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Commit 5838bd03 authored by Pierre WEISS's avatar Pierre WEISS
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Update README.md

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...@@ -20,10 +20,46 @@ https://sites.imagej.net/XXX ...@@ -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". 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?
![Drag Racing](doc/1_eigenpsf.png) 1. Open Fiji
2. Open Plugins -> Eigen_PSF -> Eigen_PSF
![Step1](doc/1_eigenpsf.png)
3. Drag and drop the images you want to open in the left pane.
![Step2](doc/2_dragimage.png)
4. You can display the selected images by clicking on the eye (show) in the left pane.
![Step3](doc/3_display.png)
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)
![Step4](doc/4_set_parameters.png)
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.
![Step5](doc/5_after_detection.png)
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.
![Step6](doc/5_after_detection.png)
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.
![Step7](doc/5_after_detection.png)
10. Finally, you can display the processed PSFs after registration, background removal and projection on the eigenPSF basis.
![Step8](doc/6_eigenpsf_montage.png)
## Future releases ## Future releases
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