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dcluet
Lipid_Droplets
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63984ef0
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63984ef0
authored
Sep 26, 2018
by
dcluet
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@@ -201,19 +201,22 @@ For some labeling with small and extremely bright noise, the **enhance signal**
**Research Engine**
===
|
|
**ORIGINAL PICTURE**
||
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**ORIGINAL PICTURE**
||
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|:------------------:|:---------------------:|:---------------------:|
||!
[
Original Picture
](
doc/Original_Picture.jpg
)
||
|!
[
Original Picture
](
doc/Original_Picture.jpg
)
|||
|First the tissue is detected on all selected slices.| | |
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**TISSUE DETECTION**
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**PARTICLES DETECTION iteration 1**
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**PARTICLES DETECTION iteration 2**
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|
`run("Gaussian Blur...", "sigma=20 slice");`
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`run("Gaussian Blur...", "sigma=1 stack");`
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`run("Gaussian Blur...", "sigma=1 stack");`
|
|!
[
Step 1
](
doc/Tissue1.jpg
)
|!
[
Step 1
](
doc/Iteration1.jpg
)
|!
[
Step 1
](
doc/Iteration1-2.jpg
)
|
||
`run("Maximum...", "radius=5 stack");`
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`run("Maximum...", "radius=5 stack");`
|
|
|!
[
Step 2
](
doc/Iteration2.jpg
)
|!
[
Step 2
](
doc/Iteration2-2.jpg
)
|
|
`
setAutoThreshold("Huang dark
");`
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`setAutoThreshold("MaxEntropy dark");`
|
`setAutoThreshold("MaxEntropy dark");`
|
|!
[
Step
2
](
doc/Tissue
2
.jpg
)
|!
[
Step 3
](
doc/Iteration3.jpg
)
|!
[
Step 3
](
doc/Iteration3-2.jpg
)
|
|
`run("Analyze Particles...", "size=100000-Infinity pixel show=Nothing add slice");`
|
`run("Analyze Particles...", "size="+ 1 +"-"+SizeMax+" add slice");`
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`run("Analyze Particles...", "size="+ 1 +"-"+SizeMax+" add slice");`
|
|
!
[
Step 3
](
doc/Tissue3.jpg
)
|!
[
Step 4
](
doc/Iteration4.jpg
)
|!
[
Step 4
](
doc/Iteration4-2.jpg
)
|
|
**This shape is used to characterize the tissue-embed particles.**
|
**Removal of all unwanted particles.**
|
**Removal of all unwanted particles.**
|
|
`setAutoThreshold("Huang dark");`
|
`run("Maximum...", "radius=5 stack");`
|
`run("Maximum...", "radius=5 stack");`
|
|
!
[
Step 2
](
doc/Tissue2.jpg
)
|!
[
Step 2
](
doc/Iteration2.jpg
)
|!
[
Step 2
](
doc/Iteration2-2.jpg
)
|
|
`
run("Analyze Particles...", "size=100000-Infinity pixel show=Nothing add slice
");`
|
`setAutoThreshold("MaxEntropy dark");`
|
`setAutoThreshold("MaxEntropy dark");`
|
|!
[
Step
3
](
doc/Tissue
3
.jpg
)
|!
[
Step 3
](
doc/Iteration3.jpg
)
|!
[
Step 3
](
doc/Iteration3-2.jpg
)
|
|
**This shape is used to characterize the<br>tissue-embed particles.**
|
`run("Analyze Particles...", "size="+ 1 +"-"+SizeMax+" add slice");`
|
`run("Analyze Particles...", "size="+ 1 +"-"+SizeMax+" add slice");`
|
|
**Continue with particles detection ->**
|!
[
Step 4
](
doc/Iteration4.jpg
)
|!
[
Step 4
](
doc/Iteration4-2.jpg
)
|
||
**Removal of all unwanted particles.**
|
**Removal of all unwanted particles.**
|
| |
**When several slices, removal of duplicates of the same particle.**
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**When several slices, removal of duplicates of the same particle.**
|
||
**RESULT ON 5 SLICES**
||
||!
[
Result
](
doc/Result.jpg
)
||
| |
**Removal of all particles on the Original Picture**
| |
||
**Continue to iteration 2 ->**
| |
|||
**RESULT ON 5 SLICES**
|
|||!
[
Result
](
doc/Result.jpg
)
|
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