Forum - Issues with alignment

From UCLA Miniscope
Jump to: navigation, search
Overview > Miniscope Discussion > Data Analysis > Issues with alignment Write a reply

I have been trying to process some of my recordings, but it seems that the alignment causes more harm than good, when there is no clear landmark visible. I tried it with the Subiculum example data set and I have a similar issue. If one calculates the max projection before and after alignment, there are extra "noise" bright spots that pop-up for the aligned case.

From what I understand, the idea is that you are supposed to use as ROI an area with some visible landmark (e.g. vessels) but ideally no cells and no dust/spots.

Has anybody experienced something similar? Any solutions/ideas?

Posted by Nikolas on 25 June 2016 at 15:21.

Hi Nikolas,

Alignment relies on stable physical features that remain visible across the entire recording. Without clear landmarks alignment can be difficult. Below are a few suggestions concerning your ROI placement and size:

  • Select an ROI roughly square and about 1/6th the total size of the frame.
  • Avoid areas with any dirt/dust.
  • Avoid placing the ROI near the edge of the frame.
Posted by DAharoni (administrator) on 5 July 2016 at 17:16.