diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
index dd7a77988..7e8afcfe5 100644
--- a/.github/workflows/Build-and-deploy-mac.yml
+++ b/.github/workflows/Build-and-deploy-mac.yml
@@ -22,7 +22,6 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: nwb-guide
-          #mamba-version: "*"
           environment-file: environments/environment-MAC.yml
           auto-activate-base: false
 
diff --git a/.github/workflows/pyflask-build-and-dist-tests.yml b/.github/workflows/pyflask-build-and-dist-tests.yml
index 5fbea858d..b2b89d50b 100644
--- a/.github/workflows/pyflask-build-and-dist-tests.yml
+++ b/.github/workflows/pyflask-build-and-dist-tests.yml
@@ -30,19 +30,16 @@ jobs:
             os: ubuntu-latest
             label: environments/environment-Linux.yml
             prefix: /usr/share/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: macos-latest
             label: environments/environment-Mac.yml
             prefix: /Users/runner/miniconda3/envs/nwb-guide
-            shorthand: unix
 
-          - python-version: "3.10"
+          - python-version: "3.9"
             os: windows-latest
             label: environments/environment-Windows.yml
             prefix: C:\Miniconda3\envs\nwb-guide
-            shorthand: win
 
     steps:
       - uses: actions/checkout@v3
@@ -88,15 +85,7 @@ jobs:
         run: rm -f /Users/runner/miniconda3/envs/nwb-guide/lib/python3.9/site-packages/sonpy/linux/sonpy.so
 
       - name: Build PyFlask distribution
-        run: npm run build:flask:${{ matrix.shorthand }}
-
-      #- if: matrix.os == 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide.exe
-
-      #- if: matrix.os != 'windows-latest'
-      #  name: Run test on build executable
-      #  run: node tests/testPyinstallerExecutable.js --script ./build/nwb-guide/nwb-guide
+        run: npm run build:flask
 
       - name: Run test on distributed executable
         run: node tests/testPyinstallerExecutable.js
diff --git a/.gitignore b/.gitignore
index 852548470..0cda7e019 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,8 +19,6 @@ semantic.json
 build/
 yarn.lock
 
-*.spec
-
 *.pyc
 src/.DS_Store
 .DS_Store
diff --git a/nwb-guide.spec b/nwb-guide.spec
new file mode 100644
index 000000000..8b4f5649d
--- /dev/null
+++ b/nwb-guide.spec
@@ -0,0 +1,74 @@
+# -*- mode: python ; coding: utf-8 -*-
+import sys
+from pathlib import Path
+
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
+from PyInstaller.utils.hooks import collect_data_files
+from PyInstaller.utils.hooks import collect_all
+
+datas = [('./paths.config.json', '.'), ('./package.json', '.')]
+binaries = []
+hiddenimports = ['scipy._distributor_init', 'scipy._lib.messagestream', 'scipy._lib._ccallback', 'scipy._lib._testutils', 'email_validator']
+datas += collect_data_files('jsonschema_specifications')
+tmp_ret = collect_all('nwbinspector')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('neuroconv')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('pynwb')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('hdmf')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ndx_dandi_icephys')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+tmp_ret = collect_all('ci_info')
+datas += tmp_ret[0]; binaries += tmp_ret[1]; hiddenimports += tmp_ret[2]
+
+
+block_cipher = None
+
+
+a = Analysis(
+    [f"{Path('pyflask') / 'app.py'}"],
+    pathex=[],
+    binaries=binaries,
+    datas=datas,
+    hiddenimports=hiddenimports,
+    hookspath=[],
+    hooksconfig={},
+    runtime_hooks=[],
+    excludes=[],
+    win_no_prefer_redirects=False,
+    win_private_assemblies=False,
+    cipher=block_cipher,
+    noarchive=False,
+)
+pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name='nwb-guide',
+    debug=False,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=True,
+    console=True,
+    disable_windowed_traceback=False,
+    argv_emulation=False,
+    target_arch=None,
+    codesign_identity=None,
+    entitlements_file=None,
+)
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.zipfiles,
+    a.datas,
+    strip=False,
+    upx=True,
+    upx_exclude=[],
+    name='nwb-guide',
+)
diff --git a/package.json b/package.json
index 3bcb3133a..28727a469 100644
--- a/package.json
+++ b/package.json
@@ -11,13 +11,14 @@
     "dev:app": "vite src/renderer",
     "dev:server": "cd pyflask && python -m flask run --port 4242",
     "build": "npm run build:app",
+    "echo": "python -c \"print('hello')\"",
     "build:app": "electron-vite build --outDir build",
-    "build:win": "npm run build && npm run build:flask:win && npm run build:electron:win",
-    "build:mac": "npm run build && npm run build:flask:unix && npm run build:electron:mac",
-    "build:linux": "npm run build && npm run build:flask:unix && npm run build:electron:linux",
-    "build:flask:base": "python -m PyInstaller --log-level DEBUG --name nwb-guide --onedir --clean --noconfirm ./pyflask/app.py --distpath ./build/flask --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ci_info --collect-all ndx_dandi_icephys --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator",
-    "build:flask:win": "npm run build:flask:base -- --add-data ./paths.config.json;. --add-data ./package.json;.",
-    "build:flask:unix": "npm run build:flask:base -- --add-data ./paths.config.json:. --add-data ./package.json:.",
+    "build:win": "npm run build && npm run build:flask && npm run build:electron:win",
+    "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
+    "build:linux": "npm run build && npm run build:flask && npm run build:electron:linux",
+    "build:flask": "python -m PyInstaller nwb-guide.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
+    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all ndx_dandi_icephys --collect-all ci_info --hidden-import scipy._distributor_init --hidden-import scipy._lib.messagestream --hidden-import scipy._lib._ccallback --hidden-import scipy._lib._testutils --hidden-import email_validator ./pyflask/app.py",
+    "build:flask:spec": "npm run build:flask:spec:base && python prepare_pyinstaller_spec.py",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
new file mode 100644
index 000000000..db06d8e91
--- /dev/null
+++ b/prepare_pyinstaller_spec.py
@@ -0,0 +1,30 @@
+"""
+Calling `pyi-makespec` regenerates the base spec file, but we need to extend the recursion limit.
+
+This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
+"""
+from pathlib import Path
+
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
+    lines = io.readlines()
+
+lines.insert(1, "import sys\n")
+lines.insert(2, "from pathlib import Path\n")
+lines.insert(3, "\n")
+lines.insert(4, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
+lines.insert(5, "\n")
+
+# Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
+# The spec file is, however, the same across platforms
+data_line_index = lines.index("datas = []\n")
+lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
+
+# Another platform specific difference is the app.py location
+app_py_line_index = next(index for index, line in enumerate(lines) if "app.py" in line)
+app_py_line = "    [f\"{Path('pyflask') / 'app.py'}\"],\n"
+lines[app_py_line_index] = app_py_line
+
+with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
+    io.writelines(lines)
+
+print("Sucessfully injected recursion depth extension and json paths!")