review April 15

[iamciera]

Overall Awesome. Let me think a little more about structuring the posts and output, but I think it is super close to publication.

Morpho_1

• This line doesn't work %matplotlib inline plots.style.use('fivethirtyeight')

• "So we see that 368 of the fishes scanned by the Bruker Skyscan 1173 have an unknown genus (or at least the value of the fish's genus was not recorded in the excel sheet provided from the data--perhaps an issue with the scope/completeness of the data?)" Maybe we can contact them to make sure.

• Maybe we can go a bit more into what "caraprotcutus" and why it is so over-represented? Contact them.

• blob.png image is missing

  • This first part is great! I love that you are explaining how to use the data without knowing Python. I think we should make this explicit in the front and have this post released at the same time as the other. Almost as a supplemental.

  Morpho_2

  • We def. cite morpho_1

  • We need to find a spot for the Morphosource_no_specimen_M16076/no_specimen_M16076-29919_no_specimen/Info.jpg data. And all the links on how and where you got the data. Just puyt another link closer to when you read in the data.

  • I think we should talk a bit about what the options are for visualizing 3D data. -Ciera.

  • We should talk a bit about openCV.

  • AND be explicit about what thresholding is.

  • Maybe put thresholding at the bottom? And do with tooth? I think it would be cool to do the thresholding with the teeth. I think if you isolated the teeth we could morphometric analysis on it pretty easy in R. Here is a tutorial I made https://iamciera.github.io/rladies_copenhagen/html/Copenhagen_Raldies_part1.html.

  • Can we find the citation for the teeth data? Maybe we can read the paper and if they didn't already do this, it could be very interesting.

[satang1]

morpho1: I should've addressed most if not all the items for morpho1, but let me know if there are still any issues with the codes or descriptions/instructions.

morpho2: I wanted to do the thresholding on the tooth, which might produce better results than the fish data, but unlike the fish data, when I downloaded the tooth data, they didn't provide a 2D side view of the reconstructed image. So instead, I did a further example on a photo I found online. I'll look for ways to incorporate the tooth data, but for now, let me know what you think about the changes, especially the descriptions on thresholding which I've changed/added to.

I've also linked the tooth data: https://www.morphosource.org/Detail/ProjectDetail/Show/project_id/73