psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring.

Over the past century, multichannel fluorescence imaging has been pivotal in myriad scientific breakthroughs by enabling the spatial visualization of proteins within a biological sample. With the shift to digital methods and visualization software, experts can now flexibly pseudocolor and combine image channels, each corresponding to a different protein, to explore their spatial relationships. We thus propose psudo, an interactive system that allows users to create optimal color palettes for multichannel spatial data. In psudo, a novel optimization method generates palettes that maximize the perceptual differences between channels while mitigating confusing color blending in overlapping channels. We integrate this method into a system that allows users to explore multi-channel image data and compare and evaluate color palettes for their data. An interactive lensing approach provides on-demand feedback on channel overlap and a color confusion metric while giving context to the underlying channel values. Color palettes can be applied globally or, using the lens, to local regions of interest. We evaluate our palette optimization approach using three graphical perception tasks in a crowdsourced user study with 150 participants, showing that users are more accurate at discerning and comparing the underlying data using our approach. Additionally, we showcase psudo in a case study exploring the complex immune responses in cancer tissue data with a biologist.

A wavelet-like filter based on neuron action potentials for analysis of human scalp electroencephalographs.

This paper describes the development and testing of a wavelet-like filter, named the SNAP, created from a neural activity simulation and used, in place of a wavelet, in a wavelet transform for improving EEG wavelet analysis, intended for brain-computer interfaces. The hypothesis is that an optimal wavelet can be approximated by deriving it from underlying components of the EEG. The SNAP was compared to standard wavelets by measuring Support Vector Machine-based EEG classification accuracy when using different wavelets/filters for EEG analysis. When classifying P300 evoked potentials, the error, as a function of the wavelet/filter used, ranged from 6.92% to 11.99%, almost twofold. Classification using the SNAP was more accurate than that with any of the six standard wavelets tested. Similarly, when differentiating between preparation for left- or right-hand movements, classification using the SNAP was more accurate (10.03% error) than for four out of five of the standard wavelets (9.54% to 12.00% error) and internationally competitive (7% error) on the 2001 NIPS competition test set. Phenomena shown only in maps of discriminatory EEG activity may explain why the SNAP appears to have promise for improving EEG wavelet analysis. It represents the initial exploration of a potential family of EEG-specific wavelets.

Reducing the number of channels for an ambulatory patient-specific EEG-based epileptic seizure detector by applying recursive feature elimination.

We are building an ambulatory version of a patient-specific epileptic seizure detector based on scalp EEG signals. Since patients have to wear the electrodes all the time, it is desirable to use the minimum number of electrodes needed to achieve good performance. In this paper, we describe a method that uses recursive feature elimination (RFE) to design detectors that use small numbers of electrodes. We also present results that indicate that the appropriate number of electrodes varies across patients. It is frequently the case that a surprisingly small number of electrodes, sometimes as few as two, suffices to construct a detector with expected performance comparable to that of detectors that use a full twenty-one-channel montage.