Welcome to plenoptic tutorial, CSHL Vision Course 2024#

This site hosts the example notebook used for the plenoptic tutorial given at the Cold Spring Harbor Labs Computational Neuroscience: Vision course in July 2024. This one-hour(ish) tutorial aims to introduce the basics of using plenoptic in order to better understand computational visual models with simple examples. We hope to explain not just plenoptic’s syntax but also the type of reasoning that it facilitates.

The presentation I gave at the beginning of this session can be found here.

This website contains two versions of the notebook we’ll use today: with and without explanatory text. Today you’ll run the version without explanatory text, which contains cells of code, while listening to my description. If later you wish to revisit this material, the version with explanatory text should help you.

You may also find the glossary useful as you go through the notebook.

You can also follow the setup instructions here to download these notebooks and run them locally, but to avoid potential installation issues in this brief period of time, we’ll use binder instead. Click on the launch binder badge on the upper left sidebar, which will then prompt you to login. Use the google account that you gave to the class organizers; if you get a 403 forbidden error or would like to use a different account, let me know so that I can give it permission. The binder instance provides a GPU with the environment necessary to run the notebook. See the section below for more details on the binder, including some important usage notes.

Setup#

Note

If you would just like to install plenoptic to use it locally, follow our installation instructions. This tutorial contains some extra packages for this specific build.

While we’ll use the binder during this tutorial, if you’d like to run the notebooks locally, you’ll need to set up a local environment. To do so:

Make sure you have git installed. It is installed by default on most Mac and Linux machines, but you may need to install it if you are on Windows. These instructions should help.

Clone the github repo for this tutorial:

git clone https://github.com/plenoptic-org/plenoptic-cshl-vision-2024.git

Create a new python 3.11 virtual environment. If you do not have a preferred way of managing your python virtual environments, we recommend miniconda. After installing it (if you have not done so already), run
```
conda create --name cshl2024 pip python=3.11
```
Activate your new environment:
```
conda activate cshl2024
```
Navigate to the cloned github repo and install the required dependencies.
```
cd plenoptic-cshl-vision-2024
pip install -r requirements.txt
```
Important

You will also need ffmpeg installed in order to view the videos in the notebook. This is likely installed on your system already if you are on Linux or Mac (run ffmpeg in your command line to check). If not, you can install it via conda: conda install -c conda-forge ffmpeg or see their install instructions.

If you have ffmpeg installed and are still having issues, try running conda update ffmpeg.
Run the setup script to prepare the notebook:
```
python scripts/setup.py
```
Important

It’s possible this step will fail (especially if you are on Windows). If so, go to the notebook on this site and download it manually.
Open up jupyter, then double-click on the introduction-stripped.ipynb notebook:
```
jupyter lab
```

Binder#

Some usage notes:

You are only allowed to have a single binder instance running at a time, so if you get the “already have an instance running error”, go to the binderhub page (or click on “check your currently running servers” on the right of the page) to join your running instance.
If you lose connection halfway through the workshop, go to the binderhub page to join your running instance rather than restarting the image.
This is important because if you restart the image, you will lose all data and progress.
The binder will be shutdown automatically after 1 day of inactivity or 7 days of total usage. Data will not persist after the binder instance shuts down, so please download any notebooks you want to keep.
I will destroy this instance in 2 weeks, so that you can use it to play around during the course. You can download your notebooks to keep them after the fact. If you do so, see the setup instructions for how to create the environment for running them locally, and let me know if you have any problems!

Contents#

See description above for an explanation of the difference between these two notebooks.