Marius Pachitariu

Both of those will work, but I would recommend merging into larger tiffs for processing speed and for generally requiring fewer parameter adjustments for registration. Yes, you would have 200...

Hi, I think it's probably the type of data. We are aware of registration issues with 1P miniscope data and are working to fix them, but we haven't really been...

Also like the Python version, the binning should be dependent on the sensor timescale.

10 tiffs please. On Wed, Oct 17, 2018, 3:26 PM Chia-Jung Chang wrote: > Oh, then do I need to split file into 13476 tiffs (cuz 13476 frames)? Or >...

It means the number of images. It will automatically take an equal number of frames from each tiff, for a total of approximately 500 (500 * ceil(500/ntiffs).

Are you working with the raw fluorescence or the spike deconvolved data? Baseline subtraction is only done prior to spike deconvolution (and never saved). If you would like the raw...

GCaMP expression in most cells has very low baselines, so they can have high SNR. As such, the baseline can sometimes be noisily estimated as 0, or below 0 and...

Yes. On Wed, Oct 17, 2018, 3:54 PM Chia-Jung Chang wrote: > Oh I see if I understand it correctly: If I have 10 tiffs in total, ntiffs > =...

The optimization stops when it finds fewer ROIs than a certain percentage of the first pass. This percentage was set to 1/20 by default. I have now increased it to...

There is no such limit, but you might have problems with