diff --git a/README.md b/README.md index 3139159479d5064d0efd11ac791de683d085be70..f3650e44b5b42129a3fb3e3ddba1f25eb77b4760 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,46 @@ https://sites.imagej.net/XXX 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. + + ## Future releases