diff --git a/poetry.lock b/poetry.lock
index f2095639..fea679c9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
 [[package]]
 name = "aiofiles"
@@ -295,14 +295,14 @@ css = ["tinycss2 (>=1.1.0,<1.2)"]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.5.7"
 description = "Python package for providing Mozilla's CA Bundle."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
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-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
+    {file = "certifi-2023.5.7.tar.gz", hash = "sha256:0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7"},
 ]
 
 [[package]]
@@ -399,14 +399,14 @@ unicode-backport = ["unicodedata2"]
 
 [[package]]
 name = "click"
-version = "8.1.6"
+version = "8.1.3"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
 ]
 
 [package.dependencies]
@@ -603,70 +603,53 @@ files = [
 
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 [[package]]
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 [[package]]
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+    {file = "fonttools-4.40.0-cp39-cp39-win_amd64.whl", hash = "sha256:7961575221e3da0841c75da53833272c520000d76f7f71274dbf43370f8a1065"},
+    {file = "fonttools-4.40.0-py3-none-any.whl", hash = "sha256:200729d12461e2038700d31f0d49ad5a7b55855dec7525074979a06b46f88505"},
+    {file = "fonttools-4.40.0.tar.gz", hash = "sha256:337b6e83d7ee73c40ea62407f2ce03b07c3459e213b6f332b94a69923b9e1cb9"},
 ]
 
 [package.extras]
@@ -908,14 +891,14 @@ tifffile = ["tifffile"]
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "6.7.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
-    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
+    {file = "importlib_metadata-6.7.0-py3-none-any.whl", hash = "sha256:cb52082e659e97afc5dac71e79de97d8681de3aa07ff18578330904a9d18e5b5"},
+    {file = "importlib_metadata-6.7.0.tar.gz", hash = "sha256:1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4"},
 ]
 
 [package.dependencies]
@@ -924,26 +907,26 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.0.0"
+version = "5.12.0"
 description = "Read resources from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
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-    {file = "importlib_resources-6.0.0.tar.gz", hash = "sha256:4cf94875a8368bd89531a756df9a9ebe1f150e0f885030b461237bc7f2d905f2"},
+    {file = "importlib_resources-5.12.0-py3-none-any.whl", hash = "sha256:7b1deeebbf351c7578e09bf2f63fa2ce8b5ffec296e0d349139d43cca061a81a"},
+    {file = "importlib_resources-5.12.0.tar.gz", hash = "sha256:4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -1177,27 +1160,25 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.18.4"
+version = "4.17.3"
 description = "An implementation of JSON Schema validation for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
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+    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
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 ]
 
 [package.dependencies]
-attrs = ">=22.2.0"
+attrs = ">=17.4.0"
 fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""}
-jsonschema-specifications = ">=2023.03.6"
-referencing = ">=0.28.4"
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
 rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
-rpds-py = ">=0.7.1"
 uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
 webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
 
@@ -1205,21 +1186,6 @@ webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-n
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
 format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
 
-[[package]]
-name = "jsonschema-specifications"
-version = "2023.7.1"
-description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "dev"
-optional = false
-python-versions = ">=3.8"
-files = [
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-
-[package.dependencies]
-referencing = ">=0.28.0"
-
 [[package]]
 name = "jupyter-client"
 version = "8.3.0"
@@ -1470,23 +1436,23 @@ test = ["coverage", "jupyter-server[test] (>=2.0.0a0)", "pytest (>=7.0)", "pytes
 
 [[package]]
 name = "jupyter-ydoc"
-version = "0.2.5"
+version = "0.2.4"
 description = "Document structures for collaborative editing using Ypy"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
 importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
-y-py = ">=0.6.0,<0.7.0"
+y-py = ">=0.5.3,<0.6.0"
 
 [package.extras]
 dev = ["click", "jupyter-releaser"]
-test = ["pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)", "ypy-websocket (>=0.8.4,<0.9.0)"]
+test = ["pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)", "ypy-websocket (>=0.3.1,<0.4.0)"]
 
 [[package]]
 name = "jupyterlab"
@@ -1531,14 +1497,14 @@ files = [
 
 [[package]]
 name = "jupyterlab-server"
-version = "2.24.0"
+version = "2.23.0"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1554,7 +1520,7 @@ requests = ">=2.28"
 [package.extras]
 docs = ["autodoc-traits", "jinja2 (<3.2.0)", "mistune (<4)", "myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinxcontrib-openapi (>0.8)"]
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+test = ["hatch", "ipykernel", "jupyterlab-server[openapi]", "openapi-spec-validator (>=0.5.1,<0.6.0)", "pytest (>=7.0)", "pytest-console-scripts", "pytest-cov", "pytest-jupyter[server] (>=0.6.2)", "pytest-timeout", "requests-mock", "sphinxcontrib-spelling", "strict-rfc3339", "werkzeug"]
 
 [[package]]
 name = "jupyterlab-widgets"
@@ -1863,53 +1829,53 @@ files = [
 
 [[package]]
 name = "matplotlib"
-version = "3.7.2"
+version = "3.7.1"
 description = "Python plotting package"
 category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -1921,7 +1887,7 @@ kiwisolver = ">=1.0.1"
 numpy = ">=1.20"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
-pyparsing = ">=2.3.1,<3.1"
+pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
@@ -1996,14 +1962,14 @@ files = [
 
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+version = "5.0.2"
 description = "Rolling backport of unittest.mock for all Pythons"
 category = "dev"
 optional = false
 python-versions = ">=3.6"
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 ]
 
 [package.extras]
@@ -2100,14 +2066,14 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 
 [[package]]
 name = "nbconvert"
-version = "7.7.2"
+version = "7.6.0"
 description = "Converting Jupyter Notebooks"
 category = "dev"
 optional = false
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 qtpdf = ["nbconvert[qtpng]"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
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-webpdf = ["playwright"]
+test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
+webpdf = ["pyppeteer (>=1,<1.1)"]
 
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 category = "dev"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -2245,37 +2211,37 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "numpy"
-version = "1.25.1"
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 [[package]]
@@ -2519,14 +2485,14 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa
 
 [[package]]
 name = "platformdirs"
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
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 python-versions = ">=3.7"
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@@ -2551,14 +2517,14 @@ testing = ["pytest", "pytest-benchmark"]
 
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 [package.extras]
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 [[package]]
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 version = "7.4.0"
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 [[package]]
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+version = "3.12.0"
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 [package.dependencies]
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 python-versions = ">=3.6"
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 ]
 
 [[package]]
 name = "ypy-websocket"
-version = "0.8.4"
+version = "0.8.2"
 description = "WebSocket connector for Ypy"
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ypy_websocket-0.8.4-py3-none-any.whl", hash = "sha256:b1ba0dfcc9762f0ca168d2378062d3ca1299d39076b0f145d961359121042be5"},
-    {file = "ypy_websocket-0.8.4.tar.gz", hash = "sha256:43a001473f5c8abcf182f603049cf305cbc855ad8deaa9dfa0f3b5a7cea9d0ff"},
+    {file = "ypy_websocket-0.8.2-py3-none-any.whl", hash = "sha256:9049d5a7d61c26c2b5a39757c9ffcbe2274bf3553adeea8de7fe1c04671d4145"},
+    {file = "ypy_websocket-0.8.2.tar.gz", hash = "sha256:491b2cc4271df4dde9be83017c15f4532b597dc43148472eb20c5aeb838a5b46"},
 ]
 
 [package.dependencies]
 aiofiles = ">=22.1.0,<23"
 aiosqlite = ">=0.17.0,<1"
-y-py = ">=0.6.0,<0.7.0"
+y-py = ">=0.5.3,<0.6.0"
 
 [package.extras]
 test = ["mypy", "pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.15.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.15.0-py3-none-any.whl", hash = "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"},
+    {file = "zipp-3.15.0.tar.gz", hash = "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "2.0"
diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 7e33dd16..7a9a43c8 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -1,6 +1,6 @@
 import logging
 import os
-import platform
+import threading
 import time
 import warnings
 from datetime import datetime
@@ -29,16 +29,16 @@ class RunStructure:
         fov_progress (dict): Whether or not an expected file has been created
     """
 
-    def __init__(self, run_folder: str, timeout: int = 10 * 60):
+    def __init__(self, run_folder: str, fov_timeout: int = 7800):
         """initializes RunStructure by parsing run json within provided run folder
 
         Args:
             run_folder (str):
                 path to run folder
-            timeout (int):
+            fov_timeout (int):
                 number of seconds to wait for non-null filesize before raising an error
         """
-        self.timeout = timeout
+        self.timeout = fov_timeout
         self.fov_progress = {}
         self.processed_fovs = []
         self.moly_points = []
@@ -183,7 +183,8 @@ def __init__(
         fov_callback: Callable[[str, str], None],
         run_callback: Callable[[str], None],
         intermediate_callback: Callable[[str], None] = None,
-        timeout: int = 1.03 * 60 * 60,
+        fov_timeout: int = 7800,
+        watcher_timeout: int = 3 * 7800,
     ):
         """Initializes FOV_EventHandler
 
@@ -198,12 +199,21 @@ def __init__(
                 callback to run over the entire run
             intermediate_callback (Callable[[None], None]):
                 run callback overriden to run on each fov
-            timeout (int):
+            fov_timeout (int):
                 number of seconds to wait for non-null filesize before raising an error
+            watcher_timeout (int):
+                length to wait for new file generation before timing out
         """
         super().__init__()
         self.run_folder = run_folder
 
+        self.last_event_time = datetime.now()
+        self.timer_thread = threading.Thread(
+            target=self.file_timer, args=(fov_timeout, watcher_timeout)
+        )
+        self.timer_thread.daemon = True
+        self.timer_thread.start()
+
         self.log_path = os.path.join(log_folder, f"{Path(run_folder).parts[-1]}_log.txt")
         if not os.path.exists(log_folder):
             os.makedirs(log_folder)
@@ -215,7 +225,7 @@ def __init__(
         )
 
         # create run structure
-        self.run_structure = RunStructure(run_folder, timeout=timeout)
+        self.run_structure = RunStructure(run_folder, fov_timeout=fov_timeout)
 
         self.fov_func = fov_callback
         self.run_func = run_callback
@@ -471,6 +481,10 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
             event (FileCreatedEvent):
                 file creation event
         """
+        # reset event creation time
+        current_time = datetime.now()
+        self.last_event_time = current_time
+
         # this happens if _check_last_fov gets called by a prior FOV, no need to reprocess
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
@@ -479,6 +493,42 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
             super().on_created(event)
             self._run_callbacks(event, check_last_fov)
 
+    def file_timer(self, fov_timeout, watcher_timeout):
+        """Checks time since last file was generated
+        Args:
+
+            fov_timeout (int):
+                how long to wait for fov data to be generated once file detected
+            watcher_timeout (int):
+                length to wait for new file generation before timing out
+        """
+        while True:
+            current_time = datetime.now()
+            time_elapsed = (current_time - self.last_event_time).total_seconds()
+
+            # 3 fov cycles and no new files --> timeout
+            if time_elapsed > watcher_timeout:
+                fov_num = self.last_fov_num_processed
+                fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
+                print(f"Timed out waiting for {fov_name} files to be generated.")
+                logging.info(
+                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
+                    f"waiting for {fov_name} files to be generated.\n"
+                )
+                logging.info(
+                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
+                    f"Running {self.run_func.__name__} on FOVs\n"
+                )
+
+                # mark remaining fovs as completed to exit watcher
+                for fov_name in list(self.run_structure.fov_progress.keys()):
+                    self.run_structure.fov_progress[fov_name] = {"json": True, "bin": True}
+
+                # trigger run callbacks
+                self.run_func(self.run_folder)
+                break
+            time.sleep(fov_timeout)
+
     def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         """Handles file renaming events
 
@@ -526,6 +576,7 @@ def start_watcher(
     run_folder_timeout: int = 5400,
     completion_check_time: int = 30,
     zero_size_timeout: int = 7800,
+    watcher_timeout: int = 3 * 7800,
 ):
     """Passes bin files to provided callback functions as they're created
 
@@ -577,7 +628,13 @@ def start_watcher(
 
     observer = Observer()
     event_handler = FOV_EventHandler(
-        run_folder, log_folder, fov_callback, run_callback, intermediate_callback, zero_size_timeout
+        run_folder,
+        log_folder,
+        fov_callback,
+        run_callback,
+        intermediate_callback,
+        zero_size_timeout,
+        watcher_timeout,
     )
     observer.schedule(event_handler, run_folder, recursive=True)
     observer.start()
diff --git a/src/toffy/json_utils.py b/src/toffy/json_utils.py
index 2a55bba3..172b70ab 100644
--- a/src/toffy/json_utils.py
+++ b/src/toffy/json_utils.py
@@ -258,3 +258,46 @@ def check_fov_resolutions(bin_file_dir, run_name, save_path=None):
         resolution_data.to_csv(save_path, index=False)
 
     return resolution_data
+
+
+def missing_fov_check(bin_file_dir, run_name):
+    """Use the run metadata to check if all FOV data was generated
+    Args:
+        bin_file_dir (str): directory containing the run json file
+        run_name (str): name of the run and corresponding run file
+
+    Raises:
+        Warning if any FOVs specified in the run file doesn't have associated bin/json files
+    """
+
+    # read in run file
+    run_file_path = os.path.join(bin_file_dir, run_name + ".json")
+    io_utils.validate_paths([run_file_path])
+    run_metadata = read_json_file(run_file_path, encoding="utf-8")
+
+    missing_fovs = {}
+    for fov in run_metadata.get("fovs", ()):
+        if fov.get("standardTarget") == "Molybdenum Foil":
+            continue
+
+        # get fov names
+        fov_number = fov.get("runOrder")
+        default_name = f"fov-{fov_number}-scan-1"
+        custom_name = fov.get("name")
+
+        # add default name and custom name for missing data
+        if not os.path.exists(
+            os.path.join(bin_file_dir, default_name + ".bin")
+        ) or not os.path.exists(os.path.join(bin_file_dir, default_name + ".json")):
+            missing_fovs[default_name] = [custom_name]
+
+        elif os.path.getsize(os.path.join(bin_file_dir, default_name + ".json")) == 0:
+            missing_fovs[default_name] = [custom_name]
+
+    if missing_fovs:
+        missing_fovs = pd.DataFrame(missing_fovs, index=[0]).T
+        missing_fovs.columns = ["fov_name"]
+        warnings.warn(
+            "The following FOVs were not processed due to missing/empty/late files: \n"
+            f"{missing_fovs}"
+        )
diff --git a/src/toffy/watcher_callbacks.py b/src/toffy/watcher_callbacks.py
index eb096f87..c058f532 100644
--- a/src/toffy/watcher_callbacks.py
+++ b/src/toffy/watcher_callbacks.py
@@ -17,6 +17,7 @@
 
 from toffy.bin_extraction import incomplete_fov_check
 from toffy.image_stitching import stitch_images
+from toffy.json_utils import missing_fov_check
 from toffy.mph_comp import combine_mph_metrics, compute_mph_metrics, visualize_mph
 from toffy.normalize import write_mph_per_mass
 from toffy.panel_utils import modify_panel_ranges
@@ -129,6 +130,13 @@ def check_incomplete_fovs(self, tiff_out_dir, **kwargs):
         """
         incomplete_fov_check(self.run_folder, tiff_out_dir)
 
+    def check_missing_fovs(self, **kwargs):
+        """Checks for associated bin/json files per FOV
+        Raises:
+            Warning if any fov data is missing
+        """
+        missing_fov_check(self.run_folder, os.path.basename(self.run_folder))
+
 
 @dataclass
 class FovCallbacks:
diff --git a/templates/3a_monitor_MIBI_run.ipynb b/templates/3a_monitor_MIBI_run.ipynb
index cfa54d7e..ba24a348 100644
--- a/templates/3a_monitor_MIBI_run.ipynb
+++ b/templates/3a_monitor_MIBI_run.ipynb
@@ -91,15 +91,19 @@
     "* The `generate_pulse_heights` FOV callback computes the median pulse heights for each mass specified in the `panel`. \n",
     "<br/> (See [4b_normalize_image_data](./4b_normalize_image_data.ipynb) for more details.)\n",
     "\n",
-    "Callbacks listed in the `run_callbacks` argument will be run only once all expected FOV's have been discovered and processed. \n",
+    "Callbacks listed in the `intermediate_callbacks` argument run and update as each new FOV is generated.\n",
+    "\n",
+    "* The `plot_qc_metrics` intermediate callback will run all currently available qc metrics on each FOV and plot the results. <br/> (See [3c_generate_qc_metrics](./3c_generate_qc_metrics.ipynb) for more details.)\n",
     "\n",
-    "* The `plot_qc_metrics` run callback will run all currently available qc metrics on each FOV, and plot the results once the run has completed. <br/> (See [3c_generate_qc_metrics](./3c_generate_qc_metrics.ipynb) for more details.)\n",
+    "* The `plot_mph_metrics` intermediate callback will compute the median pulse height data for each  FOV and plot the results. Additional arguments are: `regression` which when set to True will also plot the linear regression line for the data. <br/> (See [3d_compute_median_pulse_height](./3d_compute_median_pulse_height.ipynb) for more details.)\n",
     "\n",
-    "* The `plot_mph_metrics` run callback will compute the median pulse height data for each  FOV, and plot the results once the run has completed. Additional arguments are: `regression` which when set to True will also plot the linear regression line for the data. <br/> (See [3d_compute_median_pulse_height](./3d_compute_median_pulse_height.ipynb) for more details.)\n",
+    "Callbacks listed in the `run_callbacks` argument will be run only once all expected FOV's have been discovered and processed. \n",
     "\n",
     "* The `image_stitching` run callback will create a single image, which stitched together all FOV images for a specific channel. Additional arguments are: `channels`. <br/> (See [3e_stitch_images](./3e_stitch_images.ipynb) for more details.)\n",
     "\n",
-    "* The `check_incomplete_fovs` run callback will check the run for any partially generated images. <br/> (See [3b_extract_images_from_bin](./3b_extract_images_from_bin.ipynb) for more details.)"
+    "* The `check_incomplete_fovs` run callback will check the run for any partially generated images. <br/> (See [3b_extract_images_from_bin](./3b_extract_images_from_bin.ipynb) for more details.)\n",
+    "  \n",
+    "* The `check_missing_fovs` run callback checks that the run produces the appropriate .bin and .json all files for all FOVs included in the run file. <br/> (See [3f_FOV_checks](./3f_FOV_checks.ipynb) for more details.)"
    ]
   },
   {
@@ -109,7 +113,7 @@
    "outputs": [],
    "source": [
     "fov_callback, run_callback, intermediate_callback = build_callbacks(\n",
-    "    run_callbacks = ['image_stitching', 'check_incomplete_fovs'],\n",
+    "    run_callbacks = ['image_stitching', 'check_incomplete_fovs', 'check_missing_fovs'],\n",
     "    intermediate_callbacks = ['plot_qc_metrics', 'plot_mph_metrics'],\n",
     "    fov_callbacks = ['extract_tiffs', 'generate_pulse_heights'],\n",
     "    extract_prof=extract_prof,\n",
diff --git a/templates/3b_extract_images_from_bin.ipynb b/templates/3b_extract_images_from_bin.ipynb
index 28cb3896..e0f2a452 100644
--- a/templates/3b_extract_images_from_bin.ipynb
+++ b/templates/3b_extract_images_from_bin.ipynb
@@ -115,17 +115,17 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3c7985e3-7f9a-499c-bb42-13e72cd340e5",
+   "id": "4f366be5-5ee7-4ecf-8db1-397fd7f6c0b9",
    "metadata": {},
    "source": [
-    "## Check for any incomplete FOVs\n",
+    "## Check for any incomplete FOVs \n",
     "If the instrument is shut off part way through a run, this can result in output FOVs which are generated, but missing counts in parts of the images. The cell below will check for any incompete FOVs and warn you if any exist."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5cdf46cf-edf3-4889-b1b5-08601b5b3496",
+   "id": "6ba3af2f-d926-44cd-b688-5dab7e45513c",
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/templates/3f_check_resolutions.ipynb b/templates/3f_FOV_checks.ipynb
similarity index 66%
rename from templates/3f_check_resolutions.ipynb
rename to templates/3f_FOV_checks.ipynb
index 651cb304..574775a1 100644
--- a/templates/3f_check_resolutions.ipynb
+++ b/templates/3f_FOV_checks.ipynb
@@ -2,11 +2,11 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "4857c47b-f476-4494-9a0d-742ef35c0a85",
+   "id": "f8a1d486-4576-464a-bfe3-7e1f584f9a78",
    "metadata": {},
    "source": [
-    "# Check FOV Resolutions\n",
-    "This notebook will use the run file to check the image resolution for each FOV in the run. Consistent resolution level is important for downstream processing, so it is advised to change the image size of any problematic FOVs."
+    "# FOV checks\n",
+    "This notebook will perform two checks on your completed run which ensure all FOVs are the same resolution and verify there are no missing FOV data files."
    ]
   },
   {
@@ -17,7 +17,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from toffy.json_utils import check_fov_resolutions\n",
+    "from toffy.json_utils import check_fov_resolutions, missing_fov_check\n",
     "from toffy.image_stitching import fix_image_resolutions"
    ]
   },
@@ -45,6 +45,15 @@
     "extraction_dir = os.path.join('D:\\\\Extracted_Images', run_name) "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "adba5c6c-7b6b-4a7f-8723-b589df680317",
+   "metadata": {},
+   "source": [
+    "## FOV resolutions\n",
+    "This section will use the run file to check the image resolution for each FOV in the run. Consistent resolution level is important for downstream processing, so it is advised to change the image size of any problematic FOVs."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "b4edefe7-7f3a-4883-bcb3-47158753c837",
@@ -78,7 +87,7 @@
     "tags": []
    },
    "source": [
-    "**Step 2: Change image sizes**"
+    "**Step 2: Change image sizes (if necessary)**"
    ]
   },
   {
@@ -91,6 +100,26 @@
     "# change image size for any FOVs with inconsistent resolutions\n",
     "fix_image_resolutions(resolution_data, extraction_dir)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "23bac7b6-e67e-41ac-aee2-903cc6ab7e27",
+   "metadata": {},
+   "source": [
+    "## Missing Fovs\n",
+    "Sometimes FOVs will fail to be generated due to instrument issues, so the function below checks that each FOV specified in the run json has the corresponding (non-empty) output files."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b3f3b134-2f6d-43b7-bba9-4eb4303555ad",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# check for .bin and .json files\n",
+    "missing_fov_check(bin_file_dir, run_name)"
+   ]
   }
  ],
  "metadata": {
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index a5d03563..0dbea604 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -3,6 +3,7 @@
 import tempfile
 import time
 import warnings
+from datetime import datetime
 from multiprocessing import TimeoutError
 from multiprocessing.pool import ThreadPool as Pool
 from pathlib import Path
@@ -422,3 +423,49 @@ def test_watcher(
 
     except OSError:
         warnings.warn("Temporary file cleanup was incomplete.")
+
+
+def test_watcher_missing_fovs():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # add extra fov to run file
+        large_run_json_spoof = COMBINED_RUN_JSON_SPOOF.copy()
+        large_run_json_spoof["fovs"] = COMBINED_RUN_JSON_SPOOF["fovs"] + [
+            {
+                "runOrder": 5,
+                "scanCount": 1,
+                "frameSizePixels": {"width": 32, "height": 32},
+                "name": "missing_fov",
+            }
+        ]
+
+        run_data = os.path.join(tmpdir, "test_run")
+        os.makedirs(run_data)
+        for file in io_utils.list_files(COMBINED_DATA_PATH, substrs=[".bin", ".json"]):
+            shutil.copy(os.path.join(COMBINED_DATA_PATH, file), os.path.join(run_data, file))
+        log_out = os.path.join(tmpdir, "log_output")
+        fov_callback, run_callback, intermediate_callback = build_callbacks(
+            run_callbacks=["check_missing_fovs"],
+            intermediate_callbacks=[],
+            fov_callbacks=[],
+        )
+
+        write_json_file(
+            json_path=os.path.join(run_data, "test_run.json"),
+            json_object=large_run_json_spoof,
+            encoding="utf-8",
+        )
+
+        # watcher should raise warning for missing fov data (and not hang waiting for new file)
+        with pytest.warns(
+            warnings.warn("The following FOVs were not processed due to missing/empty/late files:"),
+        ):
+            start_watcher(
+                run_data,
+                log_out,
+                fov_callback,
+                run_callback,
+                intermediate_callback,
+                completion_check_time=1,
+                zero_size_timeout=1,
+                watcher_timeout=1,
+            )
diff --git a/tests/json_utils_test.py b/tests/json_utils_test.py
index d9365d12..1519ad0a 100644
--- a/tests/json_utils_test.py
+++ b/tests/json_utils_test.py
@@ -249,3 +249,38 @@ def test_check_fov_resolutions(capsys):
         )
 
         assert os.path.exists(os.path.join(temp_dir, "resolution_data.csv"))
+
+
+def test_missing_fov_check():
+    with tempfile.TemporaryDirectory() as temp_dir:
+        run_file_name = "test"
+        run_data = {
+            "fovs": [
+                {"runOrder": 1, "name": "image_1"},
+                {"runOrder": 2, "name": "image_2"},
+                {"runOrder": 3, "name": "image_3"},
+                {"runOrder": 4, "name": "image_3", "standardTarget": "Molybdenum Foil"},
+            ]
+        }
+        json_utils.write_json_file(
+            os.path.join(temp_dir, run_file_name + ".json"), run_data, "utf-8"
+        )
+
+        for fov in ["fov-1-scan-1", "fov-2-scan-1", "fov-3-scan-1"]:
+            json_utils.write_json_file(os.path.join(temp_dir, fov + ".json"), ["test_data"])
+            _make_blank_file(temp_dir, fov + ".bin")
+
+        # test success (ignore missing moly)
+        json_utils.missing_fov_check(temp_dir, run_file_name)
+
+        # check missing bin file raises warning
+        os.remove(os.path.join(temp_dir, "fov-1-scan-1.bin"))
+        with pytest.warns():
+            json_utils.missing_fov_check(temp_dir, run_file_name)
+        _make_blank_file(temp_dir, "fov-1-scan-1.bin")
+
+        # check empty json file raises warning
+        os.remove(os.path.join(temp_dir, "fov-2-scan-1.json"))
+        _make_blank_file(temp_dir, "fov-2-scan-1.json")
+        with pytest.warns():
+            json_utils.missing_fov_check(temp_dir, run_file_name)
diff --git a/tests/utils/test_utils.py b/tests/utils/test_utils.py
index 43a3ef6b..99b5544d 100644
--- a/tests/utils/test_utils.py
+++ b/tests/utils/test_utils.py
@@ -173,7 +173,13 @@ def generate_sample_fovs_list(fov_coords, fov_names, fov_sizes):
     "generate_mph",
     "generate_pulse_heights",
 )
-RUN_CALLBACKS = ("plot_qc_metrics", "plot_mph_metrics", "image_stitching", "check_incomplete_fovs")
+RUN_CALLBACKS = (
+    "plot_qc_metrics",
+    "plot_mph_metrics",
+    "image_stitching",
+    "check_incomplete_fovs",
+    "check_missing_fovs",
+)
 
 
 def mock_visualize_qc_metrics(
@@ -576,7 +582,13 @@ def case_default(self, intensity, replace, extract_prof):
         }
 
         return (
-            ["plot_qc_metrics", "plot_mph_metrics", "image_stitching", "check_incomplete_fovs"],
+            [
+                "plot_qc_metrics",
+                "plot_mph_metrics",
+                "image_stitching",
+                "check_incomplete_fovs",
+                "check_missing_fovs",
+            ],
             None,
             ["extract_tiffs", "generate_pulse_heights"],
             kwargs,