"ground truth" discussion

[codeneuro]

"ground truth" discussion

[agiovann]

Very good point. I would say it is also necessary to inspect a down-sampled and zero-mean version of the movie to be sure that spikes are not missed and/or that overlapping neurons are properly segmented.

cc @marius10p @agiovann @epnev @Selmaan @aaronkerlin @sofroniewn @svoboda314 @boazmohar @syncrostone

[sofroniewn]

@agiovann agreed - a great way to draw rois would be to have a mode where such a movie could be made to play in loop in the background as you are drawing on top of it

[Selmaan]

I'd agree with the idea about actually playing the (heavily temporally down-sampled) movie in the background, or some other means to check hand circling against the timeseries data. I don't think the mean or a local correlation image are a replacement for this if we want ground truth.

The ROIs will probably have some relatively inactive neurons selected because of a mean image, and active neurons not visible in the mean image. It would be useful in evaluating an algorithm's performance to do some minimal processing of the traces (e.g. %frames above 1 dF/F) to classify cells as active or inactive for this purpose.

[freeman-lab]

@Selmaan great point, if we do this redo of the ground truth, we could compute some measure of activity as you suggest, and then add a toggle for two versions of the results table, one for all neurons, and one for all neurons with activity above some threshold, @marius10p had suggested something similar.

[marius10p]

@freeman-lab sounds like a great plan to me, and definitely worth it for understanding the behavior of the algorithms. It would also allow you to compare the algorithms to inter-human agreement, which is useful information.

Not sure how you compute the local correlation map, but we find it useful to highpass filter the images at ~50um (like a background subtraction), and bandpass filter the timecourses of each pixel between 0.1 and 2 Hz (or something like that).