Papers to turn into tutorials / case studies

[jni]

I'm creating this issue as an external to-do for possible papers on which to build tutorials / examples.

• [ ] 3D structural evolution of cuttlefish shell from embryo to adult: https://royalsocietypublishing.org/doi/10.1098/rsif.2019.0175 This is a very nice example because they use thresholding and label to produce a histogram of connectivity, sizes, and tortuosity of "pillars" in the shells. I've asked the corresponding author for data.
• [ ] Single cell imaging of nuclear architecture changes: 10.3389/fcell.2019.00141. CC @jmetz — can we haz some data and scripts??? =) Very cool paper!
• [ ] Segmentation of nuclear tracks in microscopic images: 10.1002/jemt.23336.
• [ ] (This one is just super badass:) Searching for Viking Age Fortresses with Automatic Landscape Classification and Feature Detection https://www.mdpi.com/2072-4292/11/16/1881
• [ ] Tracking fungal growth https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3004-1 Code here https://github.com/modsim/mycelyso data here: https://doi.org/10.5281/zenodo.376281
• [ ] Tracking mouse paws in 3D using scipy and scikit-image (among others): https://link.springer.com/article/10.1186/s13640-019-0477-9 (includes code on github!)
• [ ] "The first day of the cenozoan" uses drill core data to infer what happened in the moments after the asteroid that killed the dinosaurs hit the Earth. https://www.pnas.org/content/early/2019/09/04/1909479116 data here: http://iodp.pangaea.de/front_content.php?idcat=601(click on "data" under "expedition 364" on the bottom left). Very interesting stuff, but the data are absolutely huge. May be more appropriate for a book chapter than a tutorial! I've asked the corresponding author for code examples. Edit: have tentatively arranged to meet the lead author at SciPy 2020! :tada:
• [ ] https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008458 some very nice images -> plots examples here!

[sciunto]

great idea!

[alexdesiqueira]

Awesome @jni! There are lots of interesting use cases around, like this, on segmentation of nuclear tracks in microscopic images :smile:

[jni]

@alexandrejaguar can you edit my initial post with a tick box for that paper? =)

[jmetz]

Sounds like a great idea @jni :+1: - though for that particular paper the main segmentation, which can be seen in the figures, was done by a colleague. My contribution was a the microfluidic cell deformation component which isn't shown in the main figures. Nonetheless I can contact the person in question and ask him for his code.

However, this project might be a better candidate, and shows a fairly common biology image analysis task - segmenting red blood cells. I've already written to the PI on this project to ask if they are happy us using the data for this purpose. I'll update once they reply!

[jmetz]

On as side-note, we might want to also consider simply using an online databank of biological images, such as https://idr.openmicroscopy.org/ or http://cellimagelibrary.org/?

[jmetz]

OK so my collaborator was ok with this; sample input files are here (as zip of jpegs): images.zip which produces the following result when analyzed:

Is that the kinda thing you were thinking?

PS the original data is in uncompressed (or at least un-lossy compressed) tiff format, but couldn't attach that here.