Registration README file updated

notebooks/03_image_registration/README.md

@@ -1,18 +1,18 @@
 # H&E-DAPI registration
 
 For each sample,
-1. Cut the DAPI via ```seperate_samples_LEVEL1.ipynb``` and save TIFF and anndata objects.
+1. Cut the DAPI via ```seperate_samples.ipynb``` and save TIFF and anndata objects.
 2. Cut H&E images via Fiji.
-3. Do the registarion with ```registration_final_elastix.ipynb```
+3. Do the registarion with ```main.py```
 
 As for visualization, we need to read the anndata for each sample, then attach the corresponding registared H&E image to it as in ```plot_example.ipynb```.
 
 
 # Phenocycler-DAPI Registration
 
-1. Cut the DAPI via ```seperate_samples_LEVEL1_slide.ipynb```
+1. Cut the DAPI via ```seperate_samples_phenocycler.ipynb```
 2. Cut Phenocycler image ```Xenium Slide_Scan1.qptiff``` via Fiji.
-3. Do the registarion with ```registration_final_elastix_phenocycler.ipynb```
+3. Do the registarion with ```main.py```
 
 
 **Cut Phenocycler image:**