View all bits in display_results method in Pixel Decoder

examples/bioprotean_mouse/04_pixeldecode.py

@@ -75,5 +75,5 @@ def decode_pixels(
         datastore.save_mtx()
 
 if __name__ == "__main__":
-    root_path = Path(r"/mnt/data/bartelle/20241108_Bartelle_MouseMERFISH_LC")
+    root_path = Path(r"/data/smFISH/12062024_Bartelle24hrcryo_sample2")
     decode_pixels(root_path=root_path,run_baysor=False)

examples/bioprotean_smFISH/smFISH_decoding.py

@@ -0,0 +1,34 @@
+from merfish3danalysis.qi2labDataStore import qi2labDataStore
+from merfish3danalysis.PixelDecoder import PixelDecoder
+from pathlib import Path
+# import numpy as np
+
+root_path = Path(r"/data/smFISH/02202025_Bartelle_control_smFISH_TqIB")
+
+# initialize datastore
+datastore_path = root_path / Path(r"qi2labdatastore")
+datastore = qi2labDataStore(datastore_path)
+merfish_bits = datastore.num_bits
+
+# initialize decodor class
+decoder = PixelDecoder(
+    datastore=datastore, 
+    use_mask=False, 
+    merfish_bits=merfish_bits, 
+    verbose=1,
+    smFISH = True
+)
+
+# decode one tile
+decoder.decode_one_tile(
+    tile_idx=0,  # Specify the tile index
+    display_results=True,  # Set to True to visualize results in Napari
+    lowpass_sigma=(3, 1, 1),  # Lowpass filter sigma
+    magnitude_threshold=0.9,  # L2-norm threshold
+    minimum_pixels=3.0,  # Minimum number of pixels for a barcode
+    use_normalization=False,  # Use normalization
+    ufish_threshold=0.5  # Ufish threshold
+)
+
+# # Save barcodes
+# decoder._save_barcodes()

examples/bioprotean_smFISH/smFISH_spot_detection.py

@@ -0,0 +1,52 @@
+from merfish3danalysis.qi2labDataStore import qi2labDataStore
+from pathlib import Path
+import pandas as pd
+
+root_path = Path(r"/data/smFISH/02202025_Bartelle_control_smFISH_TqIB")
+
+class smFISH_spotdetection:
+    def __init__(self, datastore, threshold=5):
+        self.datastore = datastore
+        self.threshold = threshold
+
+    def read_ufish_localizations(self, tile_id, bit_id):
+        self._ufish_localizations_root_path = self.datastore._ufish_localizations_root_path
+        current_ufish_localizations_path = (
+            self._ufish_localizations_root_path
+            / Path(tile_id)
+            / Path(bit_id + ".parquet")
+        )
+        if not current_ufish_localizations_path.exists():
+            raise FileNotFoundError(f"File {current_ufish_localizations_path} does not exist.")
+        return pd.read_parquet(current_ufish_localizations_path)
+
+    def get_tile_ids(self):
+        if not self.datastore._ufish_localizations_root_path.exists():
+            raise FileNotFoundError(f"Directory {self.datastore._ufish_localizations_root_path} does not exist.")
+        return sorted([p.name for p in self.datastore._ufish_localizations_root_path.iterdir() if p.is_dir()], key=lambda x: int(x.replace("tile", "")))
+
+    def get_bit_ids(self, tile_id):
+        tile_path = self.datastore._ufish_localizations_root_path / Path(tile_id)
+        if not tile_path.exists():
+            raise FileNotFoundError(f"Directory {tile_path} does not exist.")
+        return sorted([p.stem for p in tile_path.glob("*.parquet")], key=lambda x: int(x.replace("bit", "")))
+
+
+datastore_path = root_path / Path(r"qi2labdatastore")
+datastore = qi2labDataStore(datastore_path)
+smfish_class = smFISH_spotdetection(datastore)
+
+tile_ids = smfish_class.get_tile_ids()
+for tile_id in tile_ids:
+    bit_ids = smfish_class.get_bit_ids(tile_id)
+    for bit_id in bit_ids:
+        ufish_localizations_df = smfish_class.read_ufish_localizations(tile_id, bit_id)
+
+        ufish_probabilities = ufish_localizations_df.loc[:, "sum_prob_pixels"]
+        ufish_localizations_df["thresholded_probabilities"] = ufish_probabilities.where(ufish_probabilities >= smfish_class.threshold, 0)
+
+        output_path = datastore_path / "ufish_localizations_thresholded" / tile_id / f"{bit_id}_thresholded.parquet"
+        output_path.parent.mkdir(parents=True, exist_ok=True)
+        ufish_localizations_df.to_parquet(output_path)
+
+print("Thresholded probabilities saved")

src/merfish3danalysis/PixelDecoder.py

@@ -71,6 +71,7 @@ def __init__(
         use_mask: Optional[bool] = False,
         z_range: Optional[Sequence[int]] = None,
         include_blanks: Optional[bool] = True,
+        smFISH: bool = False
     ):
         self._datastore = datastore
         self._verbose = verbose
@@ -79,6 +80,10 @@ def __init__(
 
         self._n_merfish_bits = merfish_bits
 
+        # Is this data smFISH or MERFISH? 
+        # Default is False, meaning data is MERFISH
+        self._smFISH = smFISH
+
         if self._datastore.microscope_type == "2D":
             self._is_3D = False
         else:
@@ -956,8 +961,8 @@ def _extract_barcodes(
         for barcode_index in iterable_barcode:
             on_bits_indices = np.where(self._codebook_matrix[barcode_index])[0]
 
-            if len(on_bits_indices) == 1:
-                break
+            # if len(on_bits_indices) == 1:
+            #     break
 
             if self._is_3D:
                 if self._verbose > 1:
@@ -999,10 +1004,10 @@ def _extract_barcodes(
 
                 df_barcode = pd.DataFrame(props)
 
-                df_barcode["on_bit_1"] = on_bits_indices[0] + 1
-                df_barcode["on_bit_2"] = on_bits_indices[1] + 1
-                df_barcode["on_bit_3"] = on_bits_indices[2] + 1
-                df_barcode["on_bit_4"] = on_bits_indices[3] + 1
+                df_barcode["on_bit_1"] = on_bits_indices[0] + 1 if len(on_bits_indices) > 0 else 0
+                df_barcode["on_bit_2"] = on_bits_indices[1] + 1 if len(on_bits_indices) > 1 else 0
+                df_barcode["on_bit_3"] = on_bits_indices[2] + 1 if len(on_bits_indices) > 2 else 0
+                df_barcode["on_bit_4"] = on_bits_indices[3] + 1 if len(on_bits_indices) > 3 else 0
                 df_barcode["barcode_id"] = df_barcode.apply(
                     lambda x: (barcode_index + 1), axis=1
                 )
@@ -1116,10 +1121,10 @@ def _extract_barcodes(
 
                     df_barcode = pd.DataFrame(props)
 
-                    df_barcode["on_bit_1"] = on_bits_indices[0] + 1
-                    df_barcode["on_bit_2"] = on_bits_indices[1] + 1
-                    df_barcode["on_bit_3"] = on_bits_indices[2] + 1
-                    df_barcode["on_bit_4"] = on_bits_indices[3] + 1
+                    df_barcode["on_bit_1"] = on_bits_indices[0] + 1 if len(on_bits_indices) > 0 else 0
+                    df_barcode["on_bit_2"] = on_bits_indices[1] + 1 if len(on_bits_indices) > 1 else 0
+                    df_barcode["on_bit_3"] = on_bits_indices[2] + 1 if len(on_bits_indices) > 2 else 0
+                    df_barcode["on_bit_4"] = on_bits_indices[3] + 1 if len(on_bits_indices) > 3 else 0
                     df_barcode["barcode_id"] = df_barcode.apply(
                         lambda x: (barcode_index + 1), axis=1
                     )
@@ -1841,12 +1846,20 @@ def on_close_callback():
         app = QApplication.instance()
 
         app.lastWindowClosed.connect(on_close_callback)
-
-        viewer.add_image(
-            self._scaled_pixel_images,
-            scale=[self._axial_step, self._pixel_size, self._pixel_size],
-            name="pixels",
-        )
+
+        if self._smFISH:
+            for bit in range(self._datastore.num_bits):
+                viewer.add_image(
+                    self._scaled_pixel_images[bit],
+                    scale=[self._axial_step, self._pixel_size, self._pixel_size],
+                    name="pixels_" + str(bit),
+                )
+        else:
+            viewer.add_image(
+                self._scaled_pixel_images,
+                scale=[self._axial_step, self._pixel_size, self._pixel_size],
+                name="pixels",
+            )
 
         viewer.add_image(
             self._decoded_image,

src/merfish3danalysis/run_baysor.py

@@ -0,0 +1,11 @@
+
+
+
+#in pixeldecoder.py
+_reformat_barcodes_for_baysor
+
+# in qi2labdatastore.py
+
+_reformat_barcodes_for_baysor
+
+_run_baysor