@@ -26,77 +26,118 @@ def create_zstack_da(tif_path, name, add_chan=True, dims=("z", "y", "x"), fov_um
2626 da .attrs |= {f"scale_{ d } : s for d , s in zip (dims , pixel_sizes )}
2727 return da
2828
29- def get_zstack_sdata (zstack_path , zstack_masks_path , target_size , channel_names = ['gcamp' , 'dextran' ]):
30- def get_matching_metas (root ):
31- matches = []
32- for d in Path (root ).iterdir ():
33- if not d .is_dir (): continue
34- meta = _parse_stack_metadata (d ) # Extracts size and tif paths
35- if meta ['size' ] == target_size :
36- matches .append (meta )
37- return sorted (matches , key = lambda x : x ['name' ]) # Sort ensures Channel 0 -> gcamp
38-
39- img_metas = get_matching_metas (zstack_path )
40- mask_metas = get_matching_metas (zstack_masks_path )
29+ def parse_stack_metadata (folder , lookup_chans = ['gcamp' , 'dextran' ]):
30+ """Extracts size and specific channel name from naming convention."""
31+ # Pattern: Matches '400x400x450' and captures the following word (e.g., GCaMP)
32+ pattern = r'(\d+)x(\d+)x(\d+)'
33+ match = re .search (pattern , folder .name )
34+
35+ if match :
36+ width , height , depth = match .groups ()
37+ size = {"width" : int (width ), "height" : int (height ), "depth" : int (depth )}
38+ # Normalize channel name (e.g., GCaMP -> gcamp)
39+ detected_channels = [ch for ch in lookup_chans if ch in folder .name .lower ()]
40+ else :
41+ size = {"width" : None , "height" : None , "depth" : None }
42+ detected_channels = folder .name # Fallback
4143
42- sz = img_metas [0 ]['size' ]
44+ tifs = {d .name .lower (): list (d .glob ("*.tif" ))[0 ]
45+ for d in folder .iterdir () if d .is_dir () and "channel" in d .name .lower ()}
46+ jsons = {re .sub (r'.*_(registration|roi_groups|scanimage).*' , r'\1' , f .stem ): f
47+ for f in folder .glob ("*.json" )}
48+
49+ return {"size" : size , "detected_channels" : detected_channels , "tifs" : tifs , "jsons" : jsons , "name" : folder .name }
50+
51+ def get_zstack_elements (stack_folder , masks_folder , return_tables = False , chan_mapping = None , add_size_suffix = True ):
52+ if chan_mapping is None :
53+ chan_mapping = {
54+ 'channel_0_ref_0' : 'gcamp' ,
55+ 'channel_1_ref_1' : 'dextran'
56+ }
57+
58+ # Get metadata for stacks
59+ stack_meta = parse_stack_metadata (stack_folder , lookup_chans = list (chan_mapping .values ()))
60+ sz = stack_meta ['size' ]
4361 fov = (sz ['depth' ], sz ['height' ], sz ['width' ])
44- images , labels , tables = {}, {}, {}
4562
46- for i , img_meta in enumerate (img_metas ):
47- chan_name = channel_names [i ] if i < len (channel_names ) else f"channel_{ i }
48-
49- # Process Image
50- img_tif = next (iter (img_meta ['tifs' ].values ()))
51- img_da = create_zstack_da (img_tif , chan_name , add_chan = True , fov_um = fov )
52- images [chan_name ] = Image3DModel .parse (img_da , chunks = 'auto' )
63+ # Get stack channel images
64+ images = {}
65+ for chan , tif_path in stack_meta ['tifs' ].items ():
66+ chan_name = chan_mapping .get (chan , chan )
67+ img_da = create_zstack_da (tif_path , chan_name , add_chan = True , fov_um = fov )
68+ img_da .attrs .update ()
69+ images [chan_name ] = Image3DModel .parse (img_da ,
70+ c_coords = [chan_name ],
71+ chunks = 'auto' )
72+
73+ # If specified to keep names unique, add size suffix
74+ if add_size_suffix :
75+ size_suffix = f"{ fov [0 ]} { fov [1 ]} { fov [2 ]}
76+ images = {f"{ name } { size_suffix } : img for name , img in images .items ()}
77+
78+ # Use name of stack to get corresponding masks
79+ img_name = stack_meta ['name' ].split ('_registered' )[0 ]
80+ all_masks = list (masks_folder .iterdir ())
81+ matched_masks_path = [m for m in all_masks if img_name in m .name ]
82+ if matched_masks_path :
83+ matched_masks_path = matched_masks_path [0 ] if len (matched_masks_path ) == 1 else None
84+ if matched_masks_path is None :
85+ print (f"No matching mask found for { img_name } { masks_folder } )
5386
54- # Process Labels & Tables
55- if i < len (mask_metas ):
56- mask_meta = mask_metas [i ]
57- mask_tif = next (iter (mask_meta ['tifs' ].values ()))
58- label_key = f"{ chan_name }
59-
60- mask_da = create_zstack_da (mask_tif , label_key , add_chan = False , fov_um = fov )
61- labels [label_key ] = Labels3DModel .parse (mask_da , chunks = 'auto' )
62-
63- # Table logic
87+ # Get mask metadata
88+ masks_meta = parse_stack_metadata (matched_masks_path , lookup_chans = list (chan_mapping .values ()))
89+
90+ # Get labels and tables for each mask channel
91+ labels = {}
92+ tables = {}
93+ for chan , tif_path in masks_meta ['tifs' ].items ():
94+ chan_name = chan_mapping .get (chan , chan )
95+ labels_name = f"{ chan_name }
96+ if add_size_suffix :
97+ labels_name = f"{ labels_name } { size_suffix }
98+ mask_da = create_zstack_da (tif_path , labels_name , add_chan = False , fov_um = fov )
99+ labels [labels_name ] = Labels3DModel .parse (mask_da , chunks = 'auto' )
100+ if return_tables :
101+ # Corresponding table
64102 unique_ids = np .unique (mask_da .values )
65103 unique_ids = unique_ids [unique_ids > 0 ]
66104 obs = pd .DataFrame (unique_ids , columns = [f"{ chan_name } ], index = unique_ids .astype (str ))
67- obs ['region' ] = label_key
105+ obs ['region' ] = labels_name
68106 ann = ad .AnnData (obs = obs )
69- tables [f"{ chan_name } ] = TableModel .parse (ann , region = label_key , region_key = 'region' , instance_key = f"{ chan_name } )
107+ table_name = f"{ chan_name }
108+ if add_size_suffix :
109+ table_name = f"{ table_name } { size_suffix }
110+ tables [table_name ] = TableModel .parse (ann , region = labels_name , region_key = 'region' , instance_key = f"{ chan_name } )
111+
112+ return images , labels , tables
70113
71- sdata = sd .SpatialData (images = images , labels = labels , tables = tables )
114+ def get_zstacks_sdata (stacks_folder , masks_folder , return_tables = False , chan_mapping = None ):
115+ if chan_mapping is None :
116+ chan_mapping = {
117+ 'channel_0_ref_0' : 'gcamp' ,
118+ 'channel_1_ref_1' : 'dextran'
119+ }
120+ all_stacks = list (stacks_folder .iterdir ())
121+ combined_images = {}
122+ combined_labels = {}
123+ combined_tables = {}
124+ if len (all_stacks ) > 1 :
125+ add_size_suffix = True
126+ else :
127+ add_size_suffix = False
128+ for zstack_folder in all_stacks :
129+ images , labels , tables = get_zstack_elements (zstack_folder , masks_folder , return_tables = return_tables , chan_mapping = chan_mapping , add_size_suffix = add_size_suffix )
130+ combined_images .update (images )
131+ combined_labels .update (labels )
132+ if tables :
133+ combined_tables .update (tables )
72134
135+ # Combine into SpatialData
136+ sdata = sd .SpatialData (images = combined_images , labels = combined_labels , tables = combined_tables )
73137 # Apply Transformations
74138 for el_type in ['images' , 'labels' ]:
75139 for name , el in getattr (sdata , el_type ).items ():
76140 set_transformation (el , Identity (), "global" )
77141 scale = Scale ([el .attrs [f"scale_{ d } ] for d in ['z' , 'y' , 'x' ]], axes = ('z' , 'y' , 'x' ))
78142 set_transformation (el , scale , "microns" )
79-
80- return sdata
81-
82- def _parse_stack_metadata (folder ):
83- """Extracts size and specific channel name from the Allen Institute folder naming convention."""
84- # Pattern: Matches '400x400x450' and captures the following word (e.g., GCaMP)
85- pattern = r'(\d+)x(\d+)x(\d+)-([^_]+)'
86- match = re .search (pattern , folder .name )
87-
88- if match :
89- width , height , depth , channel = match .groups ()
90- size = {"width" : int (width ), "height" : int (height ), "depth" : int (depth )}
91- # Normalize channel name (e.g., GCaMP -> gcamp)
92- detected_channel = channel .lower ()
93- else :
94- size = {"width" : None , "height" : None , "depth" : None }
95- detected_channel = folder .name # Fallback
96-
97- tifs = {d .name .lower (): list (d .glob ("*.tif" ))[0 ]
98- for d in folder .iterdir () if d .is_dir () and "channel" in d .name .lower ()}
99- jsons = {re .sub (r'.*_(registration|roi_groups|scanimage).*' , r'\1' , f .stem ): f
100- for f in folder .glob ("*.json" )}
101-
102- return {"size" : size , "detected_channel" : detected_channel , "tifs" : tifs , "jsons" : jsons , "name" : folder .name }
143+ return sdata
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