mcDETECT 1.0.0__tar.gz

mcDETECT-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Chenyang Yuan
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mcDETECT-1.0.0/PKG-INFO

@@ -0,0 +1,13 @@
+Metadata-Version: 2.1
+Name: mcDETECT
+Version: 1.0.0
+Summary: mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics
+Home-page: https://github.com/chen-yang-yuan/mcDETECT
+Author: Chenyang Yuan
+Author-email: chenyang.yuan@emory.edu
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE

mcDETECT-1.0.0/mcDETECT/__init__.py

@@ -0,0 +1 @@
+from .model import mcDETECT

mcDETECT-1.0.0/mcDETECT/model.py

@@ -0,0 +1,351 @@
+import anndata
+import math
+import miniball
+import numpy as np
+import pandas as pd
+import scanpy as sc
+from rtree import index
+from scipy.spatial import cKDTree
+from scipy.stats import poisson
+from shapely.geometry import Point
+from sklearn.cluster import DBSCAN
+
+
+def closest(lst, K):
+    return lst[min(range(len(lst)), key = lambda i: abs(lst[i] - K))]
+
+
+def make_tree(d1 = None, d2 = None, d3 = None):
+    active_dimensions = [dimension for dimension in [d1, d2, d3] if dimension is not None]
+    if len(active_dimensions) == 1:
+        points = np.c_[active_dimensions[0].ravel()]
+    elif len(active_dimensions) == 2:
+        points = np.c_[active_dimensions[0].ravel(), active_dimensions[1].ravel()]
+    elif len(active_dimensions) == 3:
+        points = np.c_[active_dimensions[0].ravel(), active_dimensions[1].ravel(), active_dimensions[2].ravel()]
+    return cKDTree(points)
+
+
+def make_rtree(spheres):
+    p = index.Property()
+    idx = index.Index(properties = p)
+    for i, sphere in enumerate(spheres.itertuples()):
+        center = Point(sphere.sphere_x, sphere.sphere_y)
+        bounds = (center.x - sphere.sphere_r,
+                  center.y - sphere.sphere_r,
+                  center.x + sphere.sphere_r,
+                  center.y + sphere.sphere_r)
+        idx.insert(i, bounds)
+    return idx
+
+
+class mcDETECT:
+    
+    
+    def __init__(self, type, transcripts, syn_genes, nc_genes = None, eps = 1.5, minspl = None, grid_len = 1.0, cutoff_prob = 0.95, alpha = 5.0, low_bound = 3,
+                 size_thr = 4.0, in_nucleus_thr = (0.5, 0.5), l = 1.0, rho = 0.2, s = 1.0, nc_top = 20, nc_thr = 0.1):
+        
+        self.type = type                        # string, iST platform, now support MERSCOPE, Xenium, and CosMx
+        self.transcripts = transcripts          # dataframe, transcripts file
+        self.syn_genes = syn_genes              # list, string, all synaptic markers
+        self.nc_genes = nc_genes                # list, string, all negative controls
+        self.eps = eps                          # numeric, searching radius epsilon
+        self.minspl = minspl                    # integer, manually select min_samples, i.e., no automatic parameter selection
+        self.grid_len = grid_len                # numeric, length of grids for computing the tissue area
+        self.cutoff_prob = cutoff_prob          # numeric, cutoff probability in parameter selection for min_samples
+        self.alpha = alpha                      # numeric, scaling factor in parameter selection for min_samples
+        self.low_bound = low_bound              # integer, lower bound in parameter selection for min_samples
+        self.size_thr = size_thr                # numeric, threshold for maximum radius of an aggregation
+        self.in_nucleus_thr = in_nucleus_thr    # 2-d tuple, threshold for low- and high-in-nucleus ratio
+        self.l = l                              # numeric, scaling factor for seaching overlapped spheres
+        self.rho = rho                          # numeric, threshold for determining overlaps
+        self.s = s                              # numeric, scaling factor for merging overlapped spheres
+        self.nc_top = nc_top                    # integer, number of negative controls retained for filtering
+        self.nc_thr = nc_thr                    # numeric, threshold for negative control filtering
+    
+    
+    # [INNER] construct grids, input for tissue_area()
+    def construct_grid(self, grid_len = None):
+        if grid_len is None:
+            grid_len = self.grid_len
+        x_min, x_max = np.min(self.transcripts['global_x']), np.max(self.transcripts['global_x'])
+        y_min, y_max = np.min(self.transcripts['global_y']), np.max(self.transcripts['global_y'])
+        x_min = np.floor(x_min / grid_len) * grid_len
+        x_max = np.ceil(x_max / grid_len) * grid_len
+        y_min = np.floor(y_min / grid_len) * grid_len
+        y_max = np.ceil(y_max / grid_len) * grid_len
+        x_bins = np.arange(x_min, x_max + grid_len, grid_len)
+        y_bins = np.arange(y_min, y_max + grid_len, grid_len)
+        return x_bins, y_bins
+    
+    
+    # [INNER] calculate tissue area, input for poisson_select()
+    def tissue_area(self):
+        x_bins, y_bins = self.construct_grid(grid_len = None)
+        hist, _, _ = np.histogram2d(self.transcripts['global_x'], self.transcripts['global_y'], bins = [x_bins, y_bins])
+        area = np.count_nonzero(hist) * (self.grid_len ** 2)
+        return area
+    
+    
+    # [INNER] calculate optimal min_samples, input for dbscan()
+    def poisson_select(self, gene_name):
+        num_trans = np.sum(self.transcripts['target'] == gene_name)
+        bg_density = num_trans / self.tissue_area()
+        cutoff_density = poisson.ppf(self.cutoff_prob, mu = self.alpha * bg_density * (np.pi * self.eps ** 2))
+        optimal_m = int(max(cutoff_density, self.low_bound))
+        return optimal_m
+    
+    
+    # [INTERMEDIATE] dictionary, low- and high-in-nucleus spheres for each synaptic marker
+    def dbscan(self, target_names = None, write_csv = False, write_path = './'):
+        
+        if self.type != 'Xenium':
+            z_grid = list(np.unique(self.transcripts['global_z']))
+            z_grid.sort()
+        
+        if target_names is None:
+            target_names = self.syn_genes
+        transcripts = self.transcripts[self.transcripts['target'].isin(target_names)]
+        
+        num_individual, data_low, data_high = [], {}, {}
+        
+        for j in target_names:
+            
+            # split transcripts
+            target = transcripts[transcripts['target'] == j]
+            others = transcripts[transcripts['target'] != j]
+            tree = make_tree(d1 = np.array(others['global_x']), d2 = np.array(others['global_y']), d3 = np.array(others['global_z']))
+            
+            # 3D DBSCAN
+            if self.minspl is None:
+                min_spl = self.poisson_select(j)
+            else:
+                min_spl = self.minspl
+            X = np.array(target[['global_x', 'global_y', 'global_z']])
+            db = DBSCAN(eps = self.eps, min_samples = min_spl, algorithm = 'kd_tree').fit(X)
+            labels = db.labels_
+            n_clusters = len(set(labels)) - (1 if -1 in labels else 0)
+            
+            # iterate over all aggregations
+            sphere_x, sphere_y, sphere_z, layer_z, sphere_r, sphere_size, sphere_comp, sphere_score = [], [], [], [], [], [], [], []
+            
+            for k in range(n_clusters):
+                
+                # find minimum enclosing spheres
+                temp = target[labels == k]
+                temp_in_nucleus = np.sum(temp['overlaps_nucleus'])
+                temp_size = temp.shape[0]
+                temp = temp[['global_x', 'global_y', 'global_z']]
+                temp = temp.drop_duplicates()
+                center, r2 = miniball.get_bounding_ball(np.array(temp), epsilon=1e-8)
+                if self.type != 'Xenium':
+                    closest_z = closest(z_grid, center[2])
+                else:
+                    closest_z = center[2]
+                
+                # calculate size, composition, and in-nucleus score
+                other_idx = tree.query_ball_point([center[0], center[1], center[2]], np.sqrt(r2))
+                other_trans = others.iloc[other_idx]
+                other_in_nucleus = np.sum(other_trans['overlaps_nucleus'])
+                other_size = other_trans.shape[0]
+                other_comp = len(np.unique(other_trans['target']))
+                total_size = temp_size + other_size
+                total_comp = 1 + other_comp
+                local_score = (temp_in_nucleus + other_in_nucleus) / total_size
+                
+                # record coordinate, radius, size, composition, and in-nucleus score
+                sphere_x.append(center[0])
+                sphere_y.append(center[1])
+                sphere_z.append(center[2])
+                layer_z.append(closest_z)
+                sphere_r.append(np.sqrt(r2))
+                sphere_size.append(total_size)
+                sphere_comp.append(total_comp)
+                sphere_score.append(local_score)
+            
+            # basic features for all spheres from each synaptic marker
+            sphere = pd.DataFrame(list(zip(sphere_x, sphere_y, sphere_z, layer_z, sphere_r, sphere_size, sphere_comp, sphere_score)),
+                                  columns = ['sphere_x', 'sphere_y', 'sphere_z', 'layer_z', 'sphere_r', 'size', 'comp', 'in_nucleus'])
+            sphere['gene'] = [j] * sphere.shape[0]
+            
+            # split low- and high-in-nucleus spheres
+            sphere_low = sphere[(sphere['sphere_r'] < self.size_thr) & (sphere['in_nucleus'] < self.in_nucleus_thr[0])]
+            sphere_high = sphere[(sphere['sphere_r'] < self.size_thr) & (sphere['in_nucleus'] > self.in_nucleus_thr[1])]
+            
+            if write_csv:
+                sphere_low.to_csv(write_path + j + ' sphere.csv', index=0)
+                sphere_high.to_csv(write_path + j + ' sphere_high.csv', index=0)
+            
+            num_individual.append(sphere_low.shape[0])
+            data_low[target_names.index(j)] = sphere_low
+            data_high[target_names.index(j)] = sphere_high
+            print("{} out of {} genes processed!".format(target_names.index(j) + 1, len(target_names)))
+        
+        return np.sum(num_individual), data_low, data_high
+    
+    
+    # [INNER] merge points from two overlapped spheres, input for remove_overlaps()
+    def find_points(self, sphere_a, sphere_b):
+        transcripts = self.transcripts[self.transcripts['target'].isin(self.syn_genes)]
+        tree_temp = make_tree(d1 = np.array(transcripts['global_x']), d2 = np.array(transcripts['global_y']), d3 = np.array(transcripts['global_z']))
+        idx_a = tree_temp.query_ball_point([sphere_a['sphere_x'], sphere_a['sphere_y'], sphere_a['sphere_z']], sphere_a['sphere_r'])
+        points_a = transcripts.iloc[idx_a]
+        points_a = points_a[points_a['target'] == sphere_a['gene']]
+        idx_b = tree_temp.query_ball_point([sphere_b['sphere_x'], sphere_b['sphere_y'], sphere_b['sphere_z']], sphere_b['sphere_r'])
+        points_b = transcripts.iloc[idx_b]
+        points_b = points_b[points_b['target'] == sphere_b['gene']]
+        points = pd.concat([points_a, points_b])
+        points = points[['global_x', 'global_y', 'global_z']]
+        return points
+    
+    
+    def remove_overlaps(self, set_a, set_b):
+        
+        set_a = set_a.copy()
+        set_b = set_b.copy()
+
+        # find possible overlaps on 2D by r-tree
+        idx_b = make_rtree(set_b)
+        for i, sphere_a in set_a.iterrows():
+            center_a_3D = (sphere_a.sphere_x, sphere_a.sphere_y, sphere_a.sphere_z)
+            bounds_a = (sphere_a.sphere_x - sphere_a.sphere_r,
+                        sphere_a.sphere_y - sphere_a.sphere_r,
+                        sphere_a.sphere_x + sphere_a.sphere_r,
+                        sphere_a.sphere_y + sphere_a.sphere_r)
+            possible_overlaps = idx_b.intersection(bounds_a)
+
+            # search 3D overlaps within possible overlaps
+            for j in possible_overlaps:
+                if j in set_b.index:
+                    sphere_b = set_b.loc[j]
+                    center_b_3D = (sphere_b.sphere_x, sphere_b.sphere_y, sphere_b.sphere_z)
+                    dist = math.dist(center_a_3D, center_b_3D)
+                    radius_sum = sphere_a.sphere_r + sphere_b.sphere_r
+                    radius_diff = sphere_a.sphere_r - sphere_b.sphere_r
+
+                    # relative positions (0: internal & intersect, 1: internal, 2: intersect)
+                    c0 = (dist < self.l * radius_sum)
+                    c1 = (dist <= self.l * np.abs(radius_diff))
+                    c1_1 = (radius_diff > 0)
+                    c2_1 = (dist < self.rho * self.l * radius_sum)
+
+                    # operations on dataframes
+                    if c0:
+                        if c1 and c1_1:                             # keep A and remove B
+                            set_b.drop(index = j, inplace = True)
+                        elif c1 and not c1_1:                       # replace A with B and remove B
+                            set_a.loc[i] = set_b.loc[j]
+                            set_b.drop(index = j, inplace = True)
+                        elif not c1 and c2_1:                       # replace A with new sphere and remove B
+                            points_union = np.array(self.find_points(sphere_a, sphere_b))
+                            new_center, new_radius = miniball.get_bounding_ball(points_union, epsilon=1e-8)
+                            set_a.loc[i, 'sphere_x'] = new_center[0]
+                            set_a.loc[i, 'sphere_y'] = new_center[1]
+                            set_a.loc[i, 'sphere_z'] = new_center[2]
+                            set_a.loc[i, 'sphere_r'] = self.s * new_radius
+                            set_b.drop(index = j, inplace = True)
+        
+        set_a = set_a.reset_index(drop = True)
+        set_b = set_b.reset_index(drop = True)
+        return set_a, set_b
+    
+    
+    # [INNER] merge spheres from different synaptic markers, input for detect()
+    def merge_sphere(self, sphere_dict):
+        sphere = sphere_dict[0].copy()
+        for j in range(1, len(self.syn_genes)):
+            target_sphere = sphere_dict[j]
+            sphere, target_sphere_new = self.remove_overlaps(sphere, target_sphere)
+            sphere = pd.concat([sphere, target_sphere_new])
+            sphere = sphere.reset_index(drop = True)
+        return sphere
+    
+    
+    # [INNER] negative control filtering, input for detect()
+    def nc_filter(self, sphere_low, sphere_high):
+        
+        # negative control gene profiling
+        adata_low = self.profile(sphere_low, self.nc_genes)
+        adata_high = self.profile(sphere_high, self.nc_genes)
+        adata = anndata.concat([adata_low, adata_high], axis = 0, merge = "same")
+        adata.var['genes'] = adata.var.index
+        adata.obs_keys = list(np.arange(adata.shape[0]))
+        adata.obs['type'] = ['low'] * adata_low.shape[0] + ['high'] * adata_high.shape[0]
+        adata.obs['type'] = pd.Categorical(adata.obs['type'], categories = ["low", "high"], ordered = True)
+        
+        # DE analysis of negative control genes
+        sc.tl.rank_genes_groups(adata, 'type', method = 't-test')
+        names = adata.uns['rank_genes_groups']['names']
+        names = pd.DataFrame(names)
+        logfc = adata.uns['rank_genes_groups']['logfoldchanges']
+        logfc = pd.DataFrame(logfc)
+        pvals = adata.uns['rank_genes_groups']['pvals']
+        pvals = pd.DataFrame(pvals)
+
+        # select top upregulated negative control genes
+        df = pd.DataFrame({'names': names["high"], 'logfc': logfc["high"], 'pvals': pvals["high"]})
+        df = df[df['logfc'] >= 0]
+        df = df.sort_values(by = ['pvals'], ascending = True)
+        nc_genes_final = list(df['names'].head(self.nc_top))
+        
+        # negative control filtering
+        nc_transcripts_final = self.transcripts[self.transcripts['target'].isin(nc_genes_final)]
+        tree = make_tree(d1 = np.array(nc_transcripts_final['global_x']), d2 = np.array(nc_transcripts_final['global_y']), d3 = np.array(nc_transcripts_final['global_z']))
+        pass_idx = [0] * sphere_low.shape[0]
+        for i in range(sphere_low.shape[0]):
+            temp = sphere_low.iloc[i]
+            nc_idx = tree.query_ball_point([temp['sphere_x'], temp['sphere_y'], temp['sphere_z']], temp['sphere_r'])
+            if len(nc_idx) == 0:
+                pass_idx[i] = 1
+            elif len(nc_idx) / temp['size'] < self.nc_thr:
+                pass_idx[i] = 2
+        sphere = sphere_low[np.array(pass_idx) != 0]
+        sphere = sphere.reset_index(drop = True)
+        return sphere
+    
+    
+    # [MAIN] dataframe, metadata of identified synapses
+    def detect(self):
+        
+        _, data_low, data_high = self.dbscan()
+        
+        print("Merging spheres...")
+        sphere_low, sphere_high = self.merge_sphere(data_low), self.merge_sphere(data_high)
+        
+        if self.nc_genes is None:
+            return sphere_low
+        else:
+            print("Negative control filtering...")
+            return self.nc_filter(sphere_low, sphere_high)
+    
+    
+    # [MAIN] anndata, spatial transcriptome profile of identified synapses
+    def profile(self, synapse, genes = None, print_itr = False):
+        
+        if genes is None:
+            genes = list(np.unique(self.transcripts['target']))
+            transcripts = self.transcripts
+        else:
+            transcripts = self.transcripts[self.transcripts['target'].isin(genes)]
+        tree = make_tree(d1 = np.array(transcripts['global_x']), d2 = np.array(transcripts['global_y']), d3 = np.array(transcripts['global_z']))
+        
+        # construct gene count matrix
+        X = np.zeros((len(genes), synapse.shape[0]))
+        for i in range(synapse.shape[0]):
+            temp = synapse.iloc[i]
+            target_idx = tree.query_ball_point([temp['sphere_x'], temp['sphere_y'], temp['layer_z']], temp['sphere_r'])
+            target_trans = transcripts.iloc[target_idx]
+            target_gene = list(target_trans['target'])
+            for j in np.unique(target_gene):
+                X[genes.index(j), i] = target_gene.count(j)
+            if (print_itr) & (i % 5000 == 0):
+                print('{} out of {} synapses profiled!'.format(i, synapse.shape[0]))
+        
+        # construct spatial transcriptome profile
+        adata = anndata.AnnData(X = np.transpose(X), obs = synapse)
+        adata.obs['synapse_id'] = ['syn_{}'.format(i) for i in range(synapse.shape[0])]
+        adata.obs.rename(columns = {'sphere_x': 'global_x', 'sphere_y': 'global_y', 'sphere_z': 'global_z'}, inplace = True)
+        adata.var['genes'] = genes
+        adata.var_names = genes
+        adata.var_keys = genes
+        return adata

mcDETECT-1.0.0/mcDETECT.egg-info/PKG-INFO

@@ -0,0 +1,13 @@
+Metadata-Version: 2.1
+Name: mcDETECT
+Version: 1.0.0
+Summary: mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics
+Home-page: https://github.com/chen-yang-yuan/mcDETECT
+Author: Chenyang Yuan
+Author-email: chenyang.yuan@emory.edu
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE

mcDETECT-1.0.0/mcDETECT.egg-info/SOURCES.txt

@@ -0,0 +1,11 @@
+LICENSE
+README.md
+pyproject.toml
+setup.py
+mcDETECT/__init__.py
+mcDETECT/model.py
+mcDETECT.egg-info/PKG-INFO
+mcDETECT.egg-info/SOURCES.txt
+mcDETECT.egg-info/dependency_links.txt
+mcDETECT.egg-info/requires.txt
+mcDETECT.egg-info/top_level.txt

mcDETECT-1.0.0/mcDETECT.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

mcDETECT-1.0.0/mcDETECT.egg-info/requires.txt

@@ -0,0 +1,9 @@
+anndata
+miniball
+numpy
+pandas
+rtree
+scanpy
+scipy
+shapely
+sklearn

mcDETECT-1.0.0/mcDETECT.egg-info/top_level.txt

@@ -0,0 +1 @@
+mcDETECT

mcDETECT-1.0.0/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

mcDETECT-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

mcDETECT-1.0.0/setup.py

@@ -0,0 +1,20 @@
+from setuptools import setup, find_packages
+
+setup(
+    name = "mcDETECT",
+    version = "1.0.0",
+    packages = find_packages(),
+    install_requires = ["anndata", "miniball", "numpy", "pandas", "rtree", "scanpy", "scipy", "shapely", "sklearn"],
+    author = "Chenyang Yuan",
+    author_email = "chenyang.yuan@emory.edu",
+    description = "mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics",
+    long_description = open("README.md").read(),
+    long_description_content_type = "text/markdown",
+    url = "https://github.com/chen-yang-yuan/mcDETECT",
+    classifiers = [
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires = ">=3.6",
+)