diff --git a/dacapo/experiments/datasplits/datasets/arrays/tiff_array.py b/dacapo/experiments/datasplits/datasets/arrays/tiff_array.py
index e16ef26e0..ccdf50376 100644
--- a/dacapo/experiments/datasplits/datasets/arrays/tiff_array.py
+++ b/dacapo/experiments/datasplits/datasets/arrays/tiff_array.py
@@ -56,7 +56,7 @@ def voxel_size(self) -> Coordinate:
 
     @lazy_property.LazyProperty
     def roi(self) -> Roi:
-        return Roi(self._offset * self.shape)
+        return Roi(self._offset, self.shape)
 
     @property
     def writable(self) -> bool:
diff --git a/dacapo/experiments/model.py b/dacapo/experiments/model.py
index fe1f8e7d5..8ca2b2b9e 100644
--- a/dacapo/experiments/model.py
+++ b/dacapo/experiments/model.py
@@ -46,7 +46,7 @@ def forward(self, x):
             result = self.eval_activation(result)
         return result
 
-    def compute_output_shape(self, input_shape: Coordinate) -> Coordinate:
+    def compute_output_shape(self, input_shape: Coordinate) -> Tuple[int, Coordinate]:
         """Compute the spatial shape (i.e., not accounting for channels and
         batch dimensions) of this model, when fed a tensor of the given spatial
         shape as input."""
diff --git a/dacapo/predict.py b/dacapo/predict.py
index 340517528..afe137fcb 100644
--- a/dacapo/predict.py
+++ b/dacapo/predict.py
@@ -24,7 +24,7 @@ def predict(
     num_cpu_workers: int = 4,
     compute_context: ComputeContext = LocalTorch(),
     output_roi: Optional[Roi] = None,
-    output_dtype: Optional[np.dtype] = np.float32,  # add necessary type conversions
+    output_dtype: np.dtype = np.float32,   # type: ignore
     overwrite: bool = False,
 ):
     # get the model's input and output size
@@ -59,7 +59,6 @@ def predict(
         model.num_out_channels,
         output_voxel_size,
         output_dtype,
-        overwrite=overwrite,
     )
 
     # create gunpowder keys
diff --git a/mypy.ini b/mypy.ini
index 722c11df8..d41c2b58b 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,6 +1,8 @@
 # Global options:
 
 [mypy]
+exclude = ^(dacapo/apply\.py|dacapo/cli\.py)$
+# TODO remove this after fixing all the mypy errors @jeff
 
 # Per-module options:
 
@@ -68,4 +70,7 @@ ignore_missing_imports = True
 ignore_missing_imports = True
 
 [mypy-mwatershed.*]
-ignore_missing_imports = True
\ No newline at end of file
+ignore_missing_imports = True
+
+[mypy-numpy_indexed.*]
+ignore_missing_imports = True