Multi-electrode array recordings

A few posts describing parts of the multi-electrode array setup I've been working on in Tom Baden's lab.

Light path alignment: Align and snapshot the light path. Using a Raspberry Pi camera to capture alignment images and calculate a homography and intensity map for the light path.
Retina press: 3D-printed cap for improving contact of retinal tissue with a multi-electrode array.
Messages on the trigger line: Encode utf-8 messages on the trigger channel.

light path — Dual-projector retinal stimulation setup.

Edge Selection for the Effective use of Piecewise-Constant Distributions as Neural Network Outputs for Event Prediction (preprint)

We study the output representation of a neural network used for next event prediction. We propose partitioning the time axis into a fixed set of intervals and having a neural network output a categorical distribution over them, which we map to a (mostly) piecewise-constant probability density. We present an optimization procedure that selects interval edges in order to maximize data likelihood under the representation. The representation is well suited to processes whose inter-event distribution is a mixture of smooth and sharply peaked components—a pattern we find common in event data recorded from real-world processes. [arxiv page] [arxiv pdf]

On shifted noise for 2D receptive field estimation

An empirical test of shifted noise for estimating 2D receptive fields. Results support the idea that shifted noise cannot be thought of as a drop-in replacement for vanilla checkerboard noise. more

Four ways (two bad, two good) of calculating 2D receptive fields from spike snippets

Collecting a window of stimulus data around every spike in a recording of neurons is a common analysis step in neuroscience. The mean of these snippets is termed the spike-triggered average (STA). If you want to collapse this down to 2D, there are a few options. I've seen people use the variance of the snippets, which I think is not a good approach. A better approach is to rephrase the problem in terms of likelihood. more

Frame registration and cell detection for 2-photon recordings

3 blob detection algorithms applied to cell detection in a 2-photon recording

I worked on a project that involved carrying out 2-photon recording of the tectum of a zebrafish larva. For a single larva, we recorded 14 recordings, each 15 minutes long followed by an approximately 2-minute gap. The larva moved around, especially at the beginning, and to extract cell traces, we first needed a way to align frames and detect cells within and across recordings. more

Robust learning rate finder with Kalman smoothing

Kalman smoothing can be applied to the learning rate range test to produce smooth learning rate curves from which a learning rate can be chosen. more

Spike distance function as a learning objective for spike prediction

A learning objective that embraces the nature of spikes (or any other events): discrete points in continuous time. This learning objective allows models to predict the timing of spikes with both high and low temporal precision. For comparison, predictions when using the Poisson learning objective are also shown above. [paper page] [paper pdf]

Neural networks and color

This is a project to see if anything can be learnt by drawing parallels between human color perception and neural networks trained for vision tasks. more

Motivating ELBO from importance sampling

The evidence lower bound expression appears naturally when you try to sample the posterior distribution with an approximate distribution. I think this way of arriving at the evidence lower bound is more intuitive and reveals more about why concessions are being made. more

Inside neural network training

Some videos showing how weights, activations and gradients change at every step as a network is trained. more

Gen art

Testing out some generative networks.

Reflectance spectra

Reflectance spectra of various flowers, leaves and other objects. more

Anki notes

I've exported some of my Anki decks. Most of the content is on the answer side of each card. If you aren't using Anki, I invite you to read Michael Nielsen's argument for it.

2021's Summer of Math Exposition

The following are some posts made for 3Blue1Brown's Summer of Math Exposition. They are attempts to make clear and memorable math explainers for a wide audience.

Kevin Doran