diff --git a/cooltools/api/expected.py b/cooltools/api/expected.py
index 40273f22..b9ae9985 100644
--- a/cooltools/api/expected.py
+++ b/cooltools/api/expected.py
@@ -319,12 +319,12 @@ def make_diag_tables(clr, regions, regions2=None, clr_weight_name="weight"):
     bins = clr.bins()[:]
     if clr_weight_name is None:
         # ignore bad bins
-        sizes = dict(bins.groupby("chrom").size())
+        sizes = dict(bins.groupby("chrom", observed=True).size())
         bad_bin_dict = {
             chrom: np.zeros(sizes[chrom], dtype=bool) for chrom in sizes.keys()
         }
     elif is_cooler_balanced(clr, clr_weight_name):
-        groups = dict(iter(bins.groupby("chrom")[clr_weight_name]))
+        groups = dict(iter(bins.groupby("chrom", observed=True)[clr_weight_name]))
         bad_bin_dict = {
             chrom: np.array(groups[chrom].isnull()) for chrom in groups.keys()
         }
diff --git a/cooltools/lib/checks.py b/cooltools/lib/checks.py
index f33c6541..808d880c 100644
--- a/cooltools/lib/checks.py
+++ b/cooltools/lib/checks.py
@@ -547,7 +547,7 @@ def is_track(track, raise_errors=False):
         else:
             return False
 
-    for name, group in track.groupby(track.columns[0]):
+    for name, group in track.groupby(track.columns[0], observed=True):
         if not _is_sorted_ascending(group[track.columns[1]].values):
             if raise_errors:
                 raise ValueError(