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grp-bio-it
image-analysis-training-resources
Commits
f9d6da52
Commit
f9d6da52
authored
Apr 01, 2019
by
Christian Tischer
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EMBL Course
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code/imagej-macro/filter-objects.ijm
code/imagej-macro/filter-objects.ijm
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image_data/xy_16bit__two_values.tif
image_data/xy_16bit__two_values.tif
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image_data/xy_8bit__two_cells.tif
image_data/xy_8bit__two_cells.tif
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image_data/xy_8bit_binary__nuclei.tif
image_data/xy_8bit_binary__nuclei.tif
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image_data/xy_8bit_labels__four_objects.tif
image_data/xy_8bit_labels__four_objects.tif
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image_data/xyz_8bit_binary__spots.tif
image_data/xyz_8bit_binary__spots.tif
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workshops/.image-analysis-automation.md.swp
workshops/.image-analysis-automation.md.swp
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workshops/.image-ethics-and-data-integrity.md.swp
workshops/.image-ethics-and-data-integrity.md.swp
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workshops/bioimage-analysis-fundamentals.md
workshops/bioimage-analysis-fundamentals.md
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workshops/image-analysis-automation.md
workshops/image-analysis-automation.md
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code/imagej-macro/filter-objects.ijm
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f9d6da52
// TODO: add user interface for opening a label image file (https://imagej.net/Script_Parameters)
// TODO: add user interface for min and max area
run("Region Morphometry");
minArea = 0;
maxArea = 200;
// TODO: Duplicate the label image, in order not to loose the original one
for ( i = 0; i < Table.size; ++i )
{
area = Table.get( "Area", i );
label = Table.getString( "Label", i );
// TODO: Add some text output to tell the user what is happening...
if ( area < minArea || area > maxArea )
{
run("Replace/Remove Label(s)", "label(s)="+label+" final=0");
}
}
// TODO (Optional): Relabel the filtered label image such that labels start from 1 and none are missing
image_data/xy_16bit__two_values.tif
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image_data/xy_8bit_labels__four_objects.tif
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image_data/xyz_8bit_binary__spots.tif
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workshops/.image-analysis-automation.md.swp
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workshops/.image-ethics-and-data-integrity.md.swp
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workshops/bioimage-analysis-fundamentals.md
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workshops/image-analysis-automation.md
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# Image analysis automation
## Automated object filtering
<img src='https://g.gravizo.com/svg?
digraph G {
shift
[
fontcolor=white,color=white
]
;
label_image -> table
[
label=" measure_shape"
]
;
table -> filtered_objects;
filtered_objects -> label_image
[
label=" remove"
]
;
}
'/>
### Activity: Automatically remove objects from label image
-
Open image:
`xy_8bit_labels__four_objects.tif`
-
Devise code to automatically remove objects from the label image, e.g.
-
Remove all cells larger than N pixels in area
### Formative assessment
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