Incorporate sample datasets

[gschlafly]

Users should be able to have sample datasets in order to observe the capabilities of our plugin if they do not have their own datasets handy. How these datasets can be accessed also needs to be clear to the users.

Choice of datasets

At least two sample datasets for LF Analyze and one sample dataset for Neural Net would be great. The LF Analyze datasets could be the ant leg and a simulated GUV. The Neural Net dataset could be the mouse brain.

Sample dataset components

A dataset that gets downloaded when napari-LF is installed would include the following:

LF Analyze dataset

• light field image
• radiometry image
• dark frame image
• optical parameters
• volume parameters (default)

Neural Net dataset

• light field image
• trained model

The file names and parameters can be saved in a metadata.txt file that is located inside the corresponding project folder. The LF Analyze calibration files and the set of images used to generate the Neural Net trained model are large files. So, they can be uploaded to a different repository (or cloud location) instead.

Accessing datasets

There should be a button to switch into the project directory of the sample datasets and have the sample parameters (specified by the metadata.txt file) be loaded into the fields. napari has a built-in method to open sample data by selecting File → Open Sample, which may be useful.

Additional context

LF Analyze currently has two sample datasets: the ant leg and the sea urchin. The ant leg as the benefit of being small so it can be processed quickly. The default parameters for the sea urchin dataset is incorrect. If user switches to a different project directory and then they want to look at one of the examples, they would need to know the path of the example folder, which may be something similar to the following:

C:\Users\gschl\anaconda3\envs\napari-env\Lib\site-packages\napari_lf\examples\antleg

[gschlafly]

Desired sample datasets

1. ant leg: for LF Analyze
2. simulated GUV: for LF Analyze and Neural Net
3. mouse brain: for LF Analyze and Neural Net

Include a link to the large, trained model files stored on the cloud for the GUV and mouse brain.

[gschlafly]

Also include the experimental GUV for just the LF Analyze processing!

[gschlafly]

In order to include the mouse brain example set for both LF Analyze and Neural Net, the 3D reconstruction should be similar. Moreover, the reconstruction should be similar to the confocal stack.