Saturday 12/08/12

11:00 A – 7:30P, 8:45P – 10:00P

Cell staining

  • label with m-HP1a -405,750 and rb-H3K27me3 -488 (top) or rb-H3K27ac -488 (bottom row)

Polytene cell staining

  • label with m-HP1a-Cy3b and rb H3K4me3 -488 or rb H3K27me3-488.
  • check staining on confocal
  • some bacteria now detectable on these sections
  • mount in prolong gold, let set O/N.

Coding /Data Analysis

  • Exploring more methods to filter out non-switching dots
    • filter_nonblinkers tries use knnsearch to find nearest neighbors as a clustering approach, and then use look at variance in distribution of frames found for dots in the cluster.
    • I think the true clustering as in (Analyze_K27me3) might work better.  Need to partition image into smaller sub-images first to keep the speed.
    • Also needs a dataset with good conventional images.  My previous investigations showed differences between conventional intensity and STORM dots robustly flags regions where weak non-blinking emitters give false signal.
  • Analyzing Pc-GFP Pc data from 04/24/12 (slide 155, stain started 4/4/12).
  • Making summary slide of cluster stats for Ajaz
  • Added new manual cell boundary selection to findclusters_percell.m  For moderate numbers of cells (~100) this is a bit tedious, but more productive than specifically tuning parameters to get only half decent segmentation.  A fast 2D clustering algorithm might work alright combined with the appropriate smoothing filter…
This entry was posted in Summaries and tagged , , . Bookmark the permalink.