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grp-bio-it
image-analysis-training-resources
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Commits (1)
first draft of converted DoG module
· 3d7ddb2f
Toby Hodges
authored
Jul 30, 2019
3d7ddb2f
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_modules/filter_difference_of_gaussian.md
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3d7ddb2f
---
title
:
Difference of Gaussian
layout
:
page
layout
:
module
prerequisites
:
-
TODO
objectives
:
-
TODO
motivation
:
>
TODO
concept_map
:
>
graph TD
IM("Image") --> SBl("Small blur")
IM --> LBl("Large blur")
SBl --> NF("Noise filtered")
SBl --> SBlLBl("Small blur - Large blur")
LBl --> SBlLBl
LBl --> LB("Local background")
SBlLBl -- gives --> DoG("Differece of Gaussians (DoG)")
DoG -- is related to --> LoG("Laplacian of Gaussian (LoG)")
# figure: /path/to/image.png
# figure_legend: TODO
activity_preface
:
|
- Open image: xy_8bit__two_spots_noisy_uneven_background.tif
- Appreciate that you cannot readily threshold the spots
- Compute DoG:
- Copy image and blur with a Gaussian of small sigma -> Gs
- Copy image and blur with a Gaussian of bigger sigma -> Gb
- For the official DoG: `rb = sqrt(2) * rs`
- Create `DoG = Gs - Gb`
- Appreciate that now it is possible to threshold the spots in the DoG image
activities
:
# "TODO": /path/to/activity/file.md
exercises_preface
:
>
TODO
exercises
:
# "TODO": /path/to/exercise/file.md
learn_next
:
-
TODO
external_links
:
-
"
[Wikipedia:
Difference
of
Gaussians](https://en.wikipedia.org/wiki/Difference_of_Gaussians)"
-
"
[FeatureJ:
plugins
for
feature
extraction
from
images](https://imagescience.org/meijering/software/featurej/)"
-
"
[CellProfiler
module
for
enhancing/suppressing
features
in
an
image
(Python)](https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/modules/enhanceorsuppressfeatures.py#L4)"
---
## Difference of Gaussian (DoG)
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
image -> "small blur";
image -> "large blur";
"small blur" -> "noise filtered";
"large blur" -> "local background";
"small blur" -> "small blur - large blur" -> "DoG";
"large blur" -> "small blur - large blur" -> "DoG";
"DoG" -> "Laplacian of Gaussian (LoG)" [label=" is related"];
}
'/>
### Activity: Enhance spots in noisy image with uneven background
-
Open image: xy_8bit__two_spots_noisy_uneven_background.tif
-
Appreciate that you cannot readily threshold the spots
-
Compute DoG:
-
Copy image and blur with a Gaussian of small sigma -> Gs
-
Copy image and blur with a Gaussian of bigger sigma -> Gb
-
For the official DoG:
`rb = sqrt(2) * rs`
-
Create
`DoG = Gs - Gb`
-
Appreciate that now it is possible to threshold the spots in the DoG image
### Learn more
-
https://imagescience.org/meijering/software/featurej/
-
https://en.wikipedia.org/wiki/Difference_of_Gaussians
-
https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/modules/enhanceorsuppressfeatures.py#L4