Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization
Fig 5
Validating photocurrent subtraction with simulated mapping experiments.
a, We simulated complete circuit mapping experiments in which stimulating some cells (green) evoked direct photocurrent. We then used a connectivity inference pipeline to assess how photocurrent subtraction affected connectivity inference. b, Scatterplots of inferred vs. true weights before (left panel) and after (center panel) photocurrent subtraction. Vertical axis shows estimated weight, horizontal axis shows true weight. After subtraction, the photocurrent-inducing cells (green) are pushed closer to the identity line, while the non-photocurrent-inducing connections (purple) are largely unaffected. c, False positive rate as a function of the number of cells which induce direct photocurrents before (orange) and after (blue) subtraction. d, Traces from an example false positive in which residual current after subtraction caused us to falsely infer a connection. This typically occured due to residual photocurrent from prior trials. e, Schematic of low-latency PSCs, which can appear as scaled copies of one another when they are driven reliably. f, Example of over-subtraction that can occur in rare instances of reliable low-latency PSCs. g, We swept the minimum PSC latency used in a simulated experiment, and found that false negatives caused by PhoRC were most prevalent at very low latencies. However, even in this case they occurred rarely.