Once the site has been added, updating Fiji should cause it to download and install the plugin which can be found in "plugins"->"eigenpsf-extractor".
Once the site has been added, updating Fiji should cause it to download and install the plugin which can be found in "plugins"->"eigenpsf-extractor".
## Visual examples
## How it works?
1. Open Fiji
2. Open Plugins -> Eigen_PSF -> Eigen_PSF
3. Drag and drop the images you want to open in the left pane.
4. You can display the selected images by clicking on the eye (show) in the left pane.
5. Click on the parameters button and set the parameters. In particular, pay attention to :
- Set 2D/3D option
- Set the width of a PSF. You can also do it by drawing a square around a PSF and by clicking on get_ROI
- Set the number of EigenPSFs (this can be done afterwards)
6. Click on *Detect beads*. This may take some time. When finished, you can click on the image pane, and ROI should appear around each detected microbead.
7. The PSFs that are set as *valid* are displayed in green. Those in red are considered as *invalid* because, they are out of the distribution of observed beads. You can change the *valid*/*invalid* status by *ctrl + shift + click* or by clicking on the table at right. Note: the table contains the main beads properties. The lower the bead quality, the more likely it is for it to be a correct bead (i.e. no overlap with other beads, out of distribution features,...).
8. Click on Preprocess Patches. This will do a fine PSF registration on the detected patches and remove the background.
9. Click on Compute EigenPSF. You can also show them. You should get a result like the one below. Here we made a montage with 5 eigenPSFs extracted from the valid microbeads.
10. Finally, you can display the processed PSFs after registration, background removal and projection on the eigenPSF basis.
