diff --git a/app/scripts/nmr-cli/Dockerfile b/app/scripts/nmr-cli/Dockerfile
index 45b9abf..f7877d5 100644
--- a/app/scripts/nmr-cli/Dockerfile
+++ b/app/scripts/nmr-cli/Dockerfile
@@ -32,9 +32,6 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-# Downgrade to Node 22 for nmr-processing compatibility
-RUN npm install -g n && n 22 && hash -r
-
 COPY package.json ./
 
 RUN npm install
@@ -43,11 +40,9 @@ COPY . ./
 
 RUN npm run build
 
-# Install nmr-cli as a global package
-RUN npm install -g .
 
-# Usage examples (run after `docker run -it nmr-cli bash`):
-#   nmr-cli parse-spectra -u https://s3.uni-jena.de/nmrxiv/production/archive/1368b8fd-3af7-48f7-8b6d-13de9c1ecf8b/492-62-6.zip -s
+# Install the nmr-cli as a global package 
 # For example, nmr-cli parse-spectra -u https://s3.uni-jena.de/nmrxiv/production/archive/d5ec45db-d984-46e9-bb72-c43fd4a463fa/Sali_Eth.zip -s
 # For example, nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
 # nmr-cli predict -n "1H" --id 1 --type "nmr;1H;1d" --shifts "1" --solvent "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)" -m $"\n Ketcher  6122516162D 1   1.00000     0.00000     0\n\n 16 17  0  0  0  0  0  0  0  0999 V2000\n    1.1954   -4.6484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -4.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0622   -4.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -5.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1954   -5.6533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0644   -6.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7902   -4.1495    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6574   -4.6498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7964   -6.1512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6596   -5.6458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5228   -4.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5277   -6.1421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    6.3895   -4.6477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5216   -3.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    7.2548   -4.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1215   -4.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  3  1  2  0  0  0  0\n  1  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  4  1  0  0  0  0\n  4  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  4  9  1  0  0  0  0\n  9 10  2  0  0  0  0\n 10  8  1  0  0  0  0\n  8  7  2  0  0  0  0\n  7  2  1  0  0  0  0\n  8 11  1  0  0  0  0\n 10 12  1  0  0  0  0\n 11 13  1  0  0  0  0\n 11 14  2  0  0  0  0\n 13 15  1  0  0  0  0\n 15 16  1  0  0  0  0\nM  END"
+RUN npm install . -g
diff --git a/app/scripts/nmr-cli/package-lock.json b/app/scripts/nmr-cli/package-lock.json
index 3ae8706..6f47fd6 100644
--- a/app/scripts/nmr-cli/package-lock.json
+++ b/app/scripts/nmr-cli/package-lock.json
@@ -29,7 +29,7 @@
       },
       "devDependencies": {
         "@types/lodash.merge": "^4.6.9",
-        "@types/node": "^26.4.0",
+        "@types/node": "^26.2.0",
         "@types/yargs": "^17.0.35",
         "ts-node": "^10.9.2",
         "typescript": "^5.9.3"
@@ -128,9 +128,9 @@
       }
     },
     "node_modules/@types/node": {
-      "version": "26.4.0",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-26.4.0.tgz",
-      "integrity": "sha512-faiGnoIrLH/V8cibOMEAZ8pMw6oXqSukl29ra4mN8GdaB2ZewzeaLj+INpV5N+Z1eKWzY+IzaIZH2EIR6YZRNQ==",
+      "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": {
diff --git a/app/scripts/nmr-cli/package.json b/app/scripts/nmr-cli/package.json
index 09dafd2..c795b3a 100644
--- a/app/scripts/nmr-cli/package.json
+++ b/app/scripts/nmr-cli/package.json
@@ -32,7 +32,7 @@
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^26.4.0",
+    "@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/parse/browser-manager.ts b/app/scripts/nmr-cli/src/parse/browser-manager.ts
deleted file mode 100644
index 4a070c4..0000000
--- a/app/scripts/nmr-cli/src/parse/browser-manager.ts
+++ /dev/null
@@ -1,163 +0,0 @@
-import playwright from 'playwright';
-import type { FifoLogger } from 'fifo-logger';
-import type { SpectrumWorker } from './spectrum-worker';
-import { Spectrum } from '@zakodium/nmr-types';
-import { Snapshot } from './spectrum-snapshot';
-import { toMessage } from './utility/toMessage';
-
-// How long to wait for the NMRium "Loading" indicator to appear/disappear
-// before giving up on a single spectrum's snapshot. Prevents one stuck page
-// from hanging the entire pipeline.
-export const SNAPSHOT_LOADING_TIMEOUT_MS = 30_000;
-
-// A single flaky failure (a slow spectrum tipping over the loading timeout,
-// a one-off page hiccup) shouldn't permanently cost a spectrum its snapshot,
-// so each capture gets one retry on a fresh page before giving up.
-export const SNAPSHOT_MAX_ATTEMPTS = 2;
-
-// Owns the single shared Firefox process. Multiple lanes each get their own
-// context/page from it. `reset` is guarded so that if several lanes hit a
-// dead browser at once, only the first one actually relaunches — the rest
-// just see `current` has already changed and pick up the fresh instance.
-export class BrowserManager {
-    private current: Promise<playwright.Browser> | null = null;
-
-    async get(): Promise<playwright.Browser> {
-        if (!this.current) {
-            this.current = playwright.firefox.launch();
-        }
-        return this.current;
-    }
-
-    async reset(stale: playwright.Browser): Promise<void> {
-        if (this.current && (await this.current) === stale) {
-            const toClose = this.current;
-            this.current = null;
-            await (await toClose).close().catch(() => { });
-        }
-    }
-
-    async closeAll(): Promise<void> {
-        if (this.current) {
-            const toClose = this.current;
-            this.current = null;
-            await (await toClose).close().catch(() => { });
-        }
-    }
-}
-
-// One snapshot lane = one browser tab, reused across every spectrum it's
-// assigned. Launching the browser/context happens once per lane; every
-// spectrum after the first gets a `page.reload()` (not a new context or
-// browser) before its `nmr-wrapper:load` message, so each snapshot starts
-// from a genuinely empty NMRium instance instead of relying on `load`
-// merging vs. replacing the previous spectrum's state. A reload of an
-// already-booted SPA is far cheaper than relaunching the browser/context,
-// so this keeps the speed win while removing the state-leak risk.
-export class SnapshotLane {
-    private context: playwright.BrowserContext | null = null;
-    private page: playwright.Page | null = null;
-    private hasLoadedSpectrum = false;
-
-    constructor(private manager: BrowserManager, private url: string) { }
-
-    private async ensurePage(): Promise<playwright.Page> {
-        if (this.page && !this.page.isClosed()) {
-            if (this.hasLoadedSpectrum) {
-                await this.page.reload();
-                await this.page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
-            }
-            return this.page;
-        }
-        const browser = await this.manager.get();
-        this.context = await browser.newContext(playwright.devices['Desktop Chrome HiDPI']);
-        this.page = await this.context.newPage();
-        await this.page.goto(this.url);
-        await this.page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
-        this.hasLoadedSpectrum = false;
-        return this.page;
-    }
-
-    // Discards this lane's page/context so the next attempt (or the next
-    // spectrum, if we're giving up) starts from a clean page instead of
-    // whatever broken state caused the failure. Only escalates to a full
-    // browser relaunch if the browser process itself is gone.
-    private async recover(): Promise<void> {
-        await this.context?.close().catch(() => { });
-        this.context = null;
-        this.page = null;
-        this.hasLoadedSpectrum = false;
-
-        const browser = await this.manager.get();
-        if (!browser.isConnected()) {
-            await this.manager.reset(browser);
-        }
-    }
-
-    private async attemptCapture(
-        spectrum: Spectrum,
-        version: unknown,
-        spectrumWorker: SpectrumWorker
-    ): Promise<string> {
-        const page = await this.ensurePage();
-
-        const stringObject = await spectrumWorker.run('serialize', spectrum, version);
-
-        // Passed as a Playwright function argument rather than spliced into an
-        // evaluated script string, so a backtick or `${...}` sequence anywhere
-        // in the spectrum data can't break (or hijack) the script.
-        await page.evaluate(
-            ({ data }) => {
-                window.postMessage({ type: 'nmr-wrapper:load', data: { data, type: 'nmrium' } }, '*');
-            },
-            { data: JSON.parse(stringObject) }
-        );
-
-        await page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
-
-        const snapshot = await page.locator('#nmrSVG .container').screenshot();
-        this.hasLoadedSpectrum = true;
-        return snapshot.toString('base64');
-    }
-
-    async capture(
-        spectrum: Spectrum,
-        id: string,
-        version: unknown,
-        spectrumWorker: SpectrumWorker,
-        logger: FifoLogger
-    ): Promise<Snapshot> {
-        let lastError: unknown;
-
-        for (let attempt = 1; attempt <= SNAPSHOT_MAX_ATTEMPTS; attempt++) {
-            const start = Date.now();
-            try {
-                const image = await this.attemptCapture(spectrum, version, spectrumWorker);
-                logger.info(
-                    { id, stage: 'snapshot', attempt, durationMs: Date.now() - start },
-                    `Captured snapshot for spectrum: ${id}`
-                );
-                return { id, image };
-            } catch (e) {
-                lastError = e;
-                logger.error(
-                    { id, stage: 'snapshot', attempt, durationMs: Date.now() - start, details: toMessage(e) },
-                    `Snapshot attempt ${attempt}/${SNAPSHOT_MAX_ATTEMPTS} failed for spectrum: ${id}`
-                );
-                await this.recover();
-            }
-        }
-
-        logger.error(
-            { id, stage: 'snapshot', details: toMessage(lastError) },
-            `Giving up on snapshot for spectrum: ${id} after ${SNAPSHOT_MAX_ATTEMPTS} attempts`
-        );
-        return { id, image: null };
-    }
-
-    async dispose(): Promise<void> {
-        await this.context?.close().catch(() => { });
-        this.context = null;
-        this.page = null;
-    }
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/prase-spectra.ts b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
index 011b2bd..d4d24c4 100644
--- a/app/scripts/nmr-cli/src/parse/prase-spectra.ts
+++ b/app/scripts/nmr-cli/src/parse/prase-spectra.ts
@@ -1,26 +1,166 @@
-import { join, isAbsolute } from 'node:path';
-import type { ParsingOptions, NmriumState } from '@zakodium/nmrium-core';
-import init from '@zakodium/nmrium-core-plugins';
-import { FileCollection } from 'file-collection';
-import yargs from 'yargs';
-import { FifoLogger } from 'fifo-logger';
-import { FileOptionsArgs } from '..';
-import { runSpectraPipeline } from './run-pipeline';
-import { outputResult } from './utility/outputResult';
-import { toMessage } from './utility/toMessage';
+import { join, isAbsolute } from 'path'
+import { NmriumData, ParsingOptions, type NmriumState } from '@zakodium/nmrium-core'
+import init from '@zakodium/nmrium-core-plugins'
+import playwright from 'playwright'
+import { FileCollection } from 'file-collection'
+import { FileOptionsArgs } from '..'
+import { isSpectrum2D } from './data/data2d/isSpectrum2D'
+import { initiateDatum2D } from './data/data2d/initiateDatum2D'
+import { initiateDatum1D } from './data/data1D/initiateDatum1D'
+import { detectZones } from './data/data2d/detectZones'
+import { detectRanges } from './data/data1D/detectRanges'
+import { Filters1DManager, Filters2DManager } from 'nmr-processing'
+import yargs from 'yargs'
+import { createWriteStream } from 'fs'
+import { JsonStreamStringify } from 'json-stream-stringify';
+import { FifoLogger } from 'fifo-logger'
 
-const core = init();
+type RequiredKey<T, K extends keyof T> = Omit<T, K> & Required<Pick<T, K>>;
 
+function toMessage(e: unknown): string {
+  return e instanceof Error ? e.message : String(e)
+}
+
+
+const parsingOptions: ParsingOptions = {
+  onLoadProcessing: { autoProcessing: true },
+  selector: { general: { dataSelection: 'preferFT' } },
+  experimentalFeatures: true,
+};
 
-type RequiredKey<T, K extends keyof T> = Omit<T, K> & Required<Pick<T, K>>;
 
+interface Snapshot {
+  id: string;
+  image: string | null;
+}
+
+const core = init()
+
+function generateNMRiumURL() {
+  const baseURL = process.env['BASE_NMRIUM_URL'] || ''
+  const url = new URL(baseURL)
+  url.searchParams.append('workspace', 'embedded')
+  return url.toString()
+}
 
-function getParsingOptions(autoProcessing: boolean): ParsingOptions {
-  return {
-    onLoadProcessing: { autoProcessing },
-    selector: { general: { dataSelection: 'preferFT' } },
-    experimentalFeatures: true,
-  };
+async function launchBrowser() {
+  return playwright.firefox.launch();
+}
+
+async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>, logger: FifoLogger): Promise<Snapshot[]> {
+  const { data: { spectra } = { spectra: [] }, version } = nmriumState;
+
+  if (!spectra?.length) return [];
+
+  const url = generateNMRiumURL();
+  const snapshots: Snapshot[] = [];
+  let browser = await launchBrowser();
+
+  for (const spectrum of spectra) {
+    let context = null;
+
+    try {
+      // recreate browser if it has crashed
+      if (!browser.isConnected()) {
+        browser = await launchBrowser();
+      }
+
+      context = await browser.newContext(playwright.devices['Desktop Chrome HiDPI']);
+      const page = await context.newPage();
+
+      await page.goto(url);
+      await page.locator('text=Loading').waitFor({ state: 'hidden' });
+
+      const stringObject = JSON.stringify(
+        { version, data: { spectra: [{ ...spectrum }] } },
+        (key, value: unknown) => ArrayBuffer.isView(value) ? Array.from(value as unknown as Iterable<unknown>) : value
+      );
+
+      await page.evaluate(`
+        window.postMessage({ type: "nmr-wrapper:load", data: { data: ${stringObject}, type: "nmrium" } }, '*');
+      `);
+
+      await page.locator('text=Loading').waitFor({ state: 'hidden' });
+
+      const snapshot = await page.locator('#nmrSVG .container').screenshot();
+      snapshots.push({ id: spectrum.id, image: snapshot.toString('base64') });
+
+    } catch (e) {
+      logger.error({ id: spectrum.id, stage: 'snapshot', details: toMessage(e) }, `Failed to capture snapshot for spectrum: ${spectrum.id}`);
+      // browser crashed — close and recreate for next spectrum
+      await browser.close().catch(() => { });
+      browser = await launchBrowser();
+
+    } finally {
+      await context?.close().catch(() => { });
+    }
+  }
+
+  await browser.close().catch(() => { });
+  return snapshots;
+}
+
+
+interface ProcessSpectraOptions {
+  autoDetection: boolean; autoProcessing: boolean;
+}
+
+function processSpectra(data: NmriumData, options: ProcessSpectraOptions, logger: FifoLogger) {
+
+  const { autoDetection = false, autoProcessing = false } = options
+  for (let index = 0; index < data.spectra.length; index++) {
+    const inputSpectrum = data.spectra[index]
+    const is2D = isSpectrum2D(inputSpectrum);
+    let spectrum = null;
+
+    try {
+
+      spectrum = is2D ? initiateDatum2D(inputSpectrum) : initiateDatum1D(inputSpectrum);
+    } catch (e) {
+      logger.error({ id: inputSpectrum.id, stage: 'parsing', details: toMessage(e) }, `Failed to parse spectrum: ${inputSpectrum.id}`);
+      continue;
+    }
+
+    if (autoProcessing) {
+      try {
+
+        isSpectrum2D(spectrum) ? Filters2DManager.reapplyFilters(spectrum) : Filters1DManager.reapplyFilters(spectrum);
+        logger.info({ id: inputSpectrum.id, stage: 'processing' }, `Processed spectrum: ${inputSpectrum.id}`);
+
+      } catch (e) {
+        logger.error({ id: inputSpectrum.id, stage: 'processing', details: toMessage(e) }, `Failed to process spectrum: ${inputSpectrum.id}`);
+      }
+    }
+
+    if (autoDetection && spectrum.info.isFt) {
+      try {
+        isSpectrum2D(spectrum) ? detectZones(spectrum) : detectRanges(spectrum);
+        logger.info({ id: inputSpectrum.id, stage: 'detection' }, `Detected peaks for spectrum: ${inputSpectrum.id}`);
+      } catch (e) {
+        logger.error({ id: inputSpectrum.id, stage: 'detection', details: toMessage(e) }, `Failed to detect peaks for spectrum: ${inputSpectrum.id}`);
+      }
+    }
+
+    if (!spectrum) continue;
+
+    data.spectra[index] = spectrum;
+  }
+
+
+}
+
+function outputResult(result: any, outputPath?: string) {
+  const stream = new JsonStreamStringify(result);
+
+  if (outputPath) {
+    const writeStream = createWriteStream(outputPath);
+    stream.pipe(writeStream);
+    writeStream.on('finish', () => {
+      process.stderr.write(`Output written to: ${outputPath}\n`);
+    });
+  } else {
+    stream.pipe(process.stdout);
+  }
 }
 
 async function processAndSerialize(
@@ -30,11 +170,18 @@ async function processAndSerialize(
 ) {
   const { s: enableSnapshot = false, p: autoProcessing = false, d: autoDetection = false, o, r } = options;
 
-  const images = await runSpectraPipeline(nmriumState, { autoProcessing, autoDetection, enableSnapshot }, logger);
+  if (nmriumState.data) {
+    processSpectra(nmriumState.data, { autoDetection, autoProcessing }, logger);
+  }
+
+  const images: Snapshot[] = enableSnapshot
+    ? await captureSpectraViewAsBase64(nmriumState, logger)
+    : [];
 
   const { data, version } = core.serializeNmriumState(
     nmriumState as NmriumState,
-    { includeData: r ? 'rawData' : 'dataSource' },
+    { includeData: r ? 'rawData' : 'dataSource', },
+
   );
 
   // include the meta and info object in case of serialize as dataSource
@@ -42,67 +189,72 @@ async function processAndSerialize(
   if (!r) {
     for (let i = 0; i < spectra.length; i++) {
       const { info = {}, meta = {} } = nmriumState.data?.spectra[i] || {};
-      spectra[i] = { ...spectra[i], info, meta };
+      spectra[i] = { ...spectra[i], info, meta }
     }
   }
-  // Drop the raw processed spectra (typed arrays, filter history) now that
-  // everything needed from them has been copied into `spectra` above —
-  // otherwise they stay resident in memory alongside the serialized copy
-  // for the rest of the (potentially large, streamed) output write.
-  if (nmriumState.data) nmriumState.data.spectra = [];
   const logs = logger.getLogs();
-  await outputResult({ nmriumState: { data, version }, images, logs }, o);
+  outputResult({ nmriumState: { data, version }, images, logs }, o);
 }
 
 async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>, logger: FifoLogger) {
   const { u: url, include, exclude } = options;
 
-  const { pathname: relativePath, origin: baseURL } = new URL(url);
+  const { pathname: relativePath, origin: baseURL } = new URL(url)
   const source = {
-    entries: [{ relativePath }],
+    entries: [
+      {
+        relativePath,
+      },
+    ],
     baseURL,
-  };
+  }
+
 
-  const { state } = await core.readFromWebSource(source, { ...getParsingOptions(true), fileFilter: { include, exclude }, logger });
+  const { state } = await core.readFromWebSource(source, { ...parsingOptions, fileFilter: { include, exclude }, logger });
+
+  processAndSerialize(state, options, logger)
 
-  await processAndSerialize(state, options, logger);
 }
 
 async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'dir'>, logger: FifoLogger) {
   const { dir: path, include, exclude } = options;
 
-  const dirPath = isAbsolute(path) ? path : join(process.cwd(), path);
+  const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
 
   const fileCollection = await FileCollection.fromPath(dirPath, {
     unzip: { zipExtensions: ['zip', 'nmredata'] },
     filter: { include, exclude },
-  });
+  })
+
+  const {
+    state
+  } = await core.read(fileCollection, { ...parsingOptions, logger })
 
-  const { state } = await core.read(fileCollection, { ...getParsingOptions(true), logger });
+  processAndSerialize(state, options, logger)
 
-  await processAndSerialize(state, options, logger);
 }
 
-async function parseSpectra(argv: yargs.ArgumentsCamelCase<FileOptionsArgs>) {
+
+function parseSpectra(argv: yargs.ArgumentsCamelCase<FileOptionsArgs>
+) {
   const logger = new FifoLogger();
+
   const { u, dir } = argv;
+  // Handle parsing the spectra file logic based on argv options
+  if (u) {
+    loadSpectrumFromURL({ u, ...argv }, logger);
+  }
 
-  try {
-    // Branches are mutually exclusive and awaited so a rejection is caught
-    // here instead of becoming an unhandled promise rejection, and so -u
-    // and --dir can't race to write the same output.
-    if (u) {
-      await loadSpectrumFromURL({ u, ...argv }, logger);
-    } else if (dir) {
-      await loadSpectrumFromFilePath({ dir, ...argv }, logger);
-    } else {
-      throw new Error('Either --u (URL) or --dir (directory) must be provided.');
-    }
-  } catch (e) {
-    logger.error({ stage: 'fatal', details: toMessage(e) }, `Pipeline failed: ${toMessage(e)}`);
-    process.stderr.write(`${toMessage(e)}\n`);
-    process.exitCode = 1;
+
+  if (dir) {
+    loadSpectrumFromFilePath({ dir, ...argv }, logger);
   }
+
+
+
 }
 
-export { loadSpectrumFromFilePath, loadSpectrumFromURL, parseSpectra };
\ No newline at end of file
+
+
+
+export { loadSpectrumFromFilePath, loadSpectrumFromURL, parseSpectra }
diff --git a/app/scripts/nmr-cli/src/parse/run-concurrency.ts b/app/scripts/nmr-cli/src/parse/run-concurrency.ts
deleted file mode 100644
index 9d1f615..0000000
--- a/app/scripts/nmr-cli/src/parse/run-concurrency.ts
+++ /dev/null
@@ -1,39 +0,0 @@
-import os from 'node:os';
-
-// --- Concurrency tuning -----------------------------------------------
-// CPU-bound work (auto-processing / peak detection) is parallelized across
-// worker threads: one worker per lane, reused for every spectrum that lane
-// handles (spawning a worker reloads the whole nmr-processing module graph,
-// so lanes are long-lived, not spawned per spectrum).
-//
-// Snapshot capture is parallelized across browser tabs, but each tab is far
-// more memory-hungry than a worker thread, so it gets its own (lower) cap
-// regardless of CPU count.
-//
-// Both are overridable via env vars for tuning on a given machine.
-export const CPU_CONCURRENCY = Number(process.env['NMR_CLI_CPU_CONCURRENCY']) || Math.max(1, os.cpus().length - 1);
-export const SNAPSHOT_CONCURRENCY = Number(process.env['NMR_CLI_SNAPSHOT_CONCURRENCY']) || 3;
-
-// Runs `handler` over `items` using a fixed number of long-lived "lanes"
-// rather than firing off one promise per item. `laneIndex` is stable for the
-// lifetime of a lane, so handlers can lazily attach an expensive, reusable
-// resource (a worker thread, a browser page) to a given lane instead of
-// creating one per item.
-export async function runWithConcurrency<T>(
-    items: T[],
-    concurrency: number,
-    handler: (item: T, laneIndex: number) => Promise<void>
-): Promise<void> {
-    if (items.length === 0) return;
-    let cursor = 0;
-    const laneCount = Math.max(1, Math.min(concurrency, items.length));
-    const lanes = Array.from({ length: laneCount }, (_, laneIndex) =>
-        (async () => {
-            while (cursor < items.length) {
-                const item = items[cursor++];
-                await handler(item, laneIndex);
-            }
-        })()
-    );
-    await Promise.all(lanes);
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/run-pipeline.ts b/app/scripts/nmr-cli/src/parse/run-pipeline.ts
deleted file mode 100644
index 688a2af..0000000
--- a/app/scripts/nmr-cli/src/parse/run-pipeline.ts
+++ /dev/null
@@ -1,143 +0,0 @@
-import { isSpectrum2D, type NmriumState } from '@zakodium/nmrium-core';
-import type { FifoLogger } from 'fifo-logger';
-import { runWithConcurrency, CPU_CONCURRENCY, SNAPSHOT_CONCURRENCY } from './run-concurrency';
-import { SpectrumWorker } from './spectrum-worker';
-import { BrowserManager, SnapshotLane } from './browser-manager';
-import { Snapshot } from './spectrum-snapshot';
-import { toMessage } from './utility/toMessage';
-import { SpectrumPipelineOptions } from './type/SpectrumPipelineOptions';
-import { ParsedSpectrum } from './type/ParsedSpectrum';
-import { initiateDatum2D } from './data/data2d/initiateDatum2D';
-import { initiateDatum1D } from './data/data1D/initiateDatum1D';
-
-function getDurationMs(start: number): number {
-    return Date.now() - start;
-}
-
-function generateNMRiumURL(): string {
-    const baseURL = process.env['BASE_NMRIUM_URL'] || '';
-    const url = new URL(baseURL);
-    url.searchParams.append('workspace', 'embedded');
-    return url.toString();
-}
-
-// Each spectrum flows through the same stages — process -> detect -> snapshot
-// — but stages now run across a fixed number of concurrent "lanes" instead
-// of one spectrum at a time. Every lane owns its own worker thread (CPU
-// stages) and, if snapshots are enabled, its own persistent browser page.
-//
-// Every stage logs `durationMs` alongside its existing pass/fail log, so a
-// run's logs can be aggregated afterwards to see where time actually goes
-// (parse vs. process vs. detect vs. snapshot) instead of guessing.
-export async function runSpectraPipeline(
-    nmriumState: Partial<NmriumState>,
-    options: SpectrumPipelineOptions,
-    logger: FifoLogger
-): Promise<Snapshot[]> {
-    const data = nmriumState.data;
-    const { version } = nmriumState;
-    if (!data) return [];
-
-    const parsed = parseSpectraList(data.spectra, logger);
-
-    // Write the parsed set back so serialization later only sees spectra that
-    // actually parsed successfully.
-    data.spectra = parsed.map((d) => d.spectrum);
-    const indexById = new Map(parsed.map((d, i) => [d.id, i]));
-
-    const { autoProcessing, autoDetection, enableSnapshot } = options;
-    const snapshots: Snapshot[] = [];
-    if (parsed.length === 0) return snapshots;
-
-    const concurrency = enableSnapshot ? SNAPSHOT_CONCURRENCY : CPU_CONCURRENCY;
-    const browserManager = enableSnapshot ? new BrowserManager() : null;
-    const url = enableSnapshot ? generateNMRiumURL() : '';
-
-    const spectrumWorkers: SpectrumWorker[] = [];
-    const snapshotLanes: SnapshotLane[] = [];
-
-    const getWorker = (laneIndex: number): SpectrumWorker => {
-        if (!spectrumWorkers[laneIndex]) spectrumWorkers[laneIndex] = new SpectrumWorker();
-        return spectrumWorkers[laneIndex];
-    };
-    const getSnapshotLane = (laneIndex: number): SnapshotLane => {
-        if (!snapshotLanes[laneIndex]) snapshotLanes[laneIndex] = new SnapshotLane(browserManager!, url);
-        return snapshotLanes[laneIndex];
-    };
-
-    try {
-        await runWithConcurrency(parsed, concurrency, async ({ id, spectrum: initial }, laneIndex) => {
-            const spectrumWorker = getWorker(laneIndex);
-            let spectrum = initial;
-
-            if (autoProcessing) {
-                const start = Date.now();
-                try {
-                    spectrum = await spectrumWorker.run('process', spectrum);
-                    logger.info({ id, stage: 'processing', durationMs: getDurationMs(start) }, `Processed spectrum: ${id}`);
-                } catch (e) {
-                    logger.error(
-                        { id, stage: 'processing', durationMs: getDurationMs(start), details: toMessage(e) },
-                        `Failed to process spectrum: ${id}`
-                    );
-                }
-            }
-
-            if (autoDetection && spectrum.info.isFt) {
-                const start = Date.now();
-                try {
-                    spectrum = await spectrumWorker.run('detect', spectrum);
-                    logger.info({ id, stage: 'detection', durationMs: getDurationMs(start) }, `Detected peaks for spectrum: ${id}`);
-                } catch (e) {
-                    logger.error(
-                        { id, stage: 'detection', durationMs: getDurationMs(start), details: toMessage(e) },
-                        `Failed to detect peaks for spectrum: ${id}`
-                    );
-                }
-            }
-
-            data.spectra[indexById.get(id)!] = spectrum;
-
-            if (enableSnapshot) {
-                const lane = getSnapshotLane(laneIndex);
-                // Timing + retry for this stage live inside SnapshotLane.capture
-                // itself, since a retry needs its own per-attempt timing.
-                const snapshot = await lane.capture(spectrum, id, version, spectrumWorker, logger);
-                snapshots.push(snapshot);
-            }
-        });
-    } finally {
-        await Promise.all(spectrumWorkers.filter(Boolean).map((w) => w.terminate()));
-        await Promise.all(snapshotLanes.filter(Boolean).map((l) => l.dispose()));
-        await browserManager?.closeAll();
-    }
-
-    return snapshots;
-}
-
-
-
-
-
-
-
-function parseSpectraList(rawSpectra: any[], logger: FifoLogger): ParsedSpectrum[] {
-    const parsed: ParsedSpectrum[] = [];
-    for (const inputSpectrum of rawSpectra) {
-        const id = inputSpectrum.id;
-        const start = Date.now();
-        try {
-            const spectrum = isSpectrum2D(inputSpectrum)
-                ? initiateDatum2D(inputSpectrum)
-                : initiateDatum1D(inputSpectrum);
-            logger.info({ id, stage: 'parsing', durationMs: Date.now() - start }, `Parsed spectrum: ${id}`);
-            parsed.push({ id, spectrum });
-        } catch (e) {
-            logger.error(
-                { id, stage: 'parsing', durationMs: Date.now() - start, details: toMessage(e) },
-                `Failed to parse spectrum: ${id}`
-            );
-        }
-    }
-    return parsed;
-}
diff --git a/app/scripts/nmr-cli/src/parse/spectrum-snapshot.ts b/app/scripts/nmr-cli/src/parse/spectrum-snapshot.ts
deleted file mode 100644
index 400f9da..0000000
--- a/app/scripts/nmr-cli/src/parse/spectrum-snapshot.ts
+++ /dev/null
@@ -1,117 +0,0 @@
-import playwright, {
-    type Browser,
-    type BrowserContext,
-    type Page,
-} from 'playwright'
-
-import { SpectrumWorker } from './spectrum-worker'
-
-export interface Snapshot {
-    id: string
-    image: string | null
-}
-
-const SNAPSHOT_LOADING_TIMEOUT_MS = 30_000
-
-function generateNMRiumURL(): string {
-    const baseURL = process.env.BASE_NMRIUM_URL
-
-    if (!baseURL) {
-        throw new Error(
-            'BASE_NMRIUM_URL environment variable is not defined',
-        )
-    }
-
-    const url = new URL(baseURL)
-    url.searchParams.set('workspace', 'embedded')
-
-    return url.toString()
-}
-
-async function waitForNMRium(page: Page): Promise<void> {
-    await page.locator('text=Loading').waitFor({
-        state: 'hidden',
-        timeout: SNAPSHOT_LOADING_TIMEOUT_MS,
-    })
-}
-
-export class SpectrumSnapshot {
-    private browser: Browser | null = null
-    private context: BrowserContext | null = null
-    private page: Page | null = null
-
-    async start(): Promise<void> {
-        if (this.page) return
-
-        this.browser = await playwright.firefox.launch()
-
-        this.context = await this.browser.newContext(
-            playwright.devices['Desktop Chrome HiDPI'],
-        )
-
-        this.page = await this.context.newPage()
-
-        await this.page.goto(generateNMRiumURL())
-
-        await waitForNMRium(this.page)
-    }
-
-    async capture(
-        id: string,
-        spectrum: any,
-        version: unknown,
-        worker: SpectrumWorker,
-    ): Promise<Snapshot> {
-        if (!this.page) {
-            throw new Error(
-                'SpectrumSnapshot has not been started',
-            )
-        }
-
-        const stringObject = await worker.run(
-            'serialize',
-            spectrum,
-            version,
-        )
-
-        /*
-         * Parse the serialized data here rather than injecting
-         * the JSON string into JavaScript source code.
-         */
-        const data = JSON.parse(stringObject)
-
-        await this.page.evaluate((nmriumData) => {
-            window.postMessage(
-                {
-                    type: 'nmr-wrapper:load',
-                    data: {
-                        data: nmriumData,
-                        type: 'nmrium',
-                    },
-                },
-                '*',
-            )
-        }, data)
-
-        await waitForNMRium(this.page)
-
-        const image = await this.page
-            .locator('#nmrSVG .container')
-            .screenshot()
-
-        return {
-            id,
-            image: image.toString('base64'),
-        }
-    }
-
-    async close(): Promise<void> {
-        await this.context?.close().catch(() => { })
-        await this.browser?.close().catch(() => { })
-
-        this.page = null
-        this.context = null
-        this.browser = null
-    }
-}
-
diff --git a/app/scripts/nmr-cli/src/parse/spectrum-worker.ts b/app/scripts/nmr-cli/src/parse/spectrum-worker.ts
deleted file mode 100644
index bb7f715..0000000
--- a/app/scripts/nmr-cli/src/parse/spectrum-worker.ts
+++ /dev/null
@@ -1,71 +0,0 @@
-import { Spectrum } from '@zakodium/nmr-types';
-import { join } from 'node:path';
-import { Worker } from 'node:worker_threads';
-import { WorkerResponse } from './type/WorkerResponse';
-
-// Runs processing/detection/serialization in a separate worker thread (its
-// own V8 heap) so a heap-OOM there only terminates the worker instead of the
-// whole CLI process. One instance is created per concurrency lane (see
-// run-pipeline.ts).
-
-export class SpectrumWorker {
-    private worker: Worker | null = null;
-
-    private spawn(): Worker {
-        const worker = new Worker(join(__dirname, 'worker-entry.js'), {
-            resourceLimits: { maxOldGenerationSizeMb: 3072 },
-        });
-        worker.on('error', () => { this.worker = null; });
-        worker.on('exit', () => { this.worker = null; });
-        return worker;
-    }
-
-    private get(): Worker {
-        if (!this.worker) this.worker = this.spawn();
-        return this.worker;
-    }
-
-    run(task: 'process' | 'detect', spectrum: Spectrum): Promise<Spectrum>;
-    run(task: 'serialize', spectrum: Spectrum, version: unknown): Promise<string>;
-    run(task: 'process' | 'detect' | 'serialize', spectrum: Spectrum, version?: unknown): Promise<any> {
-        return new Promise((resolve, reject) => {
-            const worker = this.get();
-            let settled = false;
-
-            const onMessage = (msg: WorkerResponse) => {
-                settled = true;
-                cleanup();
-                if (msg.error) reject(new Error(msg.error));
-                else resolve(task === 'serialize' ? msg.stringObject : msg.spectrum);
-            };
-            const onError = (err: Error) => {
-                settled = true;
-                this.worker = null;
-                cleanup();
-                reject(err);
-            };
-            const onExit = (code: number) => {
-                this.worker = null;
-                if (!settled && code !== 0) {
-                    cleanup();
-                    reject(new Error(`Worker exited with code ${code} (likely out of memory)`));
-                }
-            };
-            const cleanup = () => {
-                worker.off('message', onMessage);
-                worker.off('error', onError);
-                worker.off('exit', onExit);
-            };
-
-            worker.on('message', onMessage);
-            worker.on('error', onError);
-            worker.on('exit', onExit);
-            worker.postMessage({ spectrum, task, version });
-        });
-    }
-
-    async terminate() {
-        await this.worker?.terminate().catch(() => { });
-        this.worker = null;
-    }
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/MoleculeExtended.ts b/app/scripts/nmr-cli/src/parse/type/MoleculeExtended.ts
index 601a66f..7e71a00 100644
--- a/app/scripts/nmr-cli/src/parse/type/MoleculeExtended.ts
+++ b/app/scripts/nmr-cli/src/parse/type/MoleculeExtended.ts
@@ -1,12 +1,11 @@
-import { StateMolecule } from '@zakodium/nmrium-core'
+import { StateMolecule } from "@zakodium/nmrium-core";
 
 export interface MoleculeExtended
-  extends
-    Required<Pick<StateMolecule, 'id' | 'molfile' | 'label'>>,
+    extends Required<Pick<StateMolecule, 'id' | 'molfile' | 'label'>>,
     Omit<StateMolecule, 'id' | 'molfile' | 'label'> {
-  mf: string
-  em: number
-  mw: number
-  svg: string
-  atoms: Record<string, number>
-}
+    mf: string;
+    em: number;
+    mw: number;
+    svg: string;
+    atoms: Record<string, number>;
+}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/ParsedSpectrum.ts b/app/scripts/nmr-cli/src/parse/type/ParsedSpectrum.ts
deleted file mode 100644
index 911550c..0000000
--- a/app/scripts/nmr-cli/src/parse/type/ParsedSpectrum.ts
+++ /dev/null
@@ -1,6 +0,0 @@
-import { Spectrum } from "@zakodium/nmr-types";
-
-export interface ParsedSpectrum {
-    id: string;
-    spectrum: Spectrum;
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/Snapshot.ts b/app/scripts/nmr-cli/src/parse/type/Snapshot.ts
deleted file mode 100644
index 0ed48cb..0000000
--- a/app/scripts/nmr-cli/src/parse/type/Snapshot.ts
+++ /dev/null
@@ -1,4 +0,0 @@
-export interface Snapshot {
-    id: string;
-    image: string | null;
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/SpectrumPipelineOptions.ts b/app/scripts/nmr-cli/src/parse/type/SpectrumPipelineOptions.ts
deleted file mode 100644
index 001b4e7..0000000
--- a/app/scripts/nmr-cli/src/parse/type/SpectrumPipelineOptions.ts
+++ /dev/null
@@ -1,5 +0,0 @@
-export interface SpectrumPipelineOptions {
-    autoProcessing: boolean;
-    autoDetection: boolean;
-    enableSnapshot: boolean;
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/WorkerRequest.ts b/app/scripts/nmr-cli/src/parse/type/WorkerRequest.ts
deleted file mode 100644
index fb39179..0000000
--- a/app/scripts/nmr-cli/src/parse/type/WorkerRequest.ts
+++ /dev/null
@@ -1,8 +0,0 @@
-import { Spectrum } from "@zakodium/nmr-types";
-
-// Message contract shared with detectWorkerEntry.ts — keep both in sync.
-export interface WorkerRequest {
-    spectrum: Spectrum;
-    task: 'process' | 'detect' | 'serialize';
-    version?: unknown;
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/type/WorkerResponse.ts b/app/scripts/nmr-cli/src/parse/type/WorkerResponse.ts
deleted file mode 100644
index 7caaa46..0000000
--- a/app/scripts/nmr-cli/src/parse/type/WorkerResponse.ts
+++ /dev/null
@@ -1,7 +0,0 @@
-import { Spectrum } from "@zakodium/nmr-types";
-
-export interface WorkerResponse {
-    spectrum?: Spectrum;
-    stringObject?: string;
-    error?: string;
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/utility/getAtom.ts b/app/scripts/nmr-cli/src/parse/utility/getAtom.ts
index da09e78..68e66ec 100644
--- a/app/scripts/nmr-cli/src/parse/utility/getAtom.ts
+++ b/app/scripts/nmr-cli/src/parse/utility/getAtom.ts
@@ -1,3 +1,3 @@
 export default function getAtom(nucleus: string): string {
-  return nucleus?.replaceAll(/\d/g, '') || ''
+  return nucleus?.replaceAll(/\d/g, '') || '';
 }
diff --git a/app/scripts/nmr-cli/src/parse/utility/isProton.ts b/app/scripts/nmr-cli/src/parse/utility/isProton.ts
index 00f3e6e..85f6e6e 100644
--- a/app/scripts/nmr-cli/src/parse/utility/isProton.ts
+++ b/app/scripts/nmr-cli/src/parse/utility/isProton.ts
@@ -1,3 +1,3 @@
 export function isProton(nucleus: string) {
-  return nucleus === '1H'
+  return nucleus === '1H';
 }
diff --git a/app/scripts/nmr-cli/src/parse/utility/outputResult.ts b/app/scripts/nmr-cli/src/parse/utility/outputResult.ts
deleted file mode 100644
index 40de4b6..0000000
--- a/app/scripts/nmr-cli/src/parse/utility/outputResult.ts
+++ /dev/null
@@ -1,24 +0,0 @@
-
-import { createWriteStream } from 'node:fs';
-import { JsonStreamStringify } from 'json-stream-stringify';
-
-export function outputResult(result: any, outputPath?: string): Promise<void> {
-    return new Promise((resolve, reject) => {
-        const stream = new JsonStreamStringify(result);
-
-        if (outputPath) {
-            const writeStream = createWriteStream(outputPath);
-            stream.pipe(writeStream);
-            writeStream.on('finish', () => {
-                process.stderr.write(`Output written to: ${outputPath}\n`);
-                resolve();
-            });
-            writeStream.on('error', reject);
-            stream.on('error', reject);
-        } else {
-            stream.pipe(process.stdout);
-            stream.on('end', () => resolve());
-            stream.on('error', reject);
-        }
-    });
-}
diff --git a/app/scripts/nmr-cli/src/parse/utility/toMessage.ts b/app/scripts/nmr-cli/src/parse/utility/toMessage.ts
deleted file mode 100644
index 6516c2c..0000000
--- a/app/scripts/nmr-cli/src/parse/utility/toMessage.ts
+++ /dev/null
@@ -1,3 +0,0 @@
-export function toMessage(e: unknown): string {
-    return e instanceof Error ? e.message : String(e);
-}
\ No newline at end of file
diff --git a/app/scripts/nmr-cli/src/parse/worker-entry.ts b/app/scripts/nmr-cli/src/parse/worker-entry.ts
deleted file mode 100644
index b78df71..0000000
--- a/app/scripts/nmr-cli/src/parse/worker-entry.ts
+++ /dev/null
@@ -1,70 +0,0 @@
-import { parentPort } from 'node:worker_threads';
-import { Filters1DManager, Filters2DManager } from 'nmr-processing';
-import { detectZones } from './data/data2d/detectZones';
-import { detectRanges } from './data/data1D/detectRanges';
-import { Spectrum } from '@zakodium/nmr-types';
-import { isSpectrum2D } from '@zakodium/nmrium-core';
-import { WorkerRequest } from './type/WorkerRequest';
-import { WorkerResponse } from './type/WorkerResponse';
-
-if (!parentPort) {
-    throw new Error('detectWorkerEntry must be run inside a worker_threads Worker');
-}
-
-// Both mutate the spectrum in place (same as the original single-threaded
-// implementation) — the return is just for a uniform call signature.
-async function runAutoProcessing(spectrum: Spectrum): Promise<Spectrum> {
-    if (isSpectrum2D(spectrum)) {
-        Filters2DManager.reapplyFilters(spectrum);
-    } else {
-        Filters1DManager.reapplyFilters(spectrum);
-    }
-    return spectrum;
-}
-
-async function runAutoDetection(spectrum: Spectrum): Promise<Spectrum> {
-    if (isSpectrum2D(spectrum)) {
-        detectZones(spectrum);
-    } else {
-        detectRanges(spectrum);
-    }
-    return spectrum;
-}
-
-// Spectra hold typed-array data (Float64Array etc.), which JSON.stringify
-// otherwise mangles into `{0: ..., 1: ...}` objects instead of arrays — the
-// replacer below converts any ArrayBuffer view to a plain array first. No
-// nmrium-core-plugins init needed here: this is a plain JSON encoding of
-// { version, data: { spectra: [spectrum] } }, matching exactly what the
-// browser's `nmr-wrapper:load` message expects.
-async function serializeSpectrum(spectrum: Spectrum, version: unknown): Promise<string> {
-    return JSON.stringify(
-        { version, data: { spectra: [spectrum] } },
-        (_key, value: unknown) => (ArrayBuffer.isView(value) ? Array.from(value as unknown as Iterable<unknown>) : value)
-    );
-}
-
-parentPort.on('message', async (msg: WorkerRequest) => {
-    const { spectrum, task, version } = msg;
-    const reply = (response: WorkerResponse) => parentPort!.postMessage(response);
-
-    try {
-        switch (task) {
-            case 'process':
-                reply({ spectrum: await runAutoProcessing(spectrum) });
-                break;
-            case 'detect':
-                reply({ spectrum: await runAutoDetection(spectrum) });
-                break;
-            case 'serialize':
-                reply({ stringObject: await serializeSpectrum(spectrum, version) });
-                break;
-            default: {
-                const exhaustive: never = task;
-                throw new Error(`Unknown task: ${exhaustive}`);
-            }
-        }
-    } catch (e) {
-        reply({ error: e instanceof Error ? e.message : String(e) });
-    }
-});
\ No newline at end of file