diff --git a/src/napari_mm3/_compile.py b/src/napari_mm3/_compile.py
index b155697..55b4bfc 100644
--- a/src/napari_mm3/_compile.py
+++ b/src/napari_mm3/_compile.py
@@ -66,42 +66,42 @@ def get_time(filepath: str) -> Union[np.int_, None]:
         return None
 
 
-def restack_planes(found_files_c1: list, found_files_c2: list, params: dict) -> None:
+def stack_channels(found_files: np.ndarray, params: dict) -> None:
     """Check if phase and fluorescence channels are separate tiffs.
     If so, restack them as one tiff file and save out to TIFF_dir.
-    Move the original files to a new directory TIFF_unstacked.
+    Move the original files to a new directory original_TIFF.
 
     Parameters
     ---------
-    found_files_c1: list of files for 1st imaging plane
-    found_files_c1: list of files for 2nd imaging plane
+    found_files: ndarray of filepaths for each imaging plane
+    params: dictionary of parameters
 
     Returns
     ---------
     None
     """
 
-    found_files_c1 = sorted(found_files_c1)
-    found_files_c2 = sorted(found_files_c2)
+    found_files = np.transpose(found_files)
 
-    for f1, f2 in zip(found_files_c1, found_files_c2):
-        information("Merging images " + str(f1) + " and " + str(f2))
-        im1 = tiff.imread(f1)
-        im2 = tiff.imread(f2)
-        im_out = np.stack((im1, im2), axis=0)
+    for files in found_files:
+        information('Merging files')
+        print(*files, sep='\n')
+        ims = [tiff.imread(f) for f in files]
+        im_out = np.stack(ims, axis=0)
 
         # need to insert regex here to catch variants
-        name_out = re.sub("c*01", "", re.IGNORECASE)
+        name_out = re.sub("c\d+", "", str(files[0]), flags = re.IGNORECASE)
         # 'minisblack' necessary to ensure that it interprets image as black/white.
         tiff.imwrite(name_out, im_out, photometric="minisblack")
 
-        ## make a new directory rather than just deleting the old images
-        old_tiff_path = params["TIFF_dir"].parent / "TIFF_unstacked"
+        ## make a new directory for the old images
+        old_tiff_path = params["TIFF_dir"].parent / "original_TIFF"
         if not old_tiff_path.exists():
             old_tiff_path.mkdir()
             information("Creating directory for original TIFFs")
-        f1.replace(str(f1).replace(str(params["TIFF_dir"]), "TIFF_unstacked"))
-        f2.replace(str(f2).replace(str(params["TIFF_dir"]), "TIFF_unstacked"))
+        
+        for f in files:
+            f.replace(str(f).replace(str(params["TIFF_dir"]), "original_TIFF"))
 
     return
 
@@ -290,7 +290,7 @@ def get_tif_metadata_filename(tif: tiff.TiffFile) -> dict:
         "t": get_time(tif.filename),  # time point
         "jd": -1 * 0.0,  # absolute julian time
         "planes": get_plane(tif.filename),
-    }  # y position on stage [um]
+    }
 
     return idata
 
@@ -1283,20 +1283,29 @@ def compile(params: dict) -> None:
 
     ## need to stack phase and fl plane if not exported from .nd2
     if params["TIFF_source"] == "BioFormats / other TIFF":
-        information("Checking if phase & fluorescence planes are separated")
+        information("Checking if imaging channels are separated")
         found_files = list(params["TIFF_dir"].glob("*.tif"))
         found_files = sorted(found_files)  # sort by timepoint
 
-        string_c1 = re.compile("c(0)*1", re.IGNORECASE)
-        string_c2 = re.compile("c(0)*2", re.IGNORECASE)
-
-        found_files_c1 = [f for f in found_files if re.search(string_c1, f.name)]
-        found_files_c2 = [f for f in found_files if re.search(string_c2, f.name)]
+        files_list = []
+        i = 0
+        while True:
+            c_string = re.compile(f"c(0)*{i}[._]", re.IGNORECASE)
+            matched_files = [f for f in found_files if re.search(c_string, f.name)]
+            if matched_files:
+                files_list.append(matched_files)
+                i+=1
+            elif i == 0:
+                # continue in case channels indexed from 1
+                i+=1
+            else:
+                break
 
-        ## if there is a second plane, stack and save them out
-        if found_files_c2:
-            information("Restacking TIFFs")
-            restack_planes(found_files_c1, found_files_c2, params)
+        files_array = np.array(files_list).squeeze()
+        if files_array.ndim > 1:
+            information("Merging TIFFs across channel")
+            stack_channels(files_array, params)
+        
         else:
             pass
 
@@ -1363,10 +1372,9 @@ def compile(params: dict) -> None:
 def load_fov(image_directory: Path, fov_id: int, filter_str: str = "") -> Union[np.ndarray, None]:
     information("getting files")
     found_files_paths = image_directory.glob("*.tif")
-    file_string = re.compile(f"xy{fov_id:02d}.*.tif", re.IGNORECASE)
+    file_string = re.compile(f"xy0*{fov_id}\w*.tif", re.IGNORECASE)
     found_files = [f.name for f in found_files_paths if re.search(file_string, f.name)]
     if filter_str:
-        # found_files = [f for f in found_files if filter_str in f]
         found_files = [
             f for f in found_files if re.search(filter_str, f, re.IGNORECASE)
         ]