diff --git a/.gitignore b/.gitignore
index c5cf332..b7fdb39 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,18 @@ dist/
 stlearn/static/*
 uploads/spatial
 uploads/filtered_feature_bc_matrix.h5
+uploads/*.h5ad
+temp_plots/
+temp_tiling/
 temp_tiling/
 temp_plots/*
+temp_plots/
+temp_tiling/
+tiling/
+.DS_Store
+uploads/*
+temp_plots/
+temp_tiling/
 tiling/
+.DS_Store
+
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..aec1ffe
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,6 @@
+FROM python:3.8
+
+WORKDIR usr/src/flask_app
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+COPY . .
diff --git a/README.md b/README.md
index c413a6d..daf44a3 100644
--- a/README.md
+++ b/README.md
@@ -1,30 +1,18 @@
-# stlearn-bokeh
-stlearn with interactive web app
+# Tutorial how to run i-stLearn
+We build a webapp version that wrap stLearn functions.
 
 ## Step 1:
 
-Install stlearn dev version by:
-
-``` git clone https://github.com/BiomedicalMachineLearning/stLearn ```
-
-``` cd stLearn ```
-
-``` python setup.py install ```
+Install stlearn by this instruction: https://stlearn.readthedocs.io/en/latest/installation.html
 
 
 ## Step 2:
 
-Clone stlearn interactive app:
-
-``` git clone https://github.com/BiomedicalMachineLearning/stlearn_interactive.git ```
-
-``` cd stlearn_interactive ```
-
-``` pip install -r requirements.txt ```
+Run the stlearn interactive app:
 
-## Step 3:
+``` stlearn launch ```
 
-Run the stlearn interactive app:
+## Step 3: Tutorial
 
-``` FLASK_APP=app.py flask run ```
+- [Tutorial - stLearn Interactive](https://github.com/BiomedicalMachineLearning/stlearn_interactive/blob/master/docs/stlearn_interactive_tutorial.pdf)
 
diff --git a/app.py b/app.py
index 12d7728..be4d8f2 100644
--- a/app.py
+++ b/app.py
@@ -14,11 +14,13 @@
 from werkzeug.utils import secure_filename
 import tempfile
 import traceback
+from datetime import timedelta
 
 import os, sys
 import stlearn
 import scanpy
 import numpy
+import numpy as np
 
 import asyncio
 from bokeh.server.server import BaseServer
@@ -45,61 +47,71 @@
     "preprocessed": [False, "Preprocessing"],
     "clustering": [False, "Clustering"],
     "psts": [False, "Spatial trajectory"],
-    "cci": [False, "Cell-cell interaction"],
     "dea": [False, "DEA"],
+    "lr": [False, "Ligand-receptor analysis"],
+    "cci": [False, "CCI"],
     # _params suffix important for templates/progress.html
     "preprocessed_params": {},
     "cci_params": {},
     "cluster_params": {},
     "psts_params": {},
     "dea_params": {},
+    "lr_params": {},
 }
 
 # print(stlearn, file=sys.stdout)
 
-app = Flask(__name__)
-app.secret_key = b'_5#y2L"F4Q8z\n\xec]/'
+server = Flask(__name__)
+server.secret_key = b'_5#y2L"F4Q8z\n\xec]/'
+server.config["PERMANENT_SESSION_LIFETIME"] = timedelta(seconds=20)
 
 UPLOAD_FOLDER = "uploads/"
 TEMPLATES_AUTO_RELOAD = True
-app.config["UPLOAD_FOLDER"] = UPLOAD_FOLDER
-app.config["SEND_FILE_MAX_AGE_DEFAULT"] = 0
-app.config["TEMPLATES_AUTO_RELOAD"] = TEMPLATES_AUTO_RELOAD
-app.config["SESSION_PERMANENT"] = False
+server.config["UPLOAD_FOLDER"] = UPLOAD_FOLDER
+server.config["SEND_FILE_MAX_AGE_DEFAULT"] = 0
+server.config["TEMPLATES_AUTO_RELOAD"] = TEMPLATES_AUTO_RELOAD
+server.config["SESSION_PERMANENT"] = False
 
 
-@app.route("/", methods=["GET"])
+@server.route("/", methods=["GET"])
 def index():
     return render_template("index.html", step_log=step_log)
 
 
-@app.route("/upload")
+@server.route("/upload")
 def upload():
     return render_template("upload.html", step_log=step_log, flash_bool=True)
 
 
-@app.route("/preprocessing", methods=["GET", "POST"])
+@server.route("/preprocessing", methods=["GET", "POST"])
 def preprocessing():
     global adata, step_log
     updated_page = views.run_preprocessing(request, adata, step_log)
     return updated_page
 
 
-@app.route("/clustering", methods=["GET", "POST"])
+@server.route("/clustering", methods=["GET", "POST"])
 def clustering():
     global adata, step_log
     updated_page = views.run_clustering(request, adata, step_log)
     return updated_page
 
 
-@app.route("/cci", methods=["GET", "POST"])
+@server.route("/lr", methods=["GET", "POST"])
+def lr():
+    global adata, step_log
+    updated_page = views.run_lr(request, adata, step_log)
+    return updated_page
+
+
+@server.route("/cci", methods=["GET", "POST"])
 def cci():
     global adata, step_log
     updated_page = views.run_cci(request, adata, step_log)
     return updated_page
 
 
-@app.route("/psts", methods=["GET", "POST"])
+@server.route("/psts", methods=["GET", "POST"])
 def psts():
     global adata, step_log
 
@@ -110,7 +122,7 @@ def psts():
         return updated_page
 
 
-@app.route("/dea", methods=["GET", "POST"])
+@server.route("/dea", methods=["GET", "POST"])
 def dea():
     global adata, step_log
     updated_page = views.run_dea(request, adata, step_log)
@@ -126,21 +138,21 @@ def dea():
 ]
 
 
-@app.route("/folder_uploader", methods=["GET", "POST"])
+@server.route("/folder_uploader", methods=["GET", "POST"])
 def folder_uploader():
     if request.method == "POST":
         # Clean uploads folder before upload a new data
         import shutil
 
-        shutil.rmtree(app.config["UPLOAD_FOLDER"])
-        os.makedirs(app.config["UPLOAD_FOLDER"])
-        open(app.config["UPLOAD_FOLDER"] + "/.gitkeep", "a").close()
+        shutil.rmtree(server.config["UPLOAD_FOLDER"])
+        os.makedirs(server.config["UPLOAD_FOLDER"])
+        open(server.config["UPLOAD_FOLDER"] + "/.gitkeep", "a").close()
         # os.mknod()
 
         # Get list of files from selected folder
         files = request.files.getlist("file")
 
-        os.mkdir(os.path.join(app.config["UPLOAD_FOLDER"], "spatial"))
+        os.mkdir(os.path.join(server.config["UPLOAD_FOLDER"], "spatial"))
 
         # allow_upload_files = list(map(lambda x: x ),allow_files)
 
@@ -150,50 +162,53 @@ def folder_uploader():
 
             filename = secure_filename(file.filename)
 
+            print(filename)
+
             if allow_files[0] in filename:
-                file.save(os.path.join(app.config["UPLOAD_FOLDER"], filename))
+                file.save(os.path.join(server.config["UPLOAD_FOLDER"], filename))
                 os.rename(
-                    os.path.join(app.config["UPLOAD_FOLDER"], filename),
-                    os.path.join(app.config["UPLOAD_FOLDER"], allow_files[0]),
+                    os.path.join(server.config["UPLOAD_FOLDER"], filename),
+                    os.path.join(server.config["UPLOAD_FOLDER"], allow_files[0]),
                 )
                 uploaded.append(allow_files[0])
 
             for allow_file in allow_files[1:]:
                 if allow_file in filename:
+
                     file.save(
-                        os.path.join(app.config["UPLOAD_FOLDER"] + "/spatial", filename)
+                        os.path.join(
+                            server.config["UPLOAD_FOLDER"] + "/spatial", filename
+                        )
                     )
                     os.rename(
                         os.path.join(
-                            app.config["UPLOAD_FOLDER"] + "/spatial", filename
+                            server.config["UPLOAD_FOLDER"] + "/spatial", filename
                         ),
                         os.path.join(
-                            app.config["UPLOAD_FOLDER"] + "/spatial", allow_file
+                            server.config["UPLOAD_FOLDER"] + "/spatial", allow_file
                         ),
                     )
 
                     uploaded.append(allow_file)
-
-            print(i)
             i += 1
             if len(uploaded) == 5:
                 flash("File uploaded successfully")
                 global adata, step_log
-                step_log = {
-                    "uploaded": [False, "Upload file"],
-                    "preprocessed": [False, "Preprocessing"],
-                    "clustering": [False, "Clustering"],
-                    "psts": [False, "Spatial trajectory"],
-                    "cci": [False, "Cell-cell interaction"],
-                    "dea": [False, "Differential expression analysis"],
-                    # _params suffix important for templates/progress.html
-                    "preprocessed_params": {},
-                    "cci_params": {},
-                    "cluster_params": {},
-                    "psts_params": {},
-                    "dea_params": {},
-                }
-                adata = stlearn.Read10X(app.config["UPLOAD_FOLDER"])
+                # step_log = {
+                #     "uploaded": [False, "Upload file"],
+                #     "preprocessed": [False, "Preprocessing"],
+                #     "clustering": [False, "Clustering"],
+                #     "psts": [False, "Spatial trajectory"],
+                #     "cci_rank": [False, "Cell-cell interaction"],
+                #     "dea": [False, "Differential expression analysis"],
+                #     # _params suffix important for templates/progress.html
+                #     "preprocessed_params": {},
+                #     "cci_params": {},
+                #     "cluster_params": {},
+                #     "psts_params": {},
+                #     "dea_params": {},
+                # }
+                adata = stlearn.Read10X(server.config["UPLOAD_FOLDER"])
                 adata.var_names_make_unique()  # removing duplicates
                 # ensuring compatible format for CCI, since need _ to pair LRs #
                 adata.var_names = numpy.array(
@@ -213,7 +228,7 @@ def folder_uploader():
             return redirect(url_for("upload"))
 
 
-@app.route("/file_uploader", methods=["GET", "POST"])
+@server.route("/file_uploader", methods=["GET", "POST"])
 def file_uploader():
     if request.method == "POST":
 
@@ -222,18 +237,19 @@ def file_uploader():
         # Clean uploads folder before upload a new data
         import shutil
 
-        shutil.rmtree(app.config["UPLOAD_FOLDER"])
-        os.makedirs(app.config["UPLOAD_FOLDER"])
-        open(app.config["UPLOAD_FOLDER"] + "/.gitkeep", "a").close()
+        shutil.rmtree(server.config["UPLOAD_FOLDER"])
+        os.makedirs(server.config["UPLOAD_FOLDER"])
+        open(server.config["UPLOAD_FOLDER"] + "/.gitkeep", "a").close()
         # os.mknod()
         f = request.files["file"]
         filename = secure_filename(f.filename)
-        f.save(os.path.join(app.config["UPLOAD_FOLDER"], filename))
+        f.save(os.path.join(server.config["UPLOAD_FOLDER"], filename))
         try:
-            adata = scanpy.read_h5ad(app.config["UPLOAD_FOLDER"] + "/" + f.filename)
+            adata = scanpy.read_h5ad(server.config["UPLOAD_FOLDER"] + "/" + f.filename)
         except:
             flash("Upload ERROR: Please choose the right AnnData file ")
 
+        ### Updating log file with current anndata state ###
         step_log["uploaded"][0] = True
 
         if "n_cells" in adata.var.columns:
@@ -247,10 +263,13 @@ def file_uploader():
         if "global_graph" in adata.uns:
             step_log["psts"][0] = True
 
+        step_log["lr"][0] = "lr_summary" in adata.uns
+        step_log["cci"][0] = np.any(["lr_cci_" in key for key in adata.uns])
+
         return redirect(url_for("upload"))
 
 
-@app.route("/choose_cluster", methods=["GET", "POST"])
+@server.route("/choose_cluster", methods=["GET", "POST"])
 def choose_cluster():
     menu = []
 
@@ -268,7 +287,7 @@ def choose_cluster():
     )
 
 
-@app.route("/convert_clusters", methods=["GET", "POST"])
+@server.route("/convert_clusters", methods=["GET", "POST"])
 def convert_clusters():
     if request.method == "POST":
         adata.obs["clusters"] = adata.obs[request.form["convert_clusters"]]
@@ -278,9 +297,11 @@ def convert_clusters():
         return redirect(url_for("psts"))
 
 
-@app.route("/gene_plot")
+@server.route("/gene_plot")
 def gene_plot():
-    script = server_document("http://127.0.0.1:5006/bokeh_gene_plot")
+    script = server_document(
+        "http://%s:5006/bokeh_gene_plot" % request.host.split(":")[0]
+    )
     return render_template(
         "gene_plot.html",
         script=script,
@@ -290,9 +311,11 @@ def gene_plot():
     )
 
 
-@app.route("/cluster_plot")
+@server.route("/cluster_plot")
 def cluster_plot():
-    script = server_document("http://127.0.0.1:5006/bokeh_cluster_plot")
+    script = server_document(
+        "http://%s:5006/bokeh_cluster_plot" % request.host.split(":")[0]
+    )
     return render_template(
         "cluster_plot.html",
         script=script,
@@ -302,11 +325,13 @@ def cluster_plot():
     )
 
 
-@app.route("/cci_plot")
-def cci_plot():
-    script = server_document("http://127.0.0.1:5006/bokeh_cci_plot")
+@server.route("/lr_plot")
+def lr_plot():
+    script = server_document(
+        "http://%s:5006/bokeh_lr_plot" % request.host.split(":")[0]
+    )
     return render_template(
-        "cci_plot.html",
+        "lr_plot.html",
         script=script,
         template="Flask",
         relative_urls=False,
@@ -314,9 +339,25 @@ def cci_plot():
     )
 
 
-@app.route("/annotate_plot")
+@server.route("/spatial_cci_plot")
+def spatial_cci_plot():
+    script = server_document(
+        "http://%s:5006/bokeh_spatial_cci_plot" % request.host.split(":")[0]
+    )
+    return render_template(
+        "spatial_cci_plot.html",
+        script=script,
+        template="Flask",
+        relative_urls=False,
+        step_log=step_log,
+    )
+
+
+@server.route("/annotate_plot")
 def annotate_plot():
-    script = server_document("http://127.0.0.1:5006/bokeh_annotate_plot")
+    script = server_document(
+        "http://%s:5006/bokeh_annotate_plot" % request.host.split(":")[0]
+    )
     return render_template(
         "annotate_plot.html",
         script=script,
@@ -326,7 +367,7 @@ def annotate_plot():
     )
 
 
-@app.route("/save_adata", methods=["POST"])
+@server.route("/save_adata", methods=["POST"])
 def save_adata():
     if request.method == "POST":
         fd, path = tempfile.mkstemp()
@@ -355,8 +396,8 @@ def save_adata():
 # sc.pp.scale(adata)g
 
 # adata.uns["lr"] = ['Gfap_Ctss']
-# st.tl.cci.lr(adata=adata)
-# st.tl.cci.permutation(adata,n_pairs=1)
+# st.tl.cci_rank.lr(adata=adata)
+# st.tl.cci_rank.permutation(adata,n_pairs=1)
 
 # sc.pp.pca(adata)
 # sc.pp.neighbors(adata)
@@ -405,16 +446,33 @@ def modify_doc_cluster_plot(doc):
         gp_object.min_logfoldchange.on_change("value", gp_object.update_data)
 
 
-def modify_doc_cci_plot(doc):
-    from stlearn.plotting.classes_bokeh import BokehCciPlot
+def modify_doc_spatial_cci_plot(doc):
+    from stlearn.plotting.classes_bokeh import BokehSpatialCciPlot
+
+    gp_object = BokehSpatialCciPlot(adata)
+    doc.add_root(row(gp_object.layout, width=800))
+
+    gp_object.annot_select.on_change("value", gp_object.update_list)
+    gp_object.annot_select.on_change("value", gp_object.update_data)
+    gp_object.lr_select.on_change("value", gp_object.update_data)
+    gp_object.data_alpha.on_change("value", gp_object.update_data)
+    gp_object.tissue_alpha.on_change("value", gp_object.update_data)
+    gp_object.spot_size.on_change("value", gp_object.update_data)
+    gp_object.list_cluster.on_change("active", gp_object.update_data)
+    gp_object.output_backend.on_change("value", gp_object.update_data)
+
+
+def modify_doc_lr_plot(doc):
+    from stlearn.plotting.classes_bokeh import BokehLRPlot
 
-    gp_object = BokehCciPlot(adata)
+    gp_object = BokehLRPlot(adata)
     doc.add_root(row(gp_object.layout, width=800))
 
     gp_object.data_alpha.on_change("value", gp_object.update_data)
     gp_object.tissue_alpha.on_change("value", gp_object.update_data)
     gp_object.spot_size.on_change("value", gp_object.update_data)
-    gp_object.het_select.on_change("value", gp_object.update_data)
+    # gp_object.het_select.on_change("value", gp_object.update_data)
+    gp_object.lr_select.on_change("value", gp_object.update_data)
     gp_object.output_backend.on_change("value", gp_object.update_data)
 
 
@@ -434,8 +492,11 @@ def modify_doc_annotate_plot(doc):
 # App for cluster_plot
 bkapp2 = Application(FunctionHandler(modify_doc_cluster_plot))
 
-# App for cci_plot
-bkapp3 = Application(FunctionHandler(modify_doc_cci_plot))
+# App for lr_plot
+bkapp3 = Application(FunctionHandler(modify_doc_lr_plot))
+
+# App for cci_spatial_plot
+bkapp3_1 = Application(FunctionHandler(modify_doc_spatial_cci_plot))
 
 # App for annotate_plot
 bkapp4 = Application(FunctionHandler(modify_doc_annotate_plot))
@@ -448,11 +509,18 @@ def bk_worker():
         {
             "/bokeh_gene_plot": bkapp,
             "/bokeh_cluster_plot": bkapp2,
-            "/bokeh_cci_plot": bkapp3,
+            # "/bokeh_cci_plot": bkapp3,
+            "/bokeh_lr_plot": bkapp3,
+            "/bokeh_spatial_cci_plot": bkapp3_1,
             "/bokeh_annotate_plot": bkapp4,
         },
         io_loop=IOLoop(),
-        allow_websocket_origin=["127.0.0.1:5000", "localhost:5000"],
+        allow_websocket_origin=[
+            "127.0.0.1:8000",
+            "localhost:8000",
+            "0.0.0.0:8000",
+            "*",
+        ],
     )
     server.start()
     server.io_loop.start()
@@ -462,5 +530,5 @@ def bk_worker():
 
 Thread(target=bk_worker).start()
 
-if __name__ == "__main__":
-    app.run(host="0.0.0.0", port=5005, debug=True, use_reloader=True)
+# if __name__ == "__main__":
+#     app.run(host="0.0.0.0", port=5005, debug=True, use_reloader=True)
diff --git a/docs/stlearn_interactive_tutorial.pdf b/docs/stlearn_interactive_tutorial.pdf
new file mode 100644
index 0000000..77dfeaa
Binary files /dev/null and b/docs/stlearn_interactive_tutorial.pdf differ
diff --git a/requirements.txt b/requirements.txt
index 7e58a80..453db43 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,6 @@
-Flask==1.1.2
-WTForms==2.3.1
+Flask==2.0.3
+flask_wtf==1.0.0
+gunicorn
+markupsafe==2.1.0
+stlearn
+WTForms==3.0.1
diff --git a/source/forms/forms.py b/source/forms/forms.py
index 21bc61b..0eef6b1 100644
--- a/source/forms/forms.py
+++ b/source/forms/forms.py
@@ -159,7 +159,71 @@ def getPreprocessForm():
     return createSuperForm(elements, element_fields, element_values)
 
 
-def getCCIForm():
+def getLRForm():
+    """Gets the LR form generated from the superform above.
+
+        Returns:
+                FlaskForm: With attributes that allow for inputs that are \
+                            related to LR analysis.
+    """
+    elements = [
+        "Species",
+        "Spot neighbourhood (-1: smallest neighbourhood, 0: within-spot mode)",
+        "Minimum spots with LR scores",
+        "N random gene pairs (permutations)",
+        "CPUs",
+    ]
+    element_fields = [
+        "SelectField",
+        "IntegerField",
+        "IntegerField",
+        "IntegerField",
+        "IntegerField",
+    ]
+    element_values = [
+        [("Human", "Human"), ("Mouse", "Mouse")],
+        -1,
+        20,
+        100,
+        2,
+    ]
+    return createSuperForm(elements, element_fields, element_values)
+
+
+def getCCIForm(adata):
+    """Gets the CCI form generated from the superform above.
+
+    Returns:
+            FlaskForm: With attributes that allow for inputs that are
+                                                    related to CCI analysis.
+    """
+    elements = [
+        "Cell information (only discrete labels available, unless mixture already in anndata.uns)",
+        "Minimum spots for LR to be considered",
+        "Spot mixture (only if the 'Cell Information' label selected available in anndata.uns)",
+        "Cell proportion cutoff (value above which cell is considered in spot if 'Spot mixture' selected)",
+        "Permutations (recommend atleast 1000)",
+    ]
+    element_fields = [
+        "SelectField",
+        "IntegerField",
+        "BooleanField",
+        "FloatField",
+        "IntegerField",
+    ]
+    if type(adata) == type(None):
+        fields = []
+        mix = False
+    else:
+        fields = [
+            key for key in adata.obs.keys() if type(adata.obs[key].values[0]) == str
+        ]
+        mix = fields[0] in adata.uns.keys()
+    element_values = [fields, 20, mix, 0.2, 100]
+    return createSuperForm(elements, element_fields, element_values)
+
+
+def getCCIForm_old():
     """Gets the CCI form generated from the superform above.
 
     Returns:
diff --git a/source/forms/views.py b/source/forms/views.py
index e0e90c7..08c89c2 100644
--- a/source/forms/views.py
+++ b/source/forms/views.py
@@ -5,6 +5,7 @@
 
 import sys
 import numpy
+import numpy as np
 from flask import flash
 from source.forms import forms
 
@@ -21,8 +22,9 @@
 
 # Creating the forms using a class generator #
 PreprocessForm = forms.getPreprocessForm()
-CCIForm = forms.getCCIForm()
+# CCIForm = forms.getCCIForm() #OLD
 ClusterForm = forms.getClusterForm()
+LRForm = forms.getLRForm()
 
 
 def run_preprocessing(request, adata, step_log):
@@ -77,90 +79,96 @@ def run_preprocessing(request, adata, step_log):
     return updated_page
 
 
+def run_lr(request, adata, step_log):
+    """Runs LR analysis."""
+
+    form = LRForm(request.form)
+
+    if not form.validate_on_submit():
+        flash_errors(form)
+
+    elif type(adata) == type(None):
+        flash("Need to load data first!")
+
+    else:
+        step_log["lr_params"] = vhs.getData(form)
+        print(step_log["lr_params"], file=sys.stdout)
+        elements = numpy.array(list(step_log["lr_params"].keys()))
+        # order: Species, Spot neighbourhood, min_spots, n_pairs, CPUs
+        element_values = list(step_log["lr_params"].values())
+        dist = element_values[1]
+        dist = dist if dist != -1 else None
+
+        # Loading the LR databases available within stlearn (from NATMI)
+        lrs = st.tl.cci.load_lrs(["connectomeDB2020_lit"], species=element_values[0])
+
+        # Running the analysis #
+        st.tl.cci.run(
+            adata,
+            lrs,
+            min_spots=element_values[2],
+            distance=dist,
+            n_pairs=element_values[3],
+            n_cpus=element_values[-1],
+        )
+        flash("LR analysis is completed!")
+
+    step_log["lr"][0] = "lr_summary" in adata.uns
+
+    updated_page = render_template(
+        "lr.html",
+        title=step_log["lr"][1],
+        lr_form=form,
+        flash_bool=True,
+        step_log=step_log,
+    )
+    return updated_page
+
+
 def run_cci(request, adata, step_log):
     """Performs CCI analysis."""
 
+    CCIForm = forms.getCCIForm(adata)
     form = CCIForm(request.form)
 
-    step_log["cci_params"] = vhs.getData(form)
-    print(step_log["cci_params"], file=sys.stdout)
-    elements = numpy.array(list(step_log["cci_params"].keys()))
-    # order: cell_het file, neighbour_dist, L-R pairs, permutations
-    element_values = list(step_log["cci_params"].values())
-
-    cell_het = type(element_values[0]) != type(None)
-    lrs, msg = vhs.getLR(element_values[2], adata.var_names)
-    print(lrs, file=sys.stdout)
-
     if not form.validate_on_submit():
         flash_errors(form)
 
     elif type(adata) == type(None):
         flash("Need to load data first!")
 
-    elif msg != "":
-        flash(msg)
-
     else:
-        """If we have been through the steps of:
-        1. Choosing with/without cell heterogeneity information.
-        2. Choosing with/without permutation testing.
-        3. Filling out information.
-        We are now ready to take the form input & perform CCI analysis.
-        """
-        try:
-            adata.uns["lr"] = lrs
-            st.tl.cci.lr(adata=adata, distance=element_values[1])
-            st.pl.het_plot(adata, use_het="cci_lr", image_alpha=0.7)
-            savePlot("cell_lr.png")
-
-            dist, n_pairs = element_values[1], element_values[-1]
-            if cell_het:  # Conduct with cell heterogeneity information #
-                print("We are using the cell heterogeneity!", file=sys.stdout)
-                # Adding the label transfer information #
-                st.add.labels(adata, element_values[0], sep="\t")
-                st.pl.cluster_plot(adata, use_label="predictions")
-                savePlot("label_transfer.png")  # saves to temp_pots
-
-                # Calculating cell heterogeneity #
-                st.tl.cci.het.count(adata, distance=dist, use_label="label_transfer")
-                st.pl.het_plot(adata, use_het="cci_het")
-                savePlot("cell_het.png")
-
-                # Merging with the lR values #
-                st.tl.cci.merge(adata, use_lr="cci_lr", use_het="cci_het")
-                st.pl.het_plot(adata, use_het="merged", cell_alpha=0.7)
-                savePlot("merged.png")
-
-            if n_pairs != 0:  # Permutation testing #
-                st.tl.cci.permutation(
-                    adata,
-                    use_het="cci_het" if cell_het else None,
-                    n_pairs=n_pairs,
-                    distance=dist,
-                )
-                st.pl.het_plot(
-                    adata,
-                    cell_alpha=0.7,
-                    use_het="merged_pvalues" if cell_het else "lr_pvalues",
-                )
-                savePlot("cci-log10pvalues.png")
-
-                st.pl.het_plot(
+        step_log["cci_params"] = vhs.getData(form)
+        print(step_log["cci_params"], file=sys.stdout)
+        elements = numpy.array(list(step_log["cci_params"].keys()))
+        # order: cell_type, min_spots, spot_mixtures, cell_prop_cutoff, sig_spots
+        #           n_perms
+        element_values = list(step_log["cci_params"].values())
+
+        if not form.validate_on_submit():
+            flash_errors(form)
+
+        else:
+            try:
+                # Running the counting of co-occurence of cell types and LR expression #
+                st.tl.cci.run_cci(
                     adata,
-                    cell_alpha=0.7,
-                    use_het="merged_sign" if cell_het else "lr_sign",
+                    element_values[0],
+                    min_spots=element_values[1],
+                    spot_mixtures=element_values[2],
+                    cell_prop_cutoff=element_values[3],
+                    sig_spots=True,  # Should make this not optional..
+                    n_perms=element_values[4],
                 )
-                savePlot("cci-sig-log10pvalues.png")
 
-            step_log["cci"][0] = True
+                flash("CCI analysis is completed!")
 
-            flash("CCI analysis is completed!")
+            except Exception as msg:
+                traceback.print_exc(file=sys.stdout)
+                flash("Analysis ERROR: " + str(msg))
+                print(msg)
 
-        except Exception as msg:
-            traceback.print_exc(file=sys.stdout)
-            flash("Analysis ERROR: " + str(msg))
-            print(msg)
+    step_log["cci"][0] = np.any(["lr_cci_" in key for key in adata.uns])
 
     updated_page = render_template(
         "cci.html",
diff --git a/source/readme.md b/source/readme.md
index ccfc47f..1ff1c27 100644
--- a/source/readme.md
+++ b/source/readme.md
@@ -1,31 +1,28 @@
 # Pre-processing Form Design Notes
 Flow of data:
 
-    app.py/preprocessing() 
+    app.py/preprocessing()
        -> source/forms/views.py/run_preprocessing(request, adata, step_log)
           -> source/forms/forms.py/getPreprocessForm()
           -> templates/preprocessing.html
              -> templates/superform.html
 
-Notes:    
-                  
+Notes:
+
     * step_log defined in app.py, keeps track whether pre-processing was run.
         -> If not run, then run_preprocessing shows just the form.
         -> If has run, shows banner that preprocessing complete.
-    
+
     * If attempt to run_preprocessing() when adata not yet loaded, shows banner
-        indicating need to upload the data first. 
-        
-    * source/forms/forms.py/getPreprocessForm() generates a WTForm class using a 
+        indicating need to upload the data first.
+
+    * source/forms/forms.py/getPreprocessForm() generates a WTForm class using a
         general WTForm generator, as defined in:
         source/forms/forms.py/createSuperForm()
-        
+
     * templates/preprocessing.html is the preprocessing page, which also injects
-        in a form to display using templates/superform.html.     
-        
-    * templates/superform.html renders a general WTForm that was created using 
+        in a form to display using templates/superform.html.
+
+    * templates/superform.html renders a general WTForm that was created using
         the source/forms/forms.py/createSuperForm() function, thereby allowing
-        easy generation of new forms if need to add extra information. 
-        
-    
-    
+        easy generation of new forms if need to add extra information.
diff --git a/static/img/Settings.gif b/static/img/Settings.gif
index 5487e4b..6c170a8 100644
Binary files a/static/img/Settings.gif and b/static/img/Settings.gif differ
diff --git a/templates/__init__.py b/templates/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/templates/base.html b/templates/base.html
index 2a14f39..e866686 100644
--- a/templates/base.html
+++ b/templates/base.html
@@ -66,6 +66,11 @@
               <i class="material-icons">settings_suggest</i>
               <p>Preprocessing</p>
             </a>
+          </li><li class="nav-item">
+            <a class="nav-link disabled" id="lr" href="/lr">
+              <i class="material-icons">cable</i>
+              <p>Ligand-receptor interaction</p>
+            </a>
           </li>
           <li class="nav-item">
             <a class="nav-link disabled" id="cci" href="/cci">
@@ -110,9 +115,15 @@
             </a>
           </li>
           <li class="nav-item">
-            <a class="nav-link disabled" id="cci_plot" href="/cci_plot">
+            <a class="nav-link disabled" id="lr_plot" href="/lr_plot">
               <i class="material-icons">calendar_view_month</i>
-              <p>Cci plot</p>
+              <p>LR plot</p>
+            </a>
+          </li>
+	        <li class="nav-item">
+            <a class="nav-link disabled" id="spatial_cci_plot" href="/spatial_cci_plot">
+              <i class="material-icons">calendar_view_month</i>
+              <p>Spatial CCI plot</p>
             </a>
           </li>
           <!-- your sidebar here -->
@@ -164,6 +175,11 @@
 
     {% if step_log.cci[0] %}
       $( "#cci_plot" ).removeClass( "disabled" )
+      $( "#spatial_cci_plot" ).removeClass( "disabled" )
+    {% endif %}
+
+    {% if step_log.lr[0] %}
+      $( "#lr_plot" ).removeClass( "disabled" )
     {% endif %}
 
     {% if step_log.clustering[0] %}
@@ -173,6 +189,7 @@
     {% endif %}
 
     {% if step_log.preprocessed[0] %}
+      $( "#lr" ).removeClass( "disabled" )
       $( "#cci" ).removeClass( "disabled" )
       $( "#clustering" ).removeClass( "disabled" )
     {% endif %}
diff --git a/templates/cci.html b/templates/cci.html
index db7c25b..958a592 100644
--- a/templates/cci.html
+++ b/templates/cci.html
@@ -15,11 +15,6 @@ <h4 class="card-title">Cell-cell interaction analysis</h4>
 	    {% include "superform.html" %}
 	    {% endwith %}
 
-		<footer>
-			<font color="red"> *Optional </font>
-			<br />
-			<font color="red"> **Required </font>
-		</footer>
 	</div>
 </div>
 {% endblock %}
diff --git a/templates/cci_old.html b/templates/cci_old.html
new file mode 100644
index 0000000..db7c25b
--- /dev/null
+++ b/templates/cci_old.html
@@ -0,0 +1,29 @@
+{% extends 'base.html' %}
+
+{% block content %}
+<div class="card">
+	<div class="card-header card-header-primary">
+		<h4 class="card-title">Cell-cell interaction analysis</h4>
+	</div>
+	<div class="card-body">
+
+		{# Gives the user errors if didn't fill out form correctly #}
+		{% include "flash_header.html" %}
+
+		{# Below is the form. #}
+	    {% with superForm=cci_form %}
+	    {% include "superform.html" %}
+	    {% endwith %}
+
+		<footer>
+			<font color="red"> *Optional </font>
+			<br />
+			<font color="red"> **Required </font>
+		</footer>
+	</div>
+</div>
+{% endblock %}
+
+{% block status %}
+{% include "progress.html" %}
+{% endblock %}
diff --git a/templates/lr.html b/templates/lr.html
new file mode 100644
index 0000000..501d12c
--- /dev/null
+++ b/templates/lr.html
@@ -0,0 +1,24 @@
+{% extends 'base.html' %}
+
+{% block content %}
+<div class="card">
+	<div class="card-header card-header-primary">
+		<h4 class="card-title">Ligand-receptor interaction analysis</h4>
+	</div>
+	<div class="card-body">
+
+		{# Gives the user errors if didn't fill out form correctly #}
+		{% include "flash_header.html" %}
+
+		{# Below is the form. #}
+	    {% with superForm=lr_form %}
+	    {% include "superform.html" %}
+	    {% endwith %}
+
+	</div>
+</div>
+{% endblock %}
+
+{% block status %}
+{% include "progress.html" %}
+{% endblock %}
diff --git a/templates/lr_plot.html b/templates/lr_plot.html
new file mode 100644
index 0000000..724ec06
--- /dev/null
+++ b/templates/lr_plot.html
@@ -0,0 +1,20 @@
+{% extends 'base.html' %}
+{% block content %}
+  <div class="card">
+   <div class="card-header card-header-primary">
+		<h4 class="card-title">Ligand-receptor significant interactions plot</h4>
+		<p class="card-category">Interactive version</p>
+   </div>
+   <div class="card-body">
+		 {{ script|safe }}
+		 <div id="overlay">
+	         <img src="{{ url_for('static', filename='img/loading_gif.gif') }}" alt="Loading" />
+	         Loading plot...
+         </div>
+   </div>
+</div>
+{% endblock %}
+
+{% block status %}
+{% include "progress.html" %}
+{% endblock %}
diff --git a/templates/spatial_cci_plot.html b/templates/spatial_cci_plot.html
new file mode 100644
index 0000000..cb7ef9c
--- /dev/null
+++ b/templates/spatial_cci_plot.html
@@ -0,0 +1,20 @@
+{% extends 'base.html' %}
+{% block content %}
+  <div class="card">
+   <div class="card-header card-header-primary">
+		<h4 class="card-title">Spatial cell-cell interactions plot</h4>
+		<p class="card-category">Interactive version</p>
+   </div>
+   <div class="card-body">
+		 {{ script|safe }}
+		 <div id="overlay">
+	         <img src="{{ url_for('static', filename='img/loading_gif.gif') }}" alt="Loading" />
+	         Loading plot...
+         </div>
+   </div>
+</div>
+{% endblock %}
+
+{% block status %}
+{% include "progress.html" %}
+{% endblock %}
diff --git a/templates/upload.html b/templates/upload.html
index c69316c..0202328 100644
--- a/templates/upload.html
+++ b/templates/upload.html
@@ -9,7 +9,7 @@ <h4 class="card-title">Uploading files</h4>
    </div>
    <div class="card-body">
 		<div class="frame">
-			<form action = "http://localhost:5000/folder_uploader" method = "POST" enctype = "multipart/form-data" class = "center">
+			<form action = "{{ url_for('folder_uploader') }}" method = "POST" enctype = "multipart/form-data" class = "center">
 				<div class="title">
 					<h2>Option 1: Open Visium data</h2>
 				</div>
@@ -32,7 +32,7 @@ <h5>Please select the path to your Visium folder. It should include: <br><b>filt
 
 		<br>
 		<div class="frame">
-			<form action = "http://localhost:5000/file_uploader" method = "POST" enctype = "multipart/form-data" class = "center">
+			<form action = "{{ url_for('file_uploader') }}" method = "POST" enctype = "multipart/form-data" class = "center">
 				<div class="title">
 					<h2>Option 2: Open AnnData object</h2>
 				</div>
diff --git a/wsgi.py b/wsgi.py
new file mode 100644
index 0000000..a209a5d
--- /dev/null
+++ b/wsgi.py
@@ -0,0 +1,4 @@
+from app import server
+
+if __name__ == "__main__":
+    server.run(host="0.0.0.0", port=8000, debug=True)