This is a plugin for fission/budding yeast cell segmentation (tested). And should also work on E.coli and other bacterias with refringent cell border (to be confirmed).
PS: you can skip the installation step described in README.md, if you need only this BF segmentation
Your bright-field image should be acquired with a Z-range of 10 micron (+-5) with a step of 0.3 micron = 34 images in total and it looks like this:
Run ImageJ with Java 1.6 +
RAM : About 400M
MAARS modules : copy maars_lib_XXX-SNAPSHOT.jar and maars_bfSeg_XXX-SNAPSHOT.jar into your plugins folder of ImageJ.
Download the Adjustable_Watershed.java for better binary segmentation,
see more details here
- Open your image.
Make sure it is calibrated, as least for x,y,z. - Find the
SegmentPombeplugin, and click on it:
- Click
loadto load your current image :
And Run!
Several seconds later, a prompt will be displayed asking whether or not to use adjustable watershed plugin to improve the segmentation by adding lines that split merged cells.
before
after
To note,for Fiji user simply install the plugin yourself by following the instuction.
Once the lines are added on the binary image (can take 1-2s). You can click on ok.
PS: If you are working on fission yeast cell, you won't need to change the parameters in Preference panel (except the Range for cell area min/max which depends on your strain). As for budding yeast, you will have to decrease the solidity threshold to around 0.7 or even lower (what is solidity). Generally, other parameters are self-explainable and you can play with them to meet your needs.