Dataset for Schistosoma mansoni motility and their true motility values

[lphilomena]

Hi，thanks for the nice work! I found some example data for running wrmXpress modules at https://zenodo.org/record/7116648, and ran some of them well. Could you please share the dataset for Schistosoma mansoni motility and their true motility values too? And also share the true motility values for Motility (96-well plate, individual wells) - Brugia malayi microfilaria: 20210819-p01-NJW_753, Motility (96-well plate, whole plate) - Brugia pahangi adults: 20220622-p02-KTR, and Motility (24-well plate, whole plate) - Brugia pahangi adults: 20220527-p02-KTR? Thank you very much!

[lphilomena]

Could you please explain how the true motility values are obtained?

[wheelern]

Hi @lphilomena 👋🏻

Let me find some S. mansoni motility videos and get back to you. At the time of publication they were too large for Zenodo (or my Wifi wasn't good enough - the upload failed every time I tried it), but I'm sure I can find another way to share them.

What exactly do you mean by "true motility values?" The motility is provided in the output CSV, either in raw form (without metadata joined) or tidy form (with metadata joined).

[lphilomena]

Hi @wheelern,

Thanks very much for your reply! Thanks for sharing S. mansoni motility videos.

In the S2 Fig. ((https://journals.plos.org/plosntds/article/file?type=supplementary&id=10.1371/journal.pntd.0010937.s003)Correlations between diagnostic “flow clouds” and motility measurements.), the third row denotes flow clouds and the fourth row denotes motility measurements. Could you show me how the motility values in the subimage in the fourth row are obtained? "true motility values" I mean there should be a ground truth motility value of S. mansoni video which can represent the real motility of the S. mansoni in that video.

I ran wrmXpress successfully with the example data "20210917-p15-NJW_913" and "20220527-p02-KTR", and got output CSV including "worm_area" and "optical_flow". There is no motility in the output CSV. Do you get the motility by dividing "optical_flow" with "worm_area" ?

[wheelern]

Optical flow is what we use as the measure of motility. In some cases, like when there are multiple worms per well, we will divide optical flow by the worm area; this normalizes the gross motility to the number of worms in the video.

I am still working on getting adult S. mansoni videos. Will keep you updated.

[wheelern]

@lphilomena - here is a link to a shared folder that includes an AVI of a video of a 96-well plate with S. mansoni adults and a YAML to use for running wrmXpress. Note that this is one video with multiple wells, so wrmXpress will split each well into its own video an analyze it.

[lphilomena]

Hi，Dr. Wheeler，

Thank you very much for sharing the S.mansoni video data. I tried the data with the YAML file. The result seems not as supposed. I will run it again. It's very kind of you to reply.

Best regards

Liu Ping

Nic Wheeler @.***> 于2023年10月7日周六 02:25写道：

@lphilomena https://github.com/lphilomena - here https://universityofwieauclaire-my.sharepoint.com/:u:/g/personal/wheelenj_uwec_edu/EVhuE8XN_6xDuCcc8WQ5TXUBa2MKt2FB82fkyxmv7Q7osg?e=0GFJFk is a link to a shared folder that includes an AVI of a video of a 96-well plate with S. mansoni adults and a YAML to use for running wrmXpress. Note that this is one video with multiple wells, so wrmXpress will split each well into its own video an analyze it.

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