Update README.md

README.md

@@ -22,42 +22,42 @@ Once the site has been added, updating Fiji should cause it to download and inst
 
 ## How  it works?
 
-1. Open Fiji
-2. Open *Plugins -> Eigen_PSF -> Eigen_PSF*
+### Step 1. Open Fiji
+### Step 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. 
+### Step 3. **Drag and drop the images** you want to open in the left pane. 
 
 ![Step2](doc/2_dragimage.png)
 
-4. **Display the selected images** by clicking on the eye (show) in the left pane. 
+### Step 4. **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 : 
+### Step 5. Click on the parameters button and set the parameters. In particular, pay attention to : 
  - **Set 2D/3D option**.
  - **Set the PSF width**. 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 as well).
 
 ![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. 
+### Step 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,...).
+### Step 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. 
+### Step 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. 
+### Step 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. 
+### Step 10. Finally, you can display the processed PSFs after registration, background removal and projection on the eigenPSF basis. 
 
 ![Step8](doc/6_eigenpsf_montage.png)