diff --git a/docs/usage/normalization_methods.md b/docs/usage/normalization_methods.md
index 8f1c0cb7..a0d945f5 100644
--- a/docs/usage/normalization_methods.md
+++ b/docs/usage/normalization_methods.md
@@ -2,7 +2,7 @@ Normalization methods
=======================
-panpipes currently supports the following normalization methods:
+`panpipes` currently supports the following normalization methods:
## RNA
@@ -16,9 +16,9 @@ Additionally, the normalized data can be scaled using scanpy's [sc.pp.scale](htt
1. clr margin= 0, normalize within each cells' counts distribution, across all features (row-wise, as you would do for RNA data)
2. clr margin= 1, normalize within each feature's distribution, across all cells (column-wise, recommended for proteomics data)
- *if you come from R, please note that the [margins are transposed](https://images.hindustantimes.com/rf/image_size_630x354/HT/p2/2017/09/21/Pictures/_78c6a162-9e94-11e7-9c3b-8e901839ece0.JPG) in the Python and anndata world*
-
-
+ *If you come from R, please note that the [margins are transposed](https://images.hindustantimes.com/rf/image_size_630x354/HT/p2/2017/09/21/Pictures/_78c6a162-9e94-11e7-9c3b-8e901839ece0.JPG) in the Python and anndata world.*
+
+
2. dsb using [muon's prot processing](https://muon.readthedocs.io/en/latest/api/generated/muon.prot.pp.html). This method is only applicable when you have raw 10x inputs (see [supported input files](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html#supported-input-filetypes)).
@@ -31,6 +31,13 @@ Additionally, the normalized data can be scaled using scanpy's [sc.pp.scale](htt
2. "logTF": logging the TF term using using [muon's atac processing](https://muon.readthedocs.io/en/latest/api/generated/muon.atac.pp.tfidf.html#muon.atac.pp.tfidf)
3. "logIDF": logging the IDF term using using [muon's atac processing](https://muon.readthedocs.io/en/latest/api/generated/muon.atac.pp.tfidf.html#muon.atac.pp.tfidf)
+## Spatial Transcriptomics
+
+1. Standard normalization using scanpy's [normalize_total](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.normalize_total.html) and [log1p](https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.log1p.html).
+
+2. Analytic Pearson Residual normalization using scanpy's [normalize_pearson_residuals](https://scanpy.readthedocs.io/en/stable/generated/scanpy.experimental.pp.normalize_pearson_residuals.html).
+
+
## Layers nomenclature within each modality
Raw, Normalised and Scaled data are saved for each modality in their specific layers:
@@ -39,13 +46,15 @@ Raw, Normalised and Scaled data are saved for each modality in their specific la
Using the following nomenclature:
-| method | layer | modality |
-| ---------------------- | --------------- | ------------- |
-| raw counts | "raw_counts" | RNA/ATAC/PROT |
-| standard log1p | "logged_counts" | RNA or ATAC |
-| scaled counts | "scaled_counts" | RNA or ATAC |
-| clr | "clr" | PROT |
-| dsb | "dsb" | PROT |
-| TFIDF (signac flavour) | "signac_norm" | ATAC |
-| TFIDF (logTF) | "logTF_norm" | ATAC |
-| TFIDF (logIDF) | "logIDF_norm" | ATAC |
+| method | layer | modality |
+| ---------------------- | -------------------- | ------------- |
+| raw counts | "raw_counts" | RNA/ATAC/PROT |
+| standard log1p | "logged_counts" | RNA or ATAC |
+| scaled counts | "scaled_counts" | RNA or ATAC |
+| clr | "clr" | PROT |
+| dsb | "dsb" | PROT |
+| TFIDF (signac flavour) | "signac_norm" | ATAC |
+| TFIDF (logTF) | "logTF_norm" | ATAC |
+| TFIDF (logIDF) | "logIDF_norm" | ATAC |
+| standard log1p | "lognorm" | Spatial |
+| Pearson Residuals | "norm_pearson_resid" | Spatial |