Tutorial
Install KICS with Plugins → Install/Uninstall Plugins…, enter KICS into
the search field and install the plugin.
Activate KICS by Plugins → napari-kics: Karyotype Widget. The KICS panel
appears on the right side of napari.
Start by loading the example karyotype image File → Open Sample → napari-kics: sample.
Adjust the threshold and blur until the highlighted (red) segmentation neatly fits the chromosome outlines.
Enter the genome size 3100 Mb and assign labels to each segmented area by clicking on Label.
You may notice that some chromosomes are labelled with several labels. These labels should be joined into one so all parts contribute to the same chromosome.
- Use the pan & zoom tool (
or press 5) to locate
defective labels. - Pick the numerical value of one of the labels with the picker tool (
or press 4) and transfer to the remaining fragments using the fill tool (
or press 3). - Generally, some defects may require using the paint brush (
or press 2) or eraser (
or press 1) tool. Use them as required. - Repeat until all defects are fixed.
The sample image contains embedded text labels that should not be labelled. To remove the corresponding labels efficiently, we scroll through the table to identify the biggest of the undesired labels.
Hint: it can be useful the activate the checkbox show selected in
layer controls.
Once we found it, we select all smaller labels in addition using ⇧ Shift + Click. Hitting ⌫ Backspace removes the labels from the image.
Hint: the FAQ lists another method for removing undesired labels
The final step is to establish chromosome names for the labels and annotate the image with the estimated sizes.
In our example this is as simple as clicking the button Automatically guess order. The X and Y chromosome will receive names 23a and 23b which must
be manually corrected by double clicking on the name in the table and entering
X and Y, respectively.
The annotations can be adjusted for better readability in step 4 of the widget. However, the settings have no effect on the SVG that is generated when saving. See next step for more details.
The results can be saved by pressing the Save button at the bottom of the
widget.
This will generated the following files in the specified folder:
| Filename | Description | Example (detail) |
|---|---|---|
| annotated.svg | Original karyotype with overlayed annotations |  |
| screenshot.png | Screenshot of the viewer |  |
| params.csv | List of parameters |  |
| labelled_color.png | Image of the labels in RGB colors |  |
| data.csv | Table of estimates, chromosome names, |  |
| thresholded.png | Result of segmentation by threshold |  |
| labelled.tiff | Labels stored as integer (image not visible in viewers) |  |
| inverted.png | Gray-scale-transformed karyotype; possibly inverted |  |
| blurred.png | Image after applying blur to inverted.png
|
 |