commented 1 year ago

Introduction

Hi, my name is Isabel Droste. I am a second year PhD Candidate at the Department of Image Physics. In my spare time I do pole dancing and bouldering.

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

My research focusses on algorithms for super-resolution microscopy. I am working on an algorithm that can detect optical aberration from microscopy data and correct for it, to eventually improve the resolution of microscopy images.

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 Yes
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

What would you like to learn during this course?

I am currently working with large (TB) datasets. I would like to learn the best practices how to handle (large) datasets, how to collaborate with other on this, and make my work understandable for others that may continue on it in the future.

Checklist assignments

enyasb commented 1 year ago

Hi @ieacdroste ! I looked at your data flow map and was wondering whether any flags apply to the data you receive from other groups, e.g., is any of it confidential?

EstherPlomp commented 1 year ago

Thanks for sharing assignment 2 @ieacdroste! It looks very concise and clear - well done!

Just two questions from my side:

ieacdroste commented 1 year ago

Hi @ieacdroste ! I looked at your data flow map and was wondering whether any flags apply to the data you receive from other groups, e.g., is any of it confidential?

Hi @enyasb, thank you for your feedback! The data that we receive from other groups indeed needs a flag because they asked us to wait till publication until they have published this data themselves.

ieacdroste commented 1 year ago

Thanks for sharing assignment 2 @ieacdroste! It looks very concise and clear - well done!

Just two questions from my side:

  • Will you also get any documentation/information about the experimental data? Or is all the information you need included within the images themselves?
  • Will you also generate your own figures? That could be seen as a new/separate dataset, along with article/chapter texts.

Thank you for your feedback @EstherPlomp! There indeed is metadata alongside the images and we create our own figures. I will add these to my data flow map

EstherPlomp commented 1 year ago

Thanks for sharing assignment 3 @ieacdroste, as well as for incorporating the feedback! It again looks very clear - well done!

Just some minor comments/thoughts from my side:

File formats

Access

Data publication

ieacdroste commented 1 year ago

Thanks @EstherPlomp for your feedback and helpful comments on Matlab and GitLab/Zenodo.

About the external programmer: This is a freelancer that helps us to implement part of the Matlab code in C++/cuda to speed up the code. In the past, we have worked with a programmer from the eScience center, but now we chose to hire a freelancer because of time constraints

msafariii commented 1 year ago

Hi @ieacdroste, your Assignment 3 appears well-defined and thoroughly explained.

I saw that your experimental microscopy data is quite extensive, totaling 10 TB in size and kind of confidential. You mentioned that you're unable to publish it until other research groups do so, but you also mentioned that it's in an open file format. This raised some confusion for me. Could you please clarify how it can be an open file format yet not allowed for publication?

ieacdroste commented 1 year ago

Thanks for you comments @msafariii. The data is saved as .tiff, which is an open file format because no commercial software is needed to read the .tiff format. Currently, the data is stored in our project storage, so it is not accessible for the public. After publication, it will be in a public data repository.

Upsiton commented 12 months ago

Hi @ieacdroste , you have a very good plan for backup and versioning of the code. As we discussed, transferring the big data stored in the U drive could be slow. You could also consider copying the frequently used data to the local drive for fast access during processing.