diff --git a/DESCRIPTION b/DESCRIPTION
index f5a0480..faa656c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,7 +7,7 @@ Description: Cell-cell Interactions at Single-Cell Resolution
 License: GPL-3
 Encoding: UTF-8
 LazyData: yes
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Depends:
     R (>= 4.0)
diff --git a/man/RunCellToCell.Rd b/man/RunCellToCell.Rd
index 0f77f19..84e45b1 100644
--- a/man/RunCellToCell.Rd
+++ b/man/RunCellToCell.Rd
@@ -4,12 +4,18 @@
 \alias{RunCellToCell}
 \title{RunCellToCell}
 \usage{
-RunCellToCell(sys.small, ground.truth, assay, meta.data.to.map, output_format)
+RunCellToCell(
+  filtered.obj,
+  ground.truth,
+  assay,
+  meta.data.to.map,
+  output_format
+)
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the SCC transformation on. Defaults to "RNA."}
 
diff --git a/man/RunCellToCellSpatial.Rd b/man/RunCellToCellSpatial.Rd
index 75268d0..24b5a29 100644
--- a/man/RunCellToCellSpatial.Rd
+++ b/man/RunCellToCellSpatial.Rd
@@ -5,7 +5,7 @@
 \title{RunCellToCellSpatial}
 \usage{
 RunCellToCellSpatial(
-  sys.small,
+  filtered.obj,
   ground.truth,
   assay,
   meta.data.to.map,
@@ -14,9 +14,9 @@ RunCellToCellSpatial(
 )
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the SCC transformation on. Defaults to "RNA."}
 
diff --git a/man/RunCellToNeighborhood.Rd b/man/RunCellToNeighborhood.Rd
index a95665a..480ff03 100644
--- a/man/RunCellToNeighborhood.Rd
+++ b/man/RunCellToNeighborhood.Rd
@@ -5,7 +5,7 @@
 \title{RunCellToNeighborhood}
 \usage{
 RunCellToNeighborhood(
-  sys.small,
+  filtered.obj,
   ground.truth,
   assay,
   meta.data.to.map,
@@ -15,9 +15,9 @@ RunCellToNeighborhood(
 )
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the SCC transformation on. Defaults to "RNA."}
 
diff --git a/man/RunCellToSystem.Rd b/man/RunCellToSystem.Rd
index 4a5e6fa..5913dc1 100644
--- a/man/RunCellToSystem.Rd
+++ b/man/RunCellToSystem.Rd
@@ -5,7 +5,7 @@
 \title{RunCellToSystem}
 \usage{
 RunCellToSystem(
-  sys.small,
+  filtered.obj,
   ground.truth,
   assay,
   blend = "mean",
@@ -14,9 +14,9 @@ RunCellToSystem(
 )
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the CellToSystem transformation on. Defaults to "RNA."}
 
diff --git a/man/RunNeighborhoodToCell.Rd b/man/RunNeighborhoodToCell.Rd
index aef0e6a..3876c49 100644
--- a/man/RunNeighborhoodToCell.Rd
+++ b/man/RunNeighborhoodToCell.Rd
@@ -5,7 +5,7 @@
 \title{RunNeighborhoodToCell}
 \usage{
 RunNeighborhoodToCell(
-  sys.small,
+  filtered.obj,
   ground.truth,
   assay,
   meta.data.to.map,
@@ -15,9 +15,9 @@ RunNeighborhoodToCell(
 )
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the SCC transformation on. Defaults to "RNA."}
 
diff --git a/man/RunSystemToCell.Rd b/man/RunSystemToCell.Rd
index 97c73e8..4e602a9 100644
--- a/man/RunSystemToCell.Rd
+++ b/man/RunSystemToCell.Rd
@@ -5,7 +5,7 @@
 \title{RunSystemToCell}
 \usage{
 RunSystemToCell(
-  sys.small,
+  filtered.obj,
   ground.truth,
   assay,
   blend = "mean",
@@ -14,9 +14,9 @@ RunSystemToCell(
 )
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
-\item{ground.truth}{Ground truth signaling mechanisms present in sys.small.}
+\item{ground.truth}{Ground truth signaling mechanisms present in filtered.obj.}
 
 \item{assay}{The assay to run the SystemToCell transformation on. Defaults to "RNA."}
 
diff --git a/man/compute_edgelist.Rd b/man/compute_edgelist.Rd
index f79e8d6..240a4bc 100644
--- a/man/compute_edgelist.Rd
+++ b/man/compute_edgelist.Rd
@@ -4,10 +4,10 @@
 \alias{compute_edgelist}
 \title{Compute an edgelist based on the spatial coordinates}
 \usage{
-compute_edgelist(sys.small, position.x, position.y, k = 4, rad.set = NULL)
+compute_edgelist(filtered.obj, position.x, position.y, k = 4, rad.set = NULL)
 }
 \arguments{
-\item{sys.small}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
+\item{filtered.obj}{A filtered Seurat object. The active identity will be used to define populations for connectomic sampling and crossings.}
 
 \item{position.x}{string. Optional. Default: NULL. The name of the meta.data column specifying location on the spatial x-axis. Only required for spatial omics data.}