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 m (→Results) |
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(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]
- Open BF image in GIMP
- Adjust (increase) Contrast to improve visibility of cell edges
- 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
Results[edit]
Pos1: File:NCIH1975 Pos1 Complete.png