diff --git a/app/routers/spectra.py b/app/routers/spectra.py
index 1e46e3c..1fa8ef9 100644
--- a/app/routers/spectra.py
+++ b/app/routers/spectra.py
@@ -3,7 +3,7 @@
 import io
 from app.schemas import HealthCheck
 from pydantic import BaseModel, HttpUrl, Field
-from typing import Optional
+from typing import Optional, List
 import subprocess
 import tempfile
 import os
@@ -50,6 +50,10 @@ class UrlParseRequest(BaseModel):
     )
     raw_data: bool = Field(
         False, description="Include raw data in the output (default: data source)")
+    include: Optional[List[str]] = Field(
+        None, description="Only include files matching pattern(s) (glob/regex string)")
+    exclude: Optional[List[str]] = Field(
+        None, description="Exclude files matching pattern(s) (glob/regex string)")
 
     model_config = {
         "json_schema_extra": {
@@ -95,6 +99,8 @@ def run_command(
     auto_processing: bool = False,
     auto_detection: bool = False,
     raw_data: bool = False,
+    include: Optional[List[str]] = None,
+    exclude: Optional[List[str]] = None,
 ) -> StreamingResponse:
     """Execute nmr-cli parse-spectra command in Docker container."""
 
@@ -113,6 +119,12 @@ def run_command(
         cmd.append("-d")
     if raw_data:
         cmd.append("-r")
+    if include:
+        cmd.append("--include")
+        cmd.extend(include)
+    if exclude:
+        cmd.append("--exclude")
+        cmd.extend(exclude)
 
     try:
         result = subprocess.run(
@@ -362,7 +374,11 @@ async def parse_spectra_from_file(
         description="Enable ranges and zones automatic detection",
     ),
     raw_data: bool = Form(
-        False, description="Include raw data in the output (default: data source references)")
+        False, description="Include raw data in the output (default: data source references)"),
+    include: Optional[List[str]] = Form(
+        None, description="Only include files matching pattern(s) (glob/regex string)"),
+    exclude: Optional[List[str]] = Form(
+        None, description="Exclude files matching pattern(s) (glob/regex string)"),
 ):
     """
     ## Parse spectra from an uploaded file
@@ -376,6 +392,8 @@ async def parse_spectra_from_file(
     | `auto_processing` | Automatically process FID → FT spectra |
     | `auto_detection` | Automatically detect ranges and zones |
     | `raw_data` | Include raw data in the output (default: data source) |
+    | `include` | Only include files matching pattern(s) |
+    | `exclude` | Exclude files matching pattern(s) |
     ### Returns
     Parsed spectra data in NMRium-compatible JSON format.
     """
@@ -405,6 +423,8 @@ async def parse_spectra_from_file(
             auto_processing=auto_processing,
             auto_detection=auto_detection,
             raw_data=raw_data,
+            include=include,
+            exclude=exclude,
         )
 
     except HTTPException:
@@ -452,6 +472,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
     | `auto_processing` | Automatically process FID → FT spectra |
     | `auto_detection` | Automatically detect ranges and zones |
     | `raw_data` | Include raw data in the output (default: data source) |
+    | `include` | Only include files matching pattern(s) |
+    | `exclude` | Exclude files matching pattern(s) |
 
     ### Returns
     Parsed spectra data in NMRium-compatible JSON format.
@@ -463,6 +485,8 @@ async def parse_spectra_from_url(request: UrlParseRequest):
             auto_processing=request.auto_processing,
             auto_detection=request.auto_detection,
             raw_data=request.raw_data,
+            include=request.include,
+            exclude=request.exclude,
         )
 
     except HTTPException:
diff --git a/app/scripts/nmr-cli/Dockerfile b/app/scripts/nmr-cli/Dockerfile
index 2e38276..f7877d5 100644
--- a/app/scripts/nmr-cli/Dockerfile
+++ b/app/scripts/nmr-cli/Dockerfile
@@ -1,13 +1,21 @@
 # build the image ` docker build --tag nmr-cli  . ` 
 # run the container ` docker run -it nmr-cli bash `
 
-FROM mcr.microsoft.com/playwright:v1.58.2-noble
+# NOTE: if `docker run` prints
+#   "Error while loading conda entry point: conda-libmamba-solver (module 'libmambapy' has no attribute 'QueryFormat')"
+# this is unrelated to this image/container — it comes from a version mismatch between
+# conda-libmamba-solver and libmambapy in your HOST shell's conda (base) environment.
+# It does not affect the container. To fix it on the host, run:
+#   conda update -n base -c conda-forge conda conda-libmamba-solver libmambapy
+# or, if that doesn't resolve it:
+#   conda install -n base -c conda-forge --force-reinstall conda-libmamba-solver libmambapy
+# or, to bypass libmamba entirely:
+#   conda config --set solver classic
+
+FROM mcr.microsoft.com/playwright:v1.62.1-noble
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
-# Downgrade to Node 22
-RUN npm install -g n && n 22 && hash -r
-
 WORKDIR /app
 
 #ENV BASE_NMRIUM_URL=https://nmrium.nmrxiv.org/
diff --git a/app/scripts/nmr-cli/package-lock.json b/app/scripts/nmr-cli/package-lock.json
index dd4eebf..6f47fd6 100644
--- a/app/scripts/nmr-cli/package-lock.json
+++ b/app/scripts/nmr-cli/package-lock.json
@@ -9,27 +9,27 @@
       "version": "1.0.0",
       "license": "ISC",
       "dependencies": {
-        "@zakodium/nmr-types": "^0.5.12",
-        "@zakodium/nmrium-core": "0.7.30",
-        "@zakodium/nmrium-core-plugins": "0.7.39",
-        "axios": "^1.13.6",
+        "@zakodium/nmr-types": "^0.5.26",
+        "@zakodium/nmrium-core": "0.7.65",
+        "@zakodium/nmrium-core-plugins": "0.7.87",
+        "axios": "^1.19.0",
         "fifo-logger": "^2.0.1",
-        "file-collection": "^6.6.1",
-        "json-stream-stringify": "^3.1.6",
+        "file-collection": "^6.7.0",
+        "json-stream-stringify": "^3.1.7",
         "lodash.merge": "^4.6.2",
-        "mf-parser": "^3.7.1",
-        "ml-spectra-processing": "^14.22.0",
-        "nmr-processing": "^22.5.2",
-        "openchemlib": "^9.20.0",
-        "playwright": "1.58.2",
-        "yargs": "^18.0.0"
+        "mf-parser": "^3.9.2",
+        "ml-spectra-processing": "^14.34.0",
+        "nmr-processing": "^22.23.6",
+        "openchemlib": "^9.25.0",
+        "playwright": "1.62.1",
+        "yargs": "^18.1.0"
       },
       "bin": {
         "nmr-cli": "build/index.js"
       },
       "devDependencies": {
         "@types/lodash.merge": "^4.6.9",
-        "@types/node": "^25.3.5",
+        "@types/node": "^26.2.0",
         "@types/yargs": "^17.0.35",
         "ts-node": "^10.9.2",
         "typescript": "^5.9.3"
@@ -128,13 +128,13 @@
       }
     },
     "node_modules/@types/node": {
-      "version": "25.3.5",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-25.3.5.tgz",
-      "integrity": "sha512-oX8xrhvpiyRCQkG1MFchB09f+cXftgIXb3a7UUa4Y3wpmZPw5tyZGTLWhlESOLq1Rq6oDlc8npVU2/9xiCuXMA==",
+      "version": "26.2.0",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-26.2.0.tgz",
+      "integrity": "sha512-5IviulTZeRNp2vAJ514cc/HUlY5nZ9fCbq9DMyC52BrhFZACo3nI0R7qBxhQmo/d27NFe96ur/b7Wwxklda+kg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "undici-types": "~7.18.0"
+        "undici-types": "~8.3.0"
       }
     },
     "node_modules/@types/yargs": {
@@ -155,73 +155,84 @@
       "license": "MIT"
     },
     "node_modules/@zakodium/nmr-types": {
-      "version": "0.5.23",
-      "resolved": "https://registry.npmjs.org/@zakodium/nmr-types/-/nmr-types-0.5.23.tgz",
-      "integrity": "sha512-a8zmplUHOevUeOQ69yFwzCNNiUi867q2RY63GXg4Clhm+3BnXonBeHXicSycOoJzSz2V0pQ4LFPuqJMxKNjLvw==",
+      "version": "0.5.26",
+      "resolved": "https://registry.npmjs.org/@zakodium/nmr-types/-/nmr-types-0.5.26.tgz",
+      "integrity": "sha512-Da7K23q8O3EK8gslzyx5Hgd3k4TXq0w8JW+Qt2pDBZNY1M+uyVE97R9vcQKtcZiGVl/O0f57+qJ3kxvqVEnRgQ==",
       "license": "CC-BY-NC-SA-4.0",
       "dependencies": {
+        "cheminfo-types": "^1.15.0",
         "ml-peak-shape-generator": "^5.5.0",
         "ml-signal-processing": "^2.2.2",
-        "ml-spectra-processing": "^14.33.0"
-      }
-    },
-    "node_modules/@zakodium/nmr-types/node_modules/ml-peak-shape-generator": {
-      "version": "5.5.0",
-      "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-5.5.0.tgz",
-      "integrity": "sha512-DyBq/u5S+/0F49Hm0OWHwWvPPM1aaCZIs/eI7/fUTWfIm86Yu03YXWMQ3874eq33MLZVgM8KguGkfeGDffCLog==",
-      "license": "MIT",
-      "dependencies": {
-        "cheminfo-types": "^1.15.0"
+        "ml-spectra-processing": "^14.33.0",
+        "zod": "^4.4.3"
       }
     },
     "node_modules/@zakodium/nmrium-core": {
-      "version": "0.7.30",
-      "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core/-/nmrium-core-0.7.30.tgz",
-      "integrity": "sha512-uds3UysKrAgm38Yt2swNnt8nmf5SHqt1LuVnewwDTolztl3Lead0RtgOYsRjnL30k6gpvGrgaoENkIMxSY0/kQ==",
+      "version": "0.7.65",
+      "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core/-/nmrium-core-0.7.65.tgz",
+      "integrity": "sha512-mXXylnGVMbYRdz23kalRziwMK6OCkJkS3HW9izjatH/6/VZgnbiSa5DBm+SazBuNe5QAutrXIFUWa+t2D/5Esw==",
       "license": "CC-BY-NC-SA-4.0",
       "dependencies": {
+        "@zakodium/utils": "^0.5.1",
         "cheminfo-types": "^1.15.0",
         "fifo-logger": "^2.0.1",
-        "file-collection": "^6.6.1",
+        "file-collection": "^6.7.0",
         "is-any-array": "^3.0.0",
         "lodash.merge": "^4.6.2",
-        "ml-spectra-processing": "^14.28.1",
-        "nmr-correlation": "^2.3.5"
+        "ml-spectra-processing": "^14.33.0"
       },
       "peerDependencies": {
         "zod": "^4.4.3"
       }
     },
     "node_modules/@zakodium/nmrium-core-plugins": {
-      "version": "0.7.39",
-      "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core-plugins/-/nmrium-core-plugins-0.7.39.tgz",
-      "integrity": "sha512-WFO8UmUB4ZGwO+eCTjC1RfUBeCtv+raQmsuVx6L7zf1/BuD0N3Lq0q+JpKkdn85sfFGckyejJr1yo2qd91EVMQ==",
+      "version": "0.7.87",
+      "resolved": "https://registry.npmjs.org/@zakodium/nmrium-core-plugins/-/nmrium-core-plugins-0.7.87.tgz",
+      "integrity": "sha512-g/JwP7tgfndzQAy8xmVBWb0PASoQc/IabMHONC7uZ+juXpYizX/XM31WwNSnmAWlbGVmKHM53xU7F+mCJX2Imw==",
       "license": "CC-BY-NC-SA-4.0",
       "dependencies": {
         "@date-fns/utc": "^2.1.1",
-        "@zakodium/nmrium-core": "^0.7.30",
+        "@zakodium/nmrium-core": "^0.7.65",
         "cheminfo-types": "^1.15.0",
-        "convert-to-jcamp": "^7.0.0",
-        "date-fns": "^4.1.0",
-        "file-collection": "^6.6.1",
+        "convert-to-jcamp": "^7.0.1",
+        "date-fns": "^4.4.0",
+        "file-collection": "^6.7.0",
         "gyromagnetic-ratio": "^2.0.0",
         "is-any-array": "^3.0.0",
-        "jcampconverter": "^12.3.3",
+        "jcampconverter": "^12.5.5",
         "linear-sum-assignment": "^1.0.9",
         "lodash.merge": "^4.6.2",
-        "ml-spectra-processing": "^14.28.1",
-        "nmr-processing": "^22.13.0",
-        "openchemlib": "^9.22.0",
-        "openchemlib-utils": "^8.15.0",
-        "sdf-parser": "^8.0.0",
+        "ml-spectra-processing": "^14.33.0",
+        "nmr-processing": "^22.23.6",
+        "openchemlib": "^9.24.0",
+        "openchemlib-utils": "^8.17.1",
+        "sdf-parser": "^9.0.0",
         "ts-pattern": "^5.9.0",
         "zod": "^4.4.3"
+      },
+      "peerDependencies": {
+        "react": "*",
+        "react-dom": "*"
+      },
+      "peerDependenciesMeta": {
+        "react": {
+          "optional": true
+        },
+        "react-dom": {
+          "optional": true
+        }
       }
     },
+    "node_modules/@zakodium/utils": {
+      "version": "0.5.1",
+      "resolved": "https://registry.npmjs.org/@zakodium/utils/-/utils-0.5.1.tgz",
+      "integrity": "sha512-aRtHXol0w/nL4ZYiVNicw/7batBasftRDmYSCXj54AWf1MvLrKZNk9hthzp8I+wm7jL938HAIv8eg/45J+XyOg==",
+      "license": "MIT"
+    },
     "node_modules/@zip.js/zip.js": {
-      "version": "2.8.23",
-      "resolved": "https://registry.npmjs.org/@zip.js/zip.js/-/zip.js-2.8.23.tgz",
-      "integrity": "sha512-RB+RLnxPJFPrGvQ9rgO+4JOcsob6lD32OcF0QE0yg24oeW9q8KnTTNlugcDaIveEcCbclobJcZP+fLQ++sH0bw==",
+      "version": "2.8.57",
+      "resolved": "https://registry.npmjs.org/@zip.js/zip.js/-/zip.js-2.8.57.tgz",
+      "integrity": "sha512-cd5a0s7CS0MOD52f7FW4ju84wc/+b+YNu5XIG72PfXRLk6rInEdvIrB/BjR8D8hS4fMKuYJOBjv6FoLh3e7DHw==",
       "license": "BSD-3-Clause",
       "engines": {
         "bun": ">=0.7.0",
@@ -255,6 +266,18 @@
         "node": ">=0.4.0"
       }
     },
+    "node_modules/agent-base": {
+      "version": "6.0.2",
+      "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
+      "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
+      "license": "MIT",
+      "dependencies": {
+        "debug": "4"
+      },
+      "engines": {
+        "node": ">= 6.0.0"
+      }
+    },
     "node_modules/ansi-regex": {
       "version": "6.2.2",
       "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz",
@@ -299,14 +322,15 @@
       "license": "MIT"
     },
     "node_modules/axios": {
-      "version": "1.13.6",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-1.13.6.tgz",
-      "integrity": "sha512-ChTCHMouEe2kn713WHbQGcuYrr6fXTBiu460OTwWrWob16g1bXn4vtz07Ope7ewMozJAnEquLk5lWQWtBig9DQ==",
+      "version": "1.19.0",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-1.19.0.tgz",
+      "integrity": "sha512-ht/iuYZXEjFxLH/Hkezgd7m6JKlHHXEUSneaDz8uZe1Gj5QZtCnpyDsckvAiEnT89OEbCLmnte4R4sn7P0EKFw==",
       "license": "MIT",
       "dependencies": {
-        "follow-redirects": "^1.15.11",
-        "form-data": "^4.0.5",
-        "proxy-from-env": "^1.1.0"
+        "follow-redirects": "^1.16.0",
+        "form-data": "^4.0.6",
+        "https-proxy-agent": "^5.0.1",
+        "proxy-from-env": "^2.1.0"
       }
     },
     "node_modules/baselines": {
@@ -341,9 +365,9 @@
       }
     },
     "node_modules/chemical-elements": {
-      "version": "2.2.2",
-      "resolved": "https://registry.npmjs.org/chemical-elements/-/chemical-elements-2.2.2.tgz",
-      "integrity": "sha512-EL7cKE8FSyTcsWbs3uECKfYtdZW6Z8tD2OAeRXK4+rRc3+AMsJUqu/Sl790Ej4qbcy11/35ErdfnI5Yy7zQopw==",
+      "version": "2.3.2",
+      "resolved": "https://registry.npmjs.org/chemical-elements/-/chemical-elements-2.3.2.tgz",
+      "integrity": "sha512-3q1h/yFUqTFitGAEShu5AcC9KWHZqtFDuiqxgnViVx77zIvrVJH1jSNHPzQGSsCkCe+czVcFdF/E9XyexOIuaw==",
       "license": "MIT"
     },
     "node_modules/chemical-groups": {
@@ -431,15 +455,32 @@
       }
     },
     "node_modules/date-fns": {
-      "version": "4.1.0",
-      "resolved": "https://registry.npmjs.org/date-fns/-/date-fns-4.1.0.tgz",
-      "integrity": "sha512-Ukq0owbQXxa/U3EGtsdVBkR1w7KOQ5gIBqdH2hkvknzZPYvBxb/aa6E8L7tmjFtkwZBu3UXBbjIgPo/Ez4xaNg==",
+      "version": "4.4.0",
+      "resolved": "https://registry.npmjs.org/date-fns/-/date-fns-4.4.0.tgz",
+      "integrity": "sha512-+1UMbeh68lH1SegH83CGWwpb6OHHbpSgr3+s5Eww5M4CAgswBpoWS0AjTOfEJ33HiYKz1hdj/KTFprzXHmq/6w==",
       "license": "MIT",
       "funding": {
         "type": "github",
         "url": "https://github.com/sponsors/kossnocorp"
       }
     },
+    "node_modules/debug": {
+      "version": "4.4.3",
+      "resolved": "https://registry.npmjs.org/debug/-/debug-4.4.3.tgz",
+      "integrity": "sha512-RGwwWnwQvkVfavKVt22FGLw+xYSdzARwm0ru6DhTVA3umU5hZc28V3kO4stgYryrTlLpuvgI9GiijltAjNbcqA==",
+      "license": "MIT",
+      "dependencies": {
+        "ms": "^2.1.3"
+      },
+      "engines": {
+        "node": ">=6.0"
+      },
+      "peerDependenciesMeta": {
+        "supports-color": {
+          "optional": true
+        }
+      }
+    },
     "node_modules/delayed-stream": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/delayed-stream/-/delayed-stream-1.0.0.tgz",
@@ -513,9 +554,9 @@
       }
     },
     "node_modules/es-object-atoms": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.1.tgz",
-      "integrity": "sha512-FGgH2h8zKNim9ljj7dankFPcICIK9Cp5bm+c2gQSYePhpaG5+esrLODihIorn+Pe6FGJzWhXQotPv73jTaldXA==",
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/es-object-atoms/-/es-object-atoms-1.1.2.tgz",
+      "integrity": "sha512-HWcBoN6NileqtSydK2FqHbS/LoDd2pqrnQHLyJzBj4kOp/ky2MWMN694xOfkK8/SnUsW2DH7EfyVlydKCsm1Zw==",
       "license": "MIT",
       "dependencies": {
         "es-errors": "^1.3.0"
@@ -564,19 +605,19 @@
       }
     },
     "node_modules/file-collection": {
-      "version": "6.6.1",
-      "resolved": "https://registry.npmjs.org/file-collection/-/file-collection-6.6.1.tgz",
-      "integrity": "sha512-YJtg82Xo3pqhfXdM3tT7+vYAYj2GgC+J4jQvhYT2GDk3UsochfrHr7BxGEiQQmjIPu05ogQx9ZJ1VclhNViPJQ==",
+      "version": "6.7.0",
+      "resolved": "https://registry.npmjs.org/file-collection/-/file-collection-6.7.0.tgz",
+      "integrity": "sha512-IQEIgbRZIJgU91DVQXMjq6zSK0lcwsG/p1Sx0HqfvdsSrCnjtvcME9xsNB5qzNVZH8TyJ9sYJDt1QvIWoVvnNQ==",
       "license": "MIT",
       "dependencies": {
-        "@zip.js/zip.js": "^2.8.15",
+        "@zip.js/zip.js": "^2.8.23",
         "cheminfo-types": "^1.10.0"
       }
     },
     "node_modules/follow-redirects": {
-      "version": "1.15.11",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.15.11.tgz",
-      "integrity": "sha512-deG2P0JfjrTxl50XGCDyfI97ZGVCxIpfKYmfyrQ54n5FO/0gfIES8C/Psl6kWVDolizcaaxZJnTS0QSMxvnsBQ==",
+      "version": "1.16.0",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.16.0.tgz",
+      "integrity": "sha512-y5rN/uOsadFT/JfYwhxRS5R7Qce+g3zG97+JrtFZlC9klX/W5hD7iiLzScI4nZqUS7DNUdhPgw4xI8W2LuXlUw==",
       "funding": [
         {
           "type": "individual",
@@ -594,16 +635,16 @@
       }
     },
     "node_modules/form-data": {
-      "version": "4.0.5",
-      "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.5.tgz",
-      "integrity": "sha512-8RipRLol37bNs2bhoV67fiTEvdTrbMUYcFTiy3+wuuOnUog2QBHCZWXDRijWQfAkhBj2Uf5UnVaiWwA5vdd82w==",
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+      "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.6.tgz",
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     "node_modules/sdf-parser": {
-      "version": "8.0.0",
-      "resolved": "https://registry.npmjs.org/sdf-parser/-/sdf-parser-8.0.0.tgz",
-      "integrity": "sha512-Mh+FbnUGfu+I7/xN0JOiuQ9GP3H36USFXg3ZpeuUMXpGmYHmzmv763poF1u152Xz76nmqRLTL2ibA4dfU0yzjw==",
+      "version": "9.0.0",
+      "resolved": "https://registry.npmjs.org/sdf-parser/-/sdf-parser-9.0.0.tgz",
+      "integrity": "sha512-yi69gjBudryiKrLsT35OkyoGmskvXbVpUjkcd9tX4M4sLVmqeptsZtcx6Etf/bvdk9Ts1Wy6PuyXVIPktn6ZNQ==",
       "license": "MIT",
       "dependencies": {
         "dynamic-typing": "^2.0.0",
@@ -1433,15 +1408,6 @@
         "ml-spectra-processing": "^14.28.1"
       }
     },
-    "node_modules/spectrum-generator/node_modules/ml-peak-shape-generator": {
-      "version": "5.5.0",
-      "resolved": "https://registry.npmjs.org/ml-peak-shape-generator/-/ml-peak-shape-generator-5.5.0.tgz",
-      "integrity": "sha512-DyBq/u5S+/0F49Hm0OWHwWvPPM1aaCZIs/eI7/fUTWfIm86Yu03YXWMQ3874eq33MLZVgM8KguGkfeGDffCLog==",
-      "license": "MIT",
-      "dependencies": {
-        "cheminfo-types": "^1.15.0"
-      }
-    },
     "node_modules/string-width": {
       "version": "7.2.0",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-7.2.0.tgz",
@@ -1545,9 +1511,9 @@
       "license": "MIT"
     },
     "node_modules/undici-types": {
-      "version": "7.18.2",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.18.2.tgz",
-      "integrity": "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w==",
+      "version": "8.3.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-8.3.0.tgz",
+      "integrity": "sha512-j375ScV60dom+YkPFIfTLcOiPxkN/buHz5GobjLhixFuANaNs3C9l4GmrWqejgXWJ7BbJcFYpTEUkS1Ge8bpZQ==",
       "dev": true,
       "license": "MIT"
     },
@@ -1585,15 +1551,15 @@
       }
     },
     "node_modules/yargs": {
-      "version": "18.0.0",
-      "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz",
-      "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==",
+      "version": "18.1.0",
+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.1.0.tgz",
+      "integrity": "sha512-2rAgRKu54VsHkqI0/tYkmluGXHD4KW7yZoycuqDQ15QOTnc2VVfy0nN/1eMhnQLO00A+dwtK20xuCnc1YGeUyg==",
       "license": "MIT",
       "dependencies": {
         "cliui": "^9.0.1",
         "escalade": "^3.1.1",
         "get-caller-file": "^2.0.5",
-        "string-width": "^7.2.0",
+        "string-width": "^8.2.1",
         "y18n": "^5.0.5",
         "yargs-parser": "^22.0.0"
       },
@@ -1610,6 +1576,22 @@
         "node": "^20.19.0 || ^22.12.0 || >=23"
       }
     },
+    "node_modules/yargs/node_modules/string-width": {
+      "version": "8.2.2",
+      "resolved": "https://registry.npmjs.org/string-width/-/string-width-8.2.2.tgz",
+      "integrity": "sha512-GaPUh5gfdrYzqeVNZvUfT23vYYxXzKYidUcnMtJg/3rxRV63EFZy3k6xfKlmfeJD0176lnUV/Usr3XcwSvFzpg==",
+      "license": "MIT",
+      "dependencies": {
+        "get-east-asian-width": "^1.5.0",
+        "strip-ansi": "^7.1.2"
+      },
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/yn": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz",
diff --git a/app/scripts/nmr-cli/package.json b/app/scripts/nmr-cli/package.json
index 0d3bd4d..c795b3a 100644
--- a/app/scripts/nmr-cli/package.json
+++ b/app/scripts/nmr-cli/package.json
@@ -15,24 +15,24 @@
     "nmr-cli": "./build/index.js"
   },
   "dependencies": {
-    "@zakodium/nmr-types": "^0.5.12",
-    "@zakodium/nmrium-core": "0.7.30",
-    "@zakodium/nmrium-core-plugins": "0.7.39",
-    "axios": "^1.13.6",
+    "@zakodium/nmr-types": "^0.5.26",
+    "@zakodium/nmrium-core": "0.7.65",
+    "@zakodium/nmrium-core-plugins": "0.7.87",
+    "axios": "^1.19.0",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^6.6.1",
-    "json-stream-stringify": "^3.1.6",
+    "file-collection": "^6.7.0",
+    "json-stream-stringify": "^3.1.7",
     "lodash.merge": "^4.6.2",
-    "mf-parser": "^3.7.1",
-    "ml-spectra-processing": "^14.22.0",
-    "nmr-processing": "^22.5.2",
-    "openchemlib": "^9.20.0",
-    "playwright": "1.58.2",
-    "yargs": "^18.0.0"
+    "mf-parser": "^3.9.2",
+    "ml-spectra-processing": "^14.34.0",
+    "nmr-processing": "^22.23.6",
+    "openchemlib": "^9.25.0",
+    "playwright": "1.62.1",
+    "yargs": "^18.1.0"
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^25.3.5",
+    "@types/node": "^26.2.0",
     "@types/yargs": "^17.0.35",
     "ts-node": "^10.9.2",
     "typescript": "^5.9.3"
diff --git a/app/scripts/nmr-cli/src/index.ts b/app/scripts/nmr-cli/src/index.ts
index 74c7000..ec4c449 100755
--- a/app/scripts/nmr-cli/src/index.ts
+++ b/app/scripts/nmr-cli/src/index.ts
@@ -26,6 +26,8 @@ Options for 'parse-spectra' command:
   -d, --auto-detection     Enable ranges and zones automatic detection.
   -o, --output             Output file path (optional)
   -r, --raw-data           Include raw data in the output instead of data source
+  --include                Include only files matching pattern(s) (glob/regex string, repeatable)
+  --exclude                Exclude files matching pattern(s) (glob/regex string, repeatable)
   
 Arguments for 'parse-publication-string' command:
   publicationString   Publication string
@@ -133,6 +135,18 @@ export interface FileOptionsArgs {
    */
   r?: boolean;
 
+  /**
+   * --include
+   * Only include files matching these pattern(s) when reading a directory (file-collection's filter.include).
+   */
+  include?: string[];
+
+  /**
+   * --exclude
+   * Exclude files matching these pattern(s) when reading a directory (file-collection's filter.exclude).
+   */
+  exclude?: string[];
+
 }
 
 // Define options for parsing a spectra file
@@ -175,6 +189,16 @@ const fileOptions: { [key in keyof FileOptionsArgs]: Options } = {
     default: false,
     description: 'Include raw data in the output (default: dataSource)',
   },
+  include: {
+    type: 'array',
+    string: true,
+    description: 'Only include files matching pattern(s) when reading a directory (glob/regex string)',
+  },
+  exclude: {
+    type: 'array',
+    string: true,
+    description: 'Exclude files matching pattern(s) when reading a directory (glob/regex string)',
+  },
 } as const
 
 const parseFileCommand: CommandModule<{}, FileOptionsArgs> = {
diff --git a/app/scripts/nmr-cli/src/parse/prase-spectra.ts b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
index 06b521d..d4d24c4 100644
--- a/app/scripts/nmr-cli/src/parse/prase-spectra.ts
+++ b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
@@ -197,7 +197,7 @@ async function processAndSerialize(
 }
 
 async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>, logger: FifoLogger) {
-  const { u: url } = options;
+  const { u: url, include, exclude } = options;
 
   const { pathname: relativePath, origin: baseURL } = new URL(url)
   const source = {
@@ -210,19 +210,20 @@ async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>, l
   }
 
 
-  const { state } = await core.readFromWebSource(source, { ...parsingOptions, logger });
+  const { state } = await core.readFromWebSource(source, { ...parsingOptions, fileFilter: { include, exclude }, logger });
 
   processAndSerialize(state, options, logger)
 
 }
 
 async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'dir'>, logger: FifoLogger) {
-  const { dir: path } = options;
+  const { dir: path, include, exclude } = options;
 
   const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
 
   const fileCollection = await FileCollection.fromPath(dirPath, {
     unzip: { zipExtensions: ['zip', 'nmredata'] },
+    filter: { include, exclude },
   })
 
   const {