Matt:LabNotes/2014-2-19

From ZhangLabWiki
Jump to navigation Jump to search

Modifying BF Confocal Images[edit]

  • Right now the BF image is mostly gray and doesn't look good (is too bright) when overlayed onto rolony images with ImageJ
  • Going to use GIMP to modify BF image

Procedure[edit]

  1. Open BF image in GIMP
  2. Adjust (increase) Contrast to improve visibility of cell edges
    • Can also play with brightness
  3. Blur/Erode
  4. Edge-detect
  5. Thresholding
  1. Gaussian Blur with radius 3
  2. Edge Detect Difference of Guardians Radius 1: 1.0 Radius 2: 16.0
    • Don't Invert
  3. Threshold so as much black as possible without losing any cells
  4. Brightness: -83
  5. Open secondary rolony polished bw images as layers
  6. Change mode to RGB, switch black bg to alpha (transparent), and add color to each layer of rolonies
  7. Flatten image and save


Results[edit]

Pos1: File:NCIH1975 Pos1 Complete.png

Pos2: File:NCIH1975 Pos2 Complete.png

Pos3: File:NCIH1975 Pos3 Complete.png