Timelapse microscopy example #452
Conversation
droumis
commented
Nov 21, 2024
droumis
commented
|
Your changes were successfully integrated in the dev site, make sure to review the pages of the projects you touched before merging this PR. |
|
The final app is too wide for the website... but I'm tempted to not change it as I want to keep the frame dimensions true to the image. Besides, you can scroll to the right to see the rest and it's not like the app is functional on the website anyways, and there's a static snapshot of what the full thing looks like right above this cell. If someone is running this in a notebook, they will be able to adjust the window size to see the full app.. 
|
There was a problem hiding this comment.
Another super solid example! I've left suggestions part of the review. My main feedback is that the annotating app still feels experimental (more than what you shared in your previous example), it's a feature that needs users and their feedback to mature. Hopefully this example will help with that!
| description: Display and annotate time-lapse microscopy in Neuroscience | ||
|
|
||
| examples_config: | ||
| created: 2024-11-21 |
There was a problem hiding this comment.
Reminder to update it before merging.
| "id": "f0de8be5-81d9-4755-b7aa-afbacd5166e3", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "For example, a dynamic process of interest could be [neural action potentials](https://en.wikipedia.org/wiki/Action_potential), and the data might come from a [miniature microscope](http://miniscope.org/)(**see image in this notebook's header**) that captures the change in fluorescence of special proteins caused by electrochemical fluctuations indicative of neuronal activity. These video-like datasets often contain many more frames in the 'Time' dimension compared to the number of pixels in the height or width of each frame.\n" |
There was a problem hiding this comment.
| "For example, a dynamic process of interest could be [neural action potentials](https://en.wikipedia.org/wiki/Action_potential), and the data might come from a [miniature microscope](http://miniscope.org/)(**see image in this notebook's header**) that captures the change in fluorescence of special proteins caused by electrochemical fluctuations indicative of neuronal activity. These video-like datasets often contain many more frames in the 'Time' dimension compared to the number of pixels in the height or width of each frame.\n" | |
| "For example, a dynamic process of interest could be [neural action potentials](https://en.wikipedia.org/wiki/Action_potential), and the data might come from a [miniature microscope](http://miniscope.org/) (**see image in this notebook's header**) that captures the change in fluorescence of special proteins caused by electrochemical fluctuations indicative of neuronal activity. These video-like datasets often contain many more frames in the 'Time' dimension compared to the number of pixels in the height or width of each frame.\n" |
| "### App Versions\n", | ||
| "We will build three different visualization approaches to cater to different use cases:\n", | ||
| "\n", | ||
| "1. **Basic Viewer:** A one-line application using `hvPlot` for quick visualization of the image stack.\n", |
There was a problem hiding this comment.
| "1. **Basic Viewer:** A one-line application using `hvPlot` for quick visualization of the image stack.\n", | |
| "1. **Basic Viewer:** A one-line application using [hvPlot](https://hvplot.holoviz.org/) for quick visualization of the image stack.\n", |
| "We will build three different visualization approaches to cater to different use cases:\n", | ||
| "\n", | ||
| "1. **Basic Viewer:** A one-line application using `hvPlot` for quick visualization of the image stack.\n", | ||
| "2. **Intermediate Viewer with Side Views:** Uses `HoloViews` for additional interactive elements, scalebars, and linked side views, aiding better navigation of the image stack and identification of regions of interest.\n", |
There was a problem hiding this comment.
| "2. **Intermediate Viewer with Side Views:** Uses `HoloViews` for additional interactive elements, scalebars, and linked side views, aiding better navigation of the image stack and identification of regions of interest.\n", | |
| "2. **Intermediate Viewer with Side Views:** Uses [HoloViews](https://holoviews.org/) for additional interactive elements, scalebars, and linked side views, aiding better navigation of the image stack and identification of regions of interest.\n", |
| "\n", | ||
| "1. **Basic Viewer:** A one-line application using `hvPlot` for quick visualization of the image stack.\n", | ||
| "2. **Intermediate Viewer with Side Views:** Uses `HoloViews` for additional interactive elements, scalebars, and linked side views, aiding better navigation of the image stack and identification of regions of interest.\n", | ||
| "3. **Advanced Viewer with Annotations and Linked Timeseries:** Building from the intermediate `HoloViews` viewer, this version adds annotation capabilities using `HoloNote`, allowing for interactive spatial annotations with linked timeseries.\n", |
There was a problem hiding this comment.
| "3. **Advanced Viewer with Annotations and Linked Timeseries:** Building from the intermediate `HoloViews` viewer, this version adds annotation capabilities using `HoloNote`, allowing for interactive spatial annotations with linked timeseries.\n", | |
| "3. **Advanced Viewer with Annotations and Linked Timeseries:** Building from the intermediate `HoloViews` viewer, this version adds annotation capabilities using [HoloNote](https://holonote.holoviz.org/), allowing for interactive spatial annotations with linked timeseries.\n", |
| "source": [ | ||
| "### Working with Annotations\n", | ||
| "\n", | ||
| "How to add new annotations: \n", |
There was a problem hiding this comment.
You could also remind the reader or let them know that there's a video that shows how it's done, once watched it all becomes much easier as the UX of HoloNote isn't super intuitive.
| "cell_type": "markdown", | ||
| "id": "c8d52e0c-eac2-429d-8658-f8ad17c2cfb1", | ||
| "metadata": {}, | ||
| "source": [ |
There was a problem hiding this comment.
As done before, it'd be nice to show the end state of the app here, so the reader can better approach where this is going.
| "id": "c8d52e0c-eac2-429d-8658-f8ad17c2cfb1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "In the final version, we'll add annotation capabilities using `HoloNote` and link these annotations to timeseries plots of mean intensity over time.\n" |
There was a problem hiding this comment.
I missed a little bit of neurosciency narrative here (even if I don't necessarily understand it!), what are we annotating and why?
| " tools=['hover', 'crosshair'],\n", | ||
| " toolbar='right',\n", | ||
| " apply_hard_bounds=True,\n", | ||
| " scalebar=True,\n", |
There was a problem hiding this comment.
There's no scalebar displayed at all in fact? Bug maybe?
There was a problem hiding this comment.
Ok the test data size is slightly more than 4MB. I guess that's fine but we have to be careful with the size of these files (all files in general), as test data files for previous projects were smaller.
|
Your changes were successfully integrated in the dev site, make sure to review the pages of the projects you touched before merging this PR. |
