diff --git a/docs/listofmaps.rst b/docs/listofmaps.rst
index dc87a08..19830b8 100644
--- a/docs/listofmaps.rst
+++ b/docs/listofmaps.rst
@@ -37,29 +37,6 @@ zhu2018-typedensity-allenccfv3-region
     # region mapping file
     # source-zhu2018_regionmapping.csv
 
-zhu2018-similarity-allenccfv3-region
-------------------------------------
-
-**Description**: Synaptic similarity
-
-**Format**: matrix
-
-**How to use**
-
-.. code:: python
-
-    # get annotation
-    fetch_annotation(source='zhu2018', desc='similarity', space='allenccfv3', res='region')
-
-    # file location
-    # $MOUSEMAPS_DATA/zhu2018
-
-    # file name
-    # source-zhu2018_desc-similarity_space-allenccfv3_res-region_matrix.csv
-
-    # region mapping file
-    # source-zhu2018_regionmapping.csv
-
 **References**
 
 ----
@@ -163,6 +140,52 @@ oh2014-pvalcontra-allenccfv3-region
     # region mapping file
     # source-oh2014_regionmapping.csv
 
+oh2014-distipsi-allenccfv3-region
+---------------------------------
+
+**Description**: Distance (mm) for ipsilateral projections
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='oh2014', desc='distipsi', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/oh2014
+
+    # file name
+    # source-oh2014_desc-distipsi_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-oh2014_regionmapping.csv
+
+oh2014-distcontra-allenccfv3-region
+-----------------------------------
+
+**Description**: Distance (mm) for contralateral projections
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='oh2014', desc='distcontra', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/oh2014
+
+    # file name
+    # source-oh2014_desc-distcontra_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-oh2014_regionmapping.csv
+
 **References**
 
 ----
@@ -226,7 +249,7 @@ lein2006amba-sagittalenergy-allenccfv3-region
     # $MOUSEMAPS_DATA/lein2006amba
 
     # file name
-    # source-lein2006amba_desc-sagittalenergy_space-allenccfv3_res-region_tabular.csv
+    # source-lein2006amba_desc-sagittalenergy_space-allenccfv3_res-region_tabular.csv.gz
 
     # region mapping file
     # source-lein2006amba_regionmapping.csv
@@ -249,7 +272,99 @@ lein2006amba-coronalenergy-allenccfv3-region
     # $MOUSEMAPS_DATA/lein2006amba
 
     # file name
-    # source-lein2006amba_desc-coronalenergy_space-allenccfv3_res-region_tabular.csv
+    # source-lein2006amba_desc-coronalenergy_space-allenccfv3_res-region_tabular.csv.gz
+
+    # region mapping file
+    # source-lein2006amba_regionmapping.csv
+
+lein2006amba-sagittaldensity-allenccfv3-region
+----------------------------------------------
+
+**Description**: Expression density of sagittal slices
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='lein2006amba', desc='sagittaldensity', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/lein2006amba
+
+    # file name
+    # source-lein2006amba_desc-sagittaldensity_space-allenccfv3_res-region_tabular.csv.gz
+
+    # region mapping file
+    # source-lein2006amba_regionmapping.csv
+
+lein2006amba-coronaldensity-allenccfv3-region
+---------------------------------------------
+
+**Description**: Expression density of coronal slices
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='lein2006amba', desc='coronaldensity', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/lein2006amba
+
+    # file name
+    # source-lein2006amba_desc-coronaldensity_space-allenccfv3_res-region_tabular.csv.gz
+
+    # region mapping file
+    # source-lein2006amba_regionmapping.csv
+
+lein2006amba-sagittalintensity-allenccfv3-region
+------------------------------------------------
+
+**Description**: Expression intensity of sagittal slices
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='lein2006amba', desc='sagittalintensity', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/lein2006amba
+
+    # file name
+    # source-lein2006amba_desc-sagittalintensity_space-allenccfv3_res-region_tabular.csv.gz
+
+    # region mapping file
+    # source-lein2006amba_regionmapping.csv
+
+lein2006amba-coronalintensity-allenccfv3-region
+-----------------------------------------------
+
+**Description**: Expression intensity of coronal slices
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='lein2006amba', desc='coronalintensity', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/lein2006amba
+
+    # file name
+    # source-lein2006amba_desc-coronalintensity_space-allenccfv3_res-region_tabular.csv.gz
 
     # region mapping file
     # source-lein2006amba_regionmapping.csv
@@ -403,6 +518,282 @@ yao2023abca-impsubsmean-allenccfv3-region
     # region mapping file
     # source-yao2023abca_substructure_regionmapping.csv
 
+yao2023abca-divictclass-allenccfv3-region
+-----------------------------------------
+
+**Description**: Cell type (class) at the division level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='divictclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-divictclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_division_regionmapping.csv
+
+yao2023abca-structclass-allenccfv3-region
+-----------------------------------------
+
+**Description**: Cell type (class) at the structure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='structclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-structclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_structure_regionmapping.csv
+
+yao2023abca-subsctclass-allenccfv3-region
+-----------------------------------------
+
+**Description**: Cell type (class) at the substructure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='subsctclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-subsctclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_substructure_regionmapping.csv
+
+yao2023abca-divictsubclass-allenccfv3-region
+--------------------------------------------
+
+**Description**: Cell type (subclass) at the division level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='divictsubclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-divictsubclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_division_regionmapping.csv
+
+yao2023abca-structsubclass-allenccfv3-region
+--------------------------------------------
+
+**Description**: Cell type (subclass) at the structure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='structsubclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-structsubclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_structure_regionmapping.csv
+
+yao2023abca-subsctsubclass-allenccfv3-region
+--------------------------------------------
+
+**Description**: Cell type (subclass) at the substructure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='subsctsubclass', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-subsctsubclass_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_substructure_regionmapping.csv
+
+yao2023abca-divictsupertype-allenccfv3-region
+---------------------------------------------
+
+**Description**: Cell type (supertype) at the division level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='divictsupertype', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-divictsupertype_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_division_regionmapping.csv
+
+yao2023abca-structsupertype-allenccfv3-region
+---------------------------------------------
+
+**Description**: Cell type (supertype) at the structure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='structsupertype', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-structsupertype_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_structure_regionmapping.csv
+
+yao2023abca-subsctsupertype-allenccfv3-region
+---------------------------------------------
+
+**Description**: Cell type (supertype) at the substructure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='subsctsupertype', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-subsctsupertype_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_substructure_regionmapping.csv
+
+yao2023abca-divictcluster-allenccfv3-region
+-------------------------------------------
+
+**Description**: Cell type (cluster) at the division level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='divictcluster', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-divictcluster_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_division_regionmapping.csv
+
+yao2023abca-structcluster-allenccfv3-region
+-------------------------------------------
+
+**Description**: Cell type (cluster) at the structure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='structcluster', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-structcluster_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_structure_regionmapping.csv
+
+yao2023abca-subsctcluster-allenccfv3-region
+-------------------------------------------
+
+**Description**: Cell type (cluster) at the substructure level
+
+**Format**: tabular
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='yao2023abca', desc='subsctcluster', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/yao2023abca
+
+    # file name
+    # source-yao2023abca_desc-subsctcluster_space-allenccfv3_res-region_tabular.csv
+
+    # region mapping file
+    # source-yao2023abca_substructure_regionmapping.csv
+
 **References**
 
 ----
@@ -483,4 +874,199 @@ zhang2023abca-subsmean-allenccfv3-region
     # region mapping file
     # source-zhang2023abca_substructure_regionmapping.csv
 
+**References**
+
+----
+
+hi-res connectome (knox2018)
+============================
+
+**Full description**
+
+ High-resolution data-driven model of the mouse connectome
+
+knox2018-conndencontra-allenccfv3-region
+----------------------------------------
+
+**Description**: Connection density (contralateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='conndencontra', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-conndencontra_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-conndenipsi-allenccfv3-region
+--------------------------------------
+
+**Description**: Connection density (ipsilateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='conndenipsi', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-conndenipsi_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-connstrcontra-allenccfv3-region
+----------------------------------------
+
+**Description**: Connection strength (contralateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='connstrcontra', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-connstrcontra_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-connstripsi-allenccfv3-region
+--------------------------------------
+
+**Description**: Connection strength (ipsilateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='connstripsi', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-connstripsi_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-normconndencontra-allenccfv3-region
+--------------------------------------------
+
+**Description**: Normalized connection density (contralateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='normconndencontra', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-normconndencontra_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-normconndenipsi-allenccfv3-region
+------------------------------------------
+
+**Description**: Normalized connection density (ipsilateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='normconndenipsi', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-normconndenipsi_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-normconnstrcontra-allenccfv3-region
+--------------------------------------------
+
+**Description**: Normalized connection strength (contralateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='normconnstrcontra', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-normconnstrcontra_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
+knox2018-normconnstripsi-allenccfv3-region
+------------------------------------------
+
+**Description**: Normalized connection strength (ipsilateral)
+
+**Format**: matrix
+
+**How to use**
+
+.. code:: python
+
+    # get annotation
+    fetch_annotation(source='knox2018', desc='normconnstripsi', space='allenccfv3', res='region')
+
+    # file location
+    # $MOUSEMAPS_DATA/knox2018
+
+    # file name
+    # source-knox2018_desc-normconnstripsi_space-allenccfv3_res-region_matrix.csv
+
+    # region mapping file
+    # source-knox2018_regionmapping.csv
+
 **References**
\ No newline at end of file
diff --git a/neuromaps_mouse/datasets/atlases.py b/neuromaps_mouse/datasets/atlases.py
index 4c828dd..fa86c1c 100644
--- a/neuromaps_mouse/datasets/atlases.py
+++ b/neuromaps_mouse/datasets/atlases.py
@@ -6,10 +6,12 @@
     get_data_dir
 )
 
+
 def get_atlas_dir(data_dir=None):
     data_dir = get_data_dir(data_dir=data_dir)
     return data_dir / "atlases"
 
+
 def fetch_allenccfv3(which=None, return_single=True, data_dir=None, verbose=1):
     data_dir = get_data_dir(data_dir=data_dir)
     atlas = MOUSEMAPS_ATLASES["allen-ccfv3"]
diff --git a/neuromaps_mouse/datasets/data/annotations-meta.json b/neuromaps_mouse/datasets/data/annotations-meta.json
index 5ad6c20..34830c5 100644
--- a/neuromaps_mouse/datasets/data/annotations-meta.json
+++ b/neuromaps_mouse/datasets/data/annotations-meta.json
@@ -5,8 +5,7 @@
       "name": "synaptome",
       "description": "Architecture of the Mouse Brain Synaptome",
       "file_desc": {
-        "typedensity": "Synaptic type density",
-        "similarity": "Synaptic similarity"
+        "typedensity": "Synaptic type density"
       },
       "comments": "Original source: ",
       "refs": [
@@ -45,7 +44,9 @@
         "wipsi": "Weighted ipsilateral strength index",
         "pvalipsi": "P values for wipsi",
         "wcontra": "Weighted contralateral strength index",
-        "pvalcontra": "P values for wcontra"
+        "pvalcontra": "P values for wcontra",
+        "distipsi": "Distance (mm) for ipsilateral projections",
+        "distcontra": "Distance (mm) for contralateral projections"
       },
       "comments": "Original source: Supplementary Table 3",
       "refs": [
@@ -148,7 +149,11 @@
       "description": "Allen Mouse Brain Atlas",
       "file_desc": {
         "sagittalenergy": "Expression energy of sagittal slices",
-        "coronalenergy": "Expression energy of coronal slices"
+        "coronalenergy": "Expression energy of coronal slices",
+        "sagittaldensity": "Expression density of sagittal slices",
+        "coronaldensity": "Expression density of coronal slices",
+        "sagittalintensity": "Expression intensity of sagittal slices",
+        "coronalintensity": "Expression intensity of coronal slices"
       },
       "comments": "",
       "warning": "This is a very large dataset, and may take a long time to download.",
@@ -232,16 +237,16 @@
         "impdivimean": "Average imputed regional gene expressions at the division level",
         "impstrumean": "Average imputed regional gene expressions at the structure level",
         "impsubsmean": "Average imputed regional gene expressions at the substructure level",
-        "divctclass": "Cell type (class) at the division level",
+        "divictclass": "Cell type (class) at the division level",
         "structclass": "Cell type (class) at the structure level",
         "subsctclass": "Cell type (class) at the substructure level",
-        "divctsubclass": "Cell type (subclass) at the division level",
+        "divictsubclass": "Cell type (subclass) at the division level",
         "structsubclass": "Cell type (subclass) at the structure level",
         "subsctsubclass": "Cell type (subclass) at the substructure level",
-        "divctsupertype": "Cell type (supertype) at the division level",
+        "divictsupertype": "Cell type (supertype) at the division level",
         "structsupertype": "Cell type (supertype) at the structure level",
         "subsctsupertype": "Cell type (supertype) at the substructure level",
-        "divctcluster": "Cell type (cluster) at the division level",
+        "divictcluster": "Cell type (cluster) at the division level",
         "structcluster": "Cell type (cluster) at the structure level",
         "subsctcluster": "Cell type (cluster) at the substructure level"
       },
diff --git a/neuromaps_mouse/datasets/utils.py b/neuromaps_mouse/datasets/utils.py
index d5417e9..a0342b1 100644
--- a/neuromaps_mouse/datasets/utils.py
+++ b/neuromaps_mouse/datasets/utils.py
@@ -14,6 +14,7 @@
 
 
 def get_data_dir(data_dir=None):
+    """Get the data directory."""
     if data_dir is None:
         data_dir = os.environ.get(
             "MOUSEMAPS_DATA", str(Path.home() / "neuromaps-mouse-data")
@@ -63,6 +64,7 @@ def _osfify_url(osf_file_id):
 
 
 def fetch_files(annotations, file_type="annotations", data_dir=None, verbose=1):
+    """Fetch files from OSF."""
     targ_fname_list = []
     for annot in annotations:
         if file_type in ["annotations", "annotations-meta"]:
@@ -139,7 +141,7 @@ def _filter_annots_by_keys(keys_dict):
     return filtered
 
 
-def _check_json(osfstorage_data):
+def _check_json(osfstorage_data, overwrite=False):
     """
     Check for errors in meta.json.
 
@@ -151,9 +153,11 @@ def _check_json(osfstorage_data):
     """
     # reload the datasets and meta json files
     from rich.console import Console
+    import importlib.resources
 
     console = Console()
 
+    # Load JSON files
     MOUSEMAPS_ATLASES = _load_resource_json("datasets/data/atlases.json")["atlases"]
     MOUSEMAPS_ANNOTS = _load_resource_json("datasets/data/annotations.json")[
         "annotations"
@@ -162,6 +166,11 @@ def _check_json(osfstorage_data):
         "annotations-meta"
     ]
 
+    # Track if any changes were made
+    atlases_updated = False
+    annots_updated = False
+    annots_meta_updated = False
+
     console.print("ATLASES")
     for atlas_k, atlas_v in MOUSEMAPS_ATLASES.items():
         console.print(f"{atlas_k} >")
@@ -170,21 +179,35 @@ def _check_json(osfstorage_data):
             if file_v["checksum"] == osfstorage_data[file_v["fname"]]["md5"]:
                 console.print("    [bold green]✓[/bold green] checksum")
             else:
-                console.print(
-                    f"    [bold red]x[/bold red] checksum local: {file_v['checksum']} remote: {osfstorage_data[file_v['fname']]['md5']}"
-                )
+                if overwrite:
+                    file_v["checksum"] = osfstorage_data[file_v["fname"]]["md5"]
+                    atlases_updated = True
+                    console.print("    [bold yellow]↻[/bold yellow] checksum updated")
+                else:
+                    console.print(
+                        f"    [bold red]x[/bold red] "
+                        f"checksum local: {file_v['checksum']} "
+                        f"remote: {osfstorage_data[file_v['fname']]['md5']}"
+                    )
 
             if file_v["url"]["osf"] == osfstorage_data[file_v["fname"]]["guid"]:
                 console.print("    [bold green]✓[/bold green] url")
             else:
-                console.print(
-                    f"    [bold red]x[/bold red] url local: {file_v['url']['osf']} remote: {osfstorage_data[file_v['fname']]['guid']}"
-                )
+                if overwrite:
+                    file_v["url"]["osf"] = osfstorage_data[file_v["fname"]]["guid"]
+                    atlases_updated = True
+                    console.print("    [bold yellow]↻[/bold yellow] url updated")
+                else:
+                    console.print(
+                        f"    [bold red]x[/bold red] "
+                        f"url local: {file_v['url']['osf']} "
+                        f"remote: {osfstorage_data[file_v['fname']]['guid']}"
+                    )
 
     console.print("\nANNOTS_META")
     for annot_meta in MOUSEMAPS_ANNOTS_META:
         console.print(f"{annot_meta['source']} {annot_meta['name']} >")
-        console.print("  \[annot files] >")
+        console.print(r"  \[annot files] >")
         for file_v in annot_meta["files"]:
             console.print(f"    {'-'.join(file_v)} >")
             try:
@@ -197,7 +220,7 @@ def _check_json(osfstorage_data):
             else:
                 console.print("      [bold red]x[/bold red] json")
 
-        console.print("  \[aux files] >")
+        console.print(r"  \[aux files] >")
         for aux_k, aux_v in annot_meta["aux_files"].items():
             console.print(f"    {aux_k} >")
 
@@ -207,21 +230,40 @@ def _check_json(osfstorage_data):
                 console.print(f"      {file_v['fname']} >")
                 if file_v["fname"] not in osfstorage_data:
                     console.print(
-                        f"        [bold red]x[/bold red] {file_v['fname']} not found in osfstorage"
+                        f"        [bold red]x[/bold red] "
+                        f"{file_v['fname']} not found in osfstorage"
                     )
                     continue
                 if file_v["checksum"] == osfstorage_data[file_v["fname"]]["md5"]:
                     console.print("        [bold green]✓[/bold green] checksum")
                 else:
-                    console.print(
-                        f"        [bold red]x[/bold red] checksum local: {file_v['checksum']} remote: {osfstorage_data[file_v['fname']]['md5']}"
-                    )
+                    if overwrite:
+                        file_v["checksum"] = osfstorage_data[file_v["fname"]]["md5"]
+                        annots_meta_updated = True
+                        console.print(
+                            "        [bold yellow]↻[/bold yellow] checksum updated"
+                        )
+                    else:
+                        console.print(
+                            f"        [bold red]x[/bold red] "
+                            f"checksum local: {file_v['checksum']} "
+                            f"remote: {osfstorage_data[file_v['fname']]['md5']}"
+                        )
                 if file_v["url"]["osf"] == osfstorage_data[file_v["fname"]]["guid"]:
                     console.print("        [bold green]✓[/bold green] url")
                 else:
-                    console.print(
-                        f"        [bold red]x[/bold red] url local: {file_v['url']['osf']} remote: {osfstorage_data[file_v['fname']]['guid']}"
-                    )
+                    if overwrite:
+                        file_v["url"]["osf"] = osfstorage_data[file_v["fname"]]["guid"]
+                        annots_meta_updated = True
+                        console.print(
+                            "        [bold yellow]↻[/bold yellow] url updated"
+                        )
+                    else:
+                        console.print(
+                            f"        [bold red]x[/bold red] "
+                            f"url local: {file_v['url']['osf']} "
+                            f"remote: {osfstorage_data[file_v['fname']]['guid']}"
+                        )
 
     console.print("\nANNOTS")
     for annot in MOUSEMAPS_ANNOTS:
@@ -230,20 +272,125 @@ def _check_json(osfstorage_data):
         )
         console.print(f"  {annotstr} >")
         if annot["fname"] not in osfstorage_data:
-            console.print(f"        [bold red]x[/bold red] {annot['fname']} not found in osfstorage")
+            console.print(
+                f"        [bold red]x[/bold red] "
+                f"{annot['fname']} not found in osfstorage"
+            )
             continue
         if annot["checksum"] == osfstorage_data[annot["fname"]]["md5"]:
             console.print("    [bold green]✓[/bold green] checksum")
         else:
-            console.print(
-                f"    [bold red]x[/bold red] checksum local: {annot['checksum']} remote: {osfstorage_data[annot['fname']]['md5']}"
-            )
+            if overwrite:
+                annot["checksum"] = osfstorage_data[annot["fname"]]["md5"]
+                annots_updated = True
+                console.print("    [bold yellow]↻[/bold yellow] checksum updated")
+            else:
+                console.print(
+                    f"    [bold red]x[/bold red] "
+                    f"checksum local: {annot['checksum']} "
+                    f"remote: {osfstorage_data[annot['fname']]['md5']}"
+                )
         if annot["url"]["osf"] == osfstorage_data[annot["fname"]]["guid"]:
             console.print("    [bold green]✓[/bold green] url")
         else:
-            console.print(
-                f"    [bold red]x[/bold red] url local: {annot['url']['osf']} remote: {osfstorage_data[annot['fname']]['guid']}"
+            if overwrite:
+                annot["url"]["osf"] = osfstorage_data[annot["fname"]]["guid"]
+                annots_updated = True
+                console.print("    [bold yellow]↻[/bold yellow] url updated")
+            else:
+                console.print(
+                    f"    [bold red]x[/bold red] "
+                    f"url local: {annot['url']['osf']} "
+                    f"remote: {osfstorage_data[annot['fname']]['guid']}"
+                )
+
+    # Write updated JSON files if changes were made
+    if atlases_updated:
+        atlases_data = {"atlases": MOUSEMAPS_ATLASES}
+        if getattr(importlib.resources, "files", None) is not None:
+            atlases_file = (
+                importlib.resources.files("neuromaps_mouse")
+                / "datasets/data/atlases.json"
             )
+        else:
+            from pkg_resources import resource_filename
+
+            atlases_file = resource_filename(
+                "neuromaps_mouse", "datasets/data/atlases.json"
+            )
+        with open(atlases_file, "w") as f:
+            json.dump(atlases_data, f, indent=2)
+        console.print("\n[bold green]✓[/bold green] Updated atlases.json")
+    if annots_updated:
+        annots_data = {"annotations": MOUSEMAPS_ANNOTS}
+        if getattr(importlib.resources, "files", None) is not None:
+            annots_file = (
+                importlib.resources.files("neuromaps_mouse")
+                / "datasets/data/annotations.json"
+            )
+        else:
+            from pkg_resources import resource_filename
+
+            annots_file = resource_filename(
+                "neuromaps_mouse", "datasets/data/annotations.json"
+            )
+        with open(annots_file, "w") as f:
+            json.dump(annots_data, f, indent=2)
+        console.print("[bold green]✓[/bold green] Updated annotations.json")
+    if annots_meta_updated:
+        annots_meta_data = {"annotations-meta": MOUSEMAPS_ANNOTS_META}
+        if getattr(importlib.resources, "files", None) is not None:
+            annots_meta_file = (
+                importlib.resources.files("neuromaps_mouse")
+                / "datasets/data/annotations-meta.json"
+            )
+        else:
+            from pkg_resources import resource_filename
+
+            annots_meta_file = resource_filename(
+                "neuromaps_mouse", "datasets/data/annotations-meta.json"
+            )
+        with open(annots_meta_file, "w") as f:
+            json.dump(annots_meta_data, f, indent=2)
+        console.print("[bold green]✓[/bold green] Updated annotations-meta.json")
+
+    # Check for files in OSF storage that are not referenced in JSON files
+    console.print("\nFILES IN OSF STORAGE NOT REFERENCED IN JSON")
+
+    # Collect all filenames referenced in JSON files
+    json_files = set()
+
+    # Atlas files
+    for atlas_v in MOUSEMAPS_ATLASES.values():
+        for file_v in atlas_v["files"].values():
+            json_files.add(file_v["fname"])
+
+    # Annotation files
+    for annot in MOUSEMAPS_ANNOTS:
+        json_files.add(annot["fname"])
+
+    # Annotation meta aux files
+    for annot_meta in MOUSEMAPS_ANNOTS_META:
+        for aux_v in annot_meta["aux_files"].values():
+            if not isinstance(aux_v, list):
+                aux_v = [aux_v]
+            for file_v in aux_v:
+                json_files.add(file_v["fname"])
+
+    # Find files in OSF storage not in JSON
+    unreferenced_files = set(osfstorage_data.keys()) - json_files
+
+    if unreferenced_files:
+        for fname in sorted(unreferenced_files):
+            console.print(f"  [bold yellow]?[/bold yellow] {fname}")
+        console.print(
+            f"\n[bold yellow]Found {len(unreferenced_files)} "
+            f"unreferenced files in OSF storage[/bold yellow]"
+        )
+    else:
+        console.print(
+            "  [bold green]✓[/bold green] All OSF storage files are referenced in JSON"
+        )
 
 
 def _check_osfstorage():
@@ -298,7 +445,9 @@ def _get_full_data(url):
                             f"      {file['attributes']['extra']['hashes']['md5']}"
                         )
                         if not file["attributes"]["guid"]:
-                            requests.get(f'https://osf.io/{OSF_NODEID}/files/osfstorage{file["attributes"]["path"]}')
+                            requests.get(
+                                f"https://osf.io/{OSF_NODEID}/files/osfstorage{file['attributes']['path']}"
+                            )
                         osfstorage_data[file["attributes"]["name"]] = {
                             "guid": file["attributes"]["guid"],
                             "md5": file["attributes"]["extra"]["hashes"]["md5"],
@@ -315,7 +464,9 @@ def _get_full_data(url):
                         f"      {file['attributes']['extra']['hashes']['md5']}"
                     )
                     if not file["attributes"]["guid"]:
-                        requests.get(f'https://osf.io/{OSF_NODEID}/files/osfstorage{file["attributes"]["path"]}')
+                        requests.get(
+                            f"https://osf.io/{OSF_NODEID}/files/osfstorage{file['attributes']['path']}"
+                        )
                     osfstorage_data[file["attributes"]["name"]] = {
                         "guid": file["attributes"]["guid"],
                         "md5": file["attributes"]["extra"]["hashes"]["md5"],
@@ -325,72 +476,16 @@ def _get_full_data(url):
     return osfstorage_data
 
 
-# def _fill_meta_json_refs(bib_file, json_file, overwrite=False, use_defaults=False):
-#     """
-#     Fill in citation information for references in a JSON file.
-
-#     For internal use only.
-
-#     Parameters
-#     ----------
-#     bib_file : str
-#         Path to BibTeX file containing references
-#     json_file : str
-#         Path to JSON file containing references
-#     overwrite : bool, optional
-#         Whether to overwrite existing citation information. Default: False
-#     use_defaults : bool, optional
-#         Whether to use default paths for `bib_file` and `json_file`. Default: False
-
-#     Returns
-#     -------
-#     None
-#     """
-#     if use_defaults:
-#         bib_file = \
-#             importlib.resources.files("neuromaps") / "datasets/data/neuromaps.bib"
-#         json_file = \
-#             importlib.resources.files("neuromaps") / "datasets/data/meta.json"
-
-#     from pybtex import PybtexEngine
-#     engine = PybtexEngine()
-
-#     def _get_citation(key):
-#         s = engine.format_from_file(
-#             filename=bib_file, style="unsrt",
-#             citations=[key], output_backend="plaintext"
-#             )
-#         return s.strip("\n").replace("[1] ", "")
-
-#     with open(json_file) as src:
-#         nm_meta = json.load(src)
-
-#     for entry in nm_meta["annotations"]:
-#         for bib_category in ["primary", "secondary"]:
-#             for bib_item in entry["refs"][bib_category]:
-#                 if bib_item["bibkey"] not in ["", None]:
-#                     if bib_item["citation"] == "" or overwrite:
-#                         bib_item["citation"] = _get_citation(bib_item["bibkey"])
-
-#     with open(json_file, "w") as dst:
-#         json.dump(nm_meta, dst, indent=4)
-
-
 def _gen_doc_listofmaps_rst(listofmaps_file):
     """
     Generate a list of maps in reStructuredText format.
 
     For internal use only.
-
-    Parameters
-    ----------
-    listofmaps_file : str
-        Path to write the list of maps
-
-    Returns
-    -------
-    None
     """
+    MOUSEMAPS_ANNOTS_META = _load_resource_json("datasets/data/annotations-meta.json")[
+        "annotations-meta"
+    ]
+
     output = []
 
     output += [
diff --git a/neuromaps_mouse/plotting.py b/neuromaps_mouse/plotting.py
index 296f259..f60217f 100644
--- a/neuromaps_mouse/plotting.py
+++ b/neuromaps_mouse/plotting.py
@@ -432,7 +432,7 @@ def plot_allenccfv3_lightbox(
             )
         else:
             ax.autoscale()
-        
+
         if view in ["sagittal", "coronal"]:
             ax.invert_yaxis()
 
diff --git a/neuromaps_mouse/resampling.py b/neuromaps_mouse/resampling.py
index de20a2e..88bfa50 100644
--- a/neuromaps_mouse/resampling.py
+++ b/neuromaps_mouse/resampling.py
@@ -1,4 +1,5 @@
 """Functions for resampling and aligning structures."""
+
 from pathlib import Path
 import subprocess
 import pandas as pd
@@ -91,16 +92,23 @@ def _get_nearest_descendant_region_allenccfv3(
 
 
 def align_structures_allenccfv3(acronyms_fixed, acronyms_moving, debug=False):
-
     df_fixed = query_structure_graph_allenccfv3(
-        acronyms_fixed, in_col="acronym", out_col=["acronym", "id", "structure_id_path"], verbose=0
+        acronyms_fixed,
+        in_col="acronym",
+        out_col=["acronym", "id", "structure_id_path"],
+        verbose=0,
     )
     df_moving = query_structure_graph_allenccfv3(
-        acronyms_moving, in_col="acronym", out_col=["acronym", "id", "structure_id_path"], verbose=0
+        acronyms_moving,
+        in_col="acronym",
+        out_col=["acronym", "id", "structure_id_path"],
+        verbose=0,
     )
 
     df_moving["id_ancestor_fixed"] = _get_nearest_ancestor_region_allenccfv3(
-        df_moving["structure_id_path"].to_list(), df_fixed["id"].to_list(), include_self=True
+        df_moving["structure_id_path"].to_list(),
+        df_fixed["id"].to_list(),
+        include_self=True,
     )
     df_moving["id_ancestor_fixed"] = df_moving["id_ancestor_fixed"].astype("Int64")
 
@@ -113,7 +121,9 @@ def align_structures_allenccfv3(acronyms_fixed, acronyms_moving, debug=False):
         )
         # also get descendant
         df_moving["id_descendant_fixed"] = _get_nearest_descendant_region_allenccfv3(
-            df_moving["id"].tolist(), df_fixed["structure_id_path"].tolist(), include_self=True
+            df_moving["id"].tolist(),
+            df_fixed["structure_id_path"].tolist(),
+            include_self=True,
         )
         df_moving["id_descendant_fixed_acronym"] = df_moving.apply(
             lambda x: get_feature_allenccfv3(
@@ -132,38 +142,49 @@ def match_structures_fuzzy_allenccfv3():
 
 
 def visualize_structure_alignment_allenccfv3(
-        acronyms_fixed, acronyms_moving, save_path=Path("./"), save_name="graphviz"
-    ):
+    acronyms_fixed, acronyms_moving, save_path=Path("./"), save_name="graphviz"
+):
     graphviz_path = shutil.which("dot")
     if graphviz_path is None:
         raise ValueError("Graphviz executable not found, please install graphviz")
-    
+
     if not isinstance(save_path, Path):
         save_path = Path(save_path)
 
     struct_csv = pd.read_csv(fetch_allenccfv3(which="structure-graph-csv"))
 
     df_fixed = query_structure_graph_allenccfv3(
-        acronyms_fixed, in_col="acronym", out_col=["acronym", "id", "structure_id_path"], verbose=0
+        acronyms_fixed,
+        in_col="acronym",
+        out_col=["acronym", "id", "structure_id_path"],
+        verbose=0,
     )
     df_moving = query_structure_graph_allenccfv3(
-        acronyms_moving, in_col="acronym", out_col=["acronym", "id", "structure_id_path"], verbose=0
+        acronyms_moving,
+        in_col="acronym",
+        out_col=["acronym", "id", "structure_id_path"],
+        verbose=0,
     )
 
     all_regions = [
-        _.strip("/").split("/") 
-        for _ in df_fixed["structure_id_path"].tolist() + df_moving["structure_id_path"].tolist()
+        _.strip("/").split("/")
+        for _ in df_fixed["structure_id_path"].tolist()
+        + df_moving["structure_id_path"].tolist()
     ]
-    all_regions = list(map(int, list(set([r for regions in all_regions for r in regions]))))
+    all_regions = list(
+        map(int, list(set([r for regions in all_regions for r in regions])))
+    )
 
     struct_csv_filtered = struct_csv[struct_csv["id"].isin(all_regions)]
-    struct_csv_filtered["parent_structure_id"] = struct_csv_filtered["parent_structure_id"].astype("Int64")
+    struct_csv_filtered["parent_structure_id"] = struct_csv_filtered[
+        "parent_structure_id"
+    ].astype("Int64")
 
     graphviz_script = [
         "digraph G {",
         'rankdir="LR";',
         'node [shape=box, fontname="Arial", fontsize=12];',
-        'edge [fontname="Arial", fontsize=10];'
+        'edge [fontname="Arial", fontsize=10];',
     ]
 
     for i, row in struct_csv_filtered.iterrows():
@@ -177,14 +198,18 @@ def visualize_structure_alignment_allenccfv3(
     for i, row in struct_csv_filtered.iterrows():
         if row["acronym"] == "root":
             continue
-        graphviz_script.append(
-            f"    {row['parent_structure_id']} -> {row['id']}"
-        )
-    graphviz_script += [
-        "}"
-    ]
+        graphviz_script.append(f"    {row['parent_structure_id']} -> {row['id']}")
+    graphviz_script += ["}"]
 
     with open(save_path / f"{save_name}.txt", "w", encoding="utf-8") as f:
         f.writelines("\n".join(graphviz_script))
 
-    subprocess.run([graphviz_path, "-Tsvg", f"{save_path / save_name}.txt", "-o", f"{save_path / save_name}.svg"])
\ No newline at end of file
+    subprocess.run(
+        [
+            graphviz_path,
+            "-Tsvg",
+            f"{save_path / save_name}.txt",
+            "-o",
+            f"{save_path / save_name}.svg",
+        ]
+    )