Editing segmented images manually
This guide was written on March 04, 2023.
Is it possible to edit the segmented branches manually and remove branches or cells from the segmented images?
Yes, you can do this manually in ImageJ or FIJI. In this guide you will find out how!
- Launch FIJI or ImageJ
- Open the output image from MotiQ Thresholder (file ending "_pBIN.tif" or "_BIN.tif") that you aim to manually edit by drag and drop into the status bar of FIJI / ImageJ.
- Launch the Auto Threshold dialog via the menu entry Image > Adjust > Auto Threshold.
- Drag both sliders to the very left so that next to the sliders "0"s are displayed. Now you can very well see what the "semi-binarized" image shows as foreground (original intensity values) and background (red).
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Move to a plane where you would like to remove a particle from the image or where you would like to separate two cells.
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Circumscribe the pixels / particle that you want to remove with an ROI. If you aim to separate two particles circumscribe a group of pixels between the two particles that you aim to separate to create a gap between the particles.
- Press the backspace key on your keyboard. It set the pixels within the selection to 0.0, so to "background".
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If the particle you aimed to remove is present in multiple z slices, remove it in all z slices where it is present by repeating steps 5-7.
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Repeat steps 5-8 until you removed all particles you aimed to remove manually.
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Save the image under a new filename (to log that you manually edited the image) by going to the menu entry File > Save As > Tiff..., selecting a new name (e.g., the old filename + the suffix "_ed" (for "edited")), and confirming the saving process.
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Close the image in FIJI.