Workshop

In this workshop, we will work through the following exercises:
 1. Segmentation using global threshold, local threshold and Deep Learning (StarDist)
 2. Cell tracking using StarDist and TrackMate
 3. Denoising using Noise2Void
 4. Bonus – 3D segmentation using StarDist and TrackMate

Prerequisite - installing required plugins in Fiji

We need to add the following three updates sites in our Fiji to install all the required plugins for this workshop:
- CSBDeep
- StarDist
- TrackMate-StarDist

Step 1: Start Fiji.
Step 2: Select Help > Update… from the menu bar.
Step 3: Click on the button “Manage update sites”.
Step 4: Scroll down the list and tick the checkboxes for update sites: CSBDeep (shown below), StarDist and TrackMate-StarDist, then click the Close button.

CSBDeep update site

Step 5: Click on “Apply changes” to install the plugins.
Step 6: Restart Fiji.
  - StarDist plugin should now be available under Plugins > StarDist > StarDist 2D.
  - Noise2Void plugin should be visible under Plugins › CSBDeep › N2V.