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image-analysis-training-resources
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grp-bio-it
image-analysis-training-resources
Commits
ec75a05b
Commit
ec75a05b
authored
Apr 02, 2019
by
Christian Tischer
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EMBL course
parent
1adbab06
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workshops/bioimage-analysis-fundamentals.md
workshops/bioimage-analysis-fundamentals.md
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workshops/bioimage-analysis-fundamentals.md
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ec75a05b
...
@@ -12,8 +12,6 @@
...
@@ -12,8 +12,6 @@
indices -> calibration;
indices -> calibration;
calibration -> coordinates;
calibration -> coordinates;
image -> calibration
[
label=" can have"
]
;
image -> calibration
[
label=" can have"
]
;
image -> data_type;
data_type -> value
[
label=" restricts"
]
;
pixel -> voxel
[
label=" 3D"
]
;
pixel -> voxel
[
label=" 3D"
]
;
}
}
'/>
'/>
...
@@ -21,12 +19,9 @@
...
@@ -21,12 +19,9 @@
### Activity
### Activity
-
Open image:
*_8bit_*
-
Open image:
*_8bit_*
-
Explore
pixel values and pixels
indices
-
Explore
different ways to inspect pixel values and
indices
-
Add image calibration
-
Add image calibration
-
Explore pixel coordinates
-
Check where the calibration is visible
-
Check whether the sofware changed indices to coordinates
-
Open image:
*_float_*
-
Explore pixel values
### Formative assessment
### Formative assessment
...
@@ -36,8 +31,6 @@ True or false?
...
@@ -36,8 +31,6 @@ True or false?
-
Changing the image calibration changes the pixel values.
-
Changing the image calibration changes the pixel values.
-
Pixel coordinates depend on image calibration.
-
Pixel coordinates depend on image calibration.
-
Pixel indices are always positive integer values.
-
Pixel indices are always positive integer values.
-
Image data type affects the possible range of pixel coordinates.
-
A pixel can take any value.
-
The lowest pixel index of a 2D image always is
`[1,1]`
.
-
The lowest pixel index of a 2D image always is
`[1,1]`
.
## Image display
## Image display
...
@@ -83,16 +76,17 @@ decrease, larger_than, increase, smaller_than
...
@@ -83,16 +76,17 @@ decrease, larger_than, increase, smaller_than
<img src='https://g.gravizo.com/svg?
<img src='https://g.gravizo.com/svg?
digraph G {
digraph G {
shift
[
fontcolor=white,color=white
]
;
shift
[
fontcolor=white,color=white
]
;
"image math" -> "pixel_values"
[
label=" changes"
]
;
"data type" -> image;
"image math" -> "pixel data type"
[
label=" does not change"
]
;
image -> "pixel values";
"pixel data type" -> "8-bit unsigned integer";
"image math" -> "pixel values"
[
label=" changes"
]
;
"image math" -> "data type"
[
label=" doesn't change"
]
;
"data type" -> "8-bit unsigned integer";
"8-bit unsigned integer" -> "0 to 255";
"8-bit unsigned integer" -> "0 to 255";
"16-bit unsigned integer" -> "0 to 65535";
"16-bit unsigned integer" -> "0 to 65535";
"N bit unsigned integer" -> "0 to 2^N - 1";
"N bit unsigned integer" -> "0 to 2^N - 1";
"pixel data type" -> "16-bit unsigned integer";
"pixel data type" -> "16-bit unsigned integer";
"pixel data type" -> "32-bit float";
"pixel data type" -> "32-bit float";
"pixel data type" -> "N-bit unsigned integer";
"pixel data type" -> "N-bit unsigned integer";
"image math" -> wrong_pixel_values
[
label = " can yield"
]
;
}
}
'/>
'/>
...
...
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