Wolfram Research

Sample Data: Gastric Mucosa Cells

Source Notebook

Locations of the gastric mucosa (the mucous membrane layer of the stomach) cells annotated with marks identifying cell type

Details

Locations of the gastric mucosa (the mucous membrane layer of the stomach) cells in the observation region Rectangle[{0., 0.}, {1., 0.81}], annotated with marks identifying cell type.

Examples

Basic Examples (1) 

In[1]:=
ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"]
Out[1]=

Summary of the spatial point data:

In[2]:=
ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"]["Summary"]
Out[2]=

Visualizations (3) 

Plot the spatial point data:

In[3]:=
ListPlot[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"], AspectRatio -> 1]
Out[3]=

Visualize points with annotations:

In[4]:=
PointValuePlot[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"], PlotLegends -> Automatic]
Out[4]=

Visualize the smooth point density:

In[5]:=
density = SmoothPointDensity[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"]]
Out[5]=
In[6]:=
Show[ContourPlot[density[{x, y}], {x, y} \[Element] ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"]["ObservationRegion"]], ListPlot[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"], PlotStyle -> Black]]
Out[6]=

Analysis (4) 

Compute probability of finding a point within given radius of an existing point - NearestNeighborG is the CDF of the nearest neighbor distribution:

In[7]:=
nnG = NearestNeighborG[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"]]
Out[7]=
In[8]:=
maxR = nnG["MaxRadius"]
Out[8]=
In[9]:=
DiscretePlot[nnG[r], {r, maxR/100, maxR, maxR/100}, AxesLabel -> {"radius", "probability"}]
Out[9]=

Mean distance between a typical point and its nearest neighbor (for positive support distribution can be approximated via a Riemann sum of 1-CDF):

In[10]:=
step = maxR/100;
partition = Table[{k, k + step}, {k, 0, maxR, step}];
values = nnG[Mean /@ partition];
In[11]:=
Total[(1 - values)*step]
Out[11]=

Test for complete spacial randomness:

In[12]:=
SpatialRandomnessTest[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"], {"PValue", "TestConclusion"}]
Out[12]=

Fit a hardcore point process to data:

In[13]:=
EstimatedPointProcess[ResourceData[\!\(\*
TagBox["\"\<Sample Data: Gastric Mucosa Cells\>\"",
#& ,
BoxID -> "ResourceTag-Sample Data: Gastric Mucosa Cells-Input",
AutoDelete->True]\), "Data"], HardcorePointProcess[\[Mu], r, 2]]
Out[13]=

Gosia Konwerska, "Sample Data: Gastric Mucosa Cells" from the Wolfram Data Repository (2021)  

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