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Documentation for napari (other than API docs)
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Add Tracks layer tutorial #32

Open kevinyamauchi opened 3 years ago

kevinyamauchi commented 3 years ago

Once https://github.com/napari/napari/pull/1361 is merged, I think we should add a tutorial on how to construct a Tracks layer. In particular:

In this comment, @sofroniewn suggested this cell tracking dataset or an SWC file as the example data to build the tutorial around. @quantumjot may have other dataset suggestions.

kevinyamauchi commented 3 years ago

@quantumjot, I am happy to take a crack at this if you don't have time. I also think it's great if you want to take this on. Just let me know which you prefer!

quantumjot commented 3 years ago

I am happy to take a crack at this if you don't have time.

That would be great! I can provide some example track data too.

kevinyamauchi commented 3 years ago

Okay, sounds good! I will start with the "fundamentals" page first, which mostly explains the parameters, init method, etc. (example for the points layer). It would be great if you could give it a review once I have a draft together to make sure I didn't make any mistakes 😛

For the "application" page, example track data would be great! Do you have some that is publicly available somewhere already? I think ideally, people who want to follow along would be able to download the same data that is used in the example. If you don't have any you can make public at this time, we can also download some from that cell tracking dataset I linked above, so no worries!

quantumjot commented 3 years ago

Great stuff! I can add some example cell track data on github for the applications page. This could be in any format, but I guess CSV files with data/properties and graph contents might be simplest.

It's probably worth using the examples from the cell tracking dataset too, but IIRC you may need to pull out the coordinates from the segmented image data.

quantumjot commented 3 years ago

I've added some example track data here and a notebook showing how they were generated.

kevinyamauchi commented 3 years ago

Hey @quantumjot , the btrack example data you linked looks like it would work nicely for the demo! How large is the corresponding image file? I think it would be cool to include images of the cells being tracked, but I understand if it's not possible to share in a convenient way.

quantumjot commented 3 years ago

How large is the corresponding image file?

The raw image data is about 2.3Gb. I'll see if we can host at UCL.

For the application page, I wondered if we should have two example sections, e.g.:

What do you think?

kevinyamauchi commented 3 years ago

How large is the corresponding image file?

The raw image data is about 2.3Gb. I'll see if we can host at UCL.

@quantumjot , that would be great. No worries if it's too much trouble!

For the application page, I wondered if we should have two example sections, e.g.:

  • Single particle tracking. For example, I converted the trackpy tutorial to work with the Tracks layer, and made a quick notebook.
  • Single cell tracking. Here we could use the output of btrack as an example. Although, perhaps it's good to use the data from the cell tracking challenge as an example, since that contains a variety of 2D and 3D data.

I think that's a great idea! In general, I think the applications pages are the perfect place to showcase integration with other parts of the scientific python ecosystem. I also like the idea of using the btrack example since I'd love to be able to link to your arboretum repo (and paper) as an example of how people could further extend their usage of the Tracks layer.

Thanks for making/linking those notebooks. If you'd like, I can have a go at writing it up over the next couple of days and then you can review/modify?

kevinyamauchi commented 3 years ago

To be a bit more concrete, a bit more about what I think can go in each "applications" tutorial:

The trackpy example can show settings up a tracks layer without a graph. Also,

The btrack example can show using a tracks with with a graph. Also,

quantumjot commented 3 years ago

That sounds amazing @kevinyamauchi! I'm happy to help with some of this too, if it helps to divide and conquer.

kevinyamauchi commented 3 years ago

That sounds amazing @kevinyamauchi! I'm happy to help with some of this too, if it helps to divide and conquer.

That would be great! Maybe I can take the trackpy one and you can take the btrack one? Also, feel free to take it as far as you can and make a PR - I am happy to finish it up if you don't have time.

The applications pages are markdown files in this folder. The "table of contents" links are in this file. Also, the gifs, screenshots, etc. are stored in this folder.

quantumjot commented 3 years ago

I've made a start on the cell tracking application over on napari/napari.github.io#91.

GenevieveBuckley commented 2 years ago

For some more demo dataset suggestions, see https://github.com/napari/napari/issues/316#issuecomment-952642188 and https://github.com/napari/napari/issues/316#issuecomment-952639095

... and this 3D cell tracking dataset is gorgeous!

C.elegans developing embryo Waterston Lab, University of Washington, Seattle, WA, USA Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-N3DH-CE.zip✱ (3.1 GB) Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-N3DH-CE.zip (1.7 GB) Microscope: Zeiss LSM 510 Meta Objective lens: Plan-Apochromat 63x/1.4 (oil) Voxel size (microns): 0.09 x 0.09 x 1.0 Time step (min): 1 (1.5) Additional information: Nature Methods, 2008

For cell tracking, this dataset could be really interesting (there's a very speedy cell, and also a cell splitting in two). It's from this website: http://celltrackingchallenge.net/

Human hepatocarcinoma-derived cells expressing the fusion protein YFP-TIA-1 Dr. Alessia Ruggieri and Philipp Klein, Centre for Integrative Infectious Disease Research (CIID), University Hospital Heidelberg, Germany Training dataset: http://data.celltrackingchallenge.net/training-datasets/Fluo-C2DL-Huh7.zip (36 MB) Challenge dataset: http://data.celltrackingchallenge.net/challenge-datasets/Fluo-C2DL-Huh7.zip (36 MB) Microscope: Nikon Eclipse Ti2 Objective lens: CFI Plan Apo Lambda 20x/0.75 Pixel size (microns): 0.65 x 0.65 Time step (min): 15 Additional information: Cell Host & Microbe, 2012