Matt:LabNotes/2014-2-19: Difference between revisions

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>Mzcai
(Created page with "==Modifying BF Confocal Images== *Right now the BF image is mostly gray and doesn't look good when overlayed onto rolony images with ImageJ *Going to use GIMP to modify BF ima...")
 
>Mzcai
 
(3 intermediate revisions by the same user not shown)
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==Modifying BF Confocal Images==
==Modifying BF Confocal Images==
*Right now the BF image is mostly gray and doesn't look good when overlayed onto rolony images with ImageJ
*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
*Going to use GIMP to modify BF image


Line 7: Line 7:
#Adjust (increase) Contrast to improve visibility of cell edges
#Adjust (increase) Contrast to improve visibility of cell edges
#*Can also play with brightness
#*Can also play with brightness
#
#Blur/Erode
#Edge-detect
#Thresholding
 
#Gaussian Blur with radius 3
#Edge Detect Difference of Guardians Radius 1: 1.0 Radius 2: 16.0
#*Don't Invert
#Threshold so as much black as possible without losing any cells
#Brightness: -83
#Open secondary rolony polished bw images as layers
#Change mode to RGB, switch black bg to alpha (transparent), and add color to each layer of rolonies
#Flatten image and save
 
<!--
#Adjust (increase) Contrast to improve visibility of cell edges
#*Can also play with brightness
#Blur/Erode
#Edge-detect
#Thresholding
 
--first time--
#Adjust brightness and contrast
#Invert
#Select left and threshold
#Select invert and threshold-->
 
===Results===
Pos1: [[File:NCIH1975_Pos1_Complete.png | 450px]]<br>
 
Pos2: [[File:NCIH1975_Pos2_Complete.png | 450px]]<br>
 
Pos3: [[File:NCIH1975_Pos3_Complete.png | 450px]]<br>

Latest revision as of 07:02, 20 February 2014

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