FileHop for Researchers
A private desktop workspace for the files you work on every day — papers, figures, scans, interview transcripts. Sits next to your reference manager, runs entirely on your machine.
Built for academic, industry, and independent researchers. Runs on Mac and Windows. No per-seat subscription, no cloud account.
Download FileHop FreeSix file workflows researchers do every day
And that your reference manager does not.
Annotate papers for a literature review
Highlight, sticky-note for marginalia, freehand for diagrams, stamp for 'READ' / 'CITE' workflow signals. Annotation Memory resumes your markup state when you reopen the file. Your reference library stays in Zotero; the markup stays on your disk.
Anonymize a manuscript for double-blind submission
Convert Word to clean PDF, strip the PDF's metadata (author, timestamps, tracked-changes residue), batch-strip EXIF on every embedded figure. Practical workflow for the 'Word File > Properties > Author' problem.
OCR a scanned research archive locally (coming soon)
Image-only PDFs from old papers, multipage TIFF, handwritten lab notebooks, scanned figures. Local on-device OCR is coming soon — it will run as a downloadable model so no archival material leaves your machine.
Organize a mixed-file research project
PDFs, screenshots, figure exports, and draft notes. Combine the right subset into one annotated dossier for an advisor, co-author, or supervisor. Your knowledge graph (Notion, Obsidian, OneNote) stays where it is; FileHop is where files come together before they leave the lab.
Redact an interview transcript before sharing
Destructive redaction: text glyphs and image pixels inside the redaction box are removed and the output is re-walked to confirm nothing redactable survives. Anonymize participant names, locations, and identifiers in qualitative data before sharing with a co-author — IRB and FERPA hygiene at the file layer.
Prepare figures for journal submission
Batch convert PNG, JPG, and TIFF figures to journal-target format at the right DPI. Strip EXIF metadata (camera model, GPS, edit history, embedded software and user name) before submission — the under-discussed double-blind de-anonymization vector.
Where FileHop fits in your stack
Your reference manager (Zotero / Mendeley / EndNote / Papers / Citavi / Paperpile)
↓ owns citations, library, BibTeX — when a file leaves it …
FileHop — file workspace. Annotate, redact, anonymize, convert, compress, combine (OCR coming soon).
↓ goes back to your co-authors, journal, preprint server, or archive
Submission portal · journal · data repository · collaborator
FileHop sits beside your citation library, not on top of it. Your reference manager owns the bibliography. FileHop owns the file work that happens around each paper — once it leaves the citation pane and before it reaches the journal, archive, or co-author.
What 'local-first' actually solves — and what it doesn't
What local-first solves
- ✓ Exposure of unpublished manuscripts to third-party servers during routine file work.
- ✓ Peer-review confidentiality violations from pasting reviewer copies into cloud LLMs.
- ✓ IRB-restricted interview data passing through transcription APIs.
- ✓ Metadata leakage that de-anonymizes double-blind submissions (Word properties, PDF document properties, EXIF on figures).
- ✓ 'Free' online OCR or conversion sites whose terms of service grant the operator rights to your uploaded text or figures.
- ✓ Vendor lock-in to a specific PDF cloud or reference-manager file format.
What local-first does NOT solve
- — Citation management, bibliography, or BibTeX export — your reference manager owns this.
- — Qualitative-coding analysis — NVivo, Atlas.ti, MAXQDA, and Dedoose own this.
- — Statistical analysis or notebook environments — R, Stata, SPSS, Jupyter, and RStudio own this.
- — Plagiarism or similarity detection — iThenticate and Turnitin own this.
- — Systematic-review screening — Covidence, Rayyan, and DistillerSR own this.
- — Your institution's IRB protocol, data-use agreement, or data-classification policy — those remain your responsibility.
- — Verifying that your own anonymization, redaction, and metadata removal worked before submission or sharing — always check.
The FileHop tools, in research terms
The same toolkit your daily file work needs, named the way you'd say it in a lab meeting.
| Workflow | FileHop tool |
|---|---|
| Strip identifying metadata from a manuscript draft for double-blind submission | Compress PDF (with opt-in metadata removal) → |
| Hit a journal submission system's PDF size cap | Compress to 5MB → |
| Combine paper + figures + supplementary into one PDF for advisor circulation | Merge PDF → |
| Split a 600-page archive scan into chapters or sections | Split PDF → |
| Password-protect an IRB consent form for secure transport | Protect PDF → |
| Open a password-protected file a collaborator sent (with the password) | Unlock PDF → |
| Extract the methods section or a single appendix as a standalone PDF | Extract Pages → |
| Reorder appendices and supplementary sections | Reorder Pages → |
| Rotate a sideways-scanned archive page | Rotate PDF → |
| Convert a draft PDF back into an editable Word document | PDF to Word → |
| Convert legacy TIFF figures to journal-acceptable formats | TIFF to JPG → |
| Batch-convert dozens of figure exports at once | Batch Image Converter → |
| OCR a stack of image-only archival PDFs locally | Extract Text from Image (local OCR coming soon) → |
How the privacy story actually works
- · Files are processed on your computer. Conversion, compression, merging, redaction, and annotation all run locally in the FileHop desktop app — your file does not transit our servers for any of these tasks.
- · Local OCR is coming soon — it will run as a downloadable on-device model, so no page image or extracted text leaves your machine.
- · When OCR ships, a cloud option will be available as an opt-in alternative for machines that cannot run the local model. It will be off by default and ask for explicit consent per task.
- · Audio transcription is coming soon and will run locally, so interview audio stays on your computer.
- · No telemetry on file contents. We do not log what you opened, what you converted, what you redacted, or what you annotated.
- · No AI training on your files. We do not use your documents to train models.
- · Open output formats. FileHop writes standard PDF, DOCX, JPG, PNG, TIFF, MP4, CSV, and MD — no proprietary container, no lock-in.
- · One-time install, no account required for local features.
Reference reading
Cited as public reference points only — not endorsements of FileHop.
- Springer / Annals of Biomedical Engineering — hidden prompts in manuscripts
- Nature — anonymization checklist for double-blind peer review
- Elsevier — risks of AI-assisted academic writing
- noScribe (GitHub) — local offline transcription precedent for IRB-restricted material
Where researchers in different contexts put FileHop to work
Light treatment — FileHop is one workspace, not a separate product per discipline.
Academic (PhD / postdoc / faculty)
Literature-review annotation across 60+ papers, double-blind anonymization for journal submission, organizing archival material that can't legally leave the institution (local OCR coming soon).
Qualitative / social science
Interview-transcript redaction for IRB and FERPA compliance, mixed-file project organization (transcripts, field notes, consent forms). Local audio transcription coming soon.
STEM / lab science
Figure preparation for journal submission (TIFF / PNG / DPI / EXIF strip), batch image conversion across dozens of plots, supplementary-file combining for submission.
Medical / clinical
HIPAA-aware local workflow for IRB-restricted documents, scan-and-redact patient-adjacent material. Caveat: no compliance certification — FileHop handles the file-layer; your protocol and institutional review remain your responsibility.
Industry research / R&D
Proprietary-document handling, batch metadata strip for external sharing, offline competitive-document review without uploading to a free converter or cloud LLM.
Independent researcher / archive / library
Converting old scan formats, organizing mixed-format archives. Local OCR for legacy collections coming soon.
What FileHop is not
Honest scope keeps everyone out of trouble. FileHop is a file workspace, not a research-tech suite.
- · Not a reference manager. Keep using Zotero, Mendeley, EndNote, Papers, Citavi, or Paperpile for citations, library, and BibTeX.
- · Not an AI research assistant. We don't search papers, write literature reviews, or synthesize findings — Elicit, Scite, SciSpace, Consensus, and Undermind own that lane.
- · Not a qualitative-coding platform. Use NVivo, Atlas.ti, MAXQDA, or Dedoose for coding analysis and theme querying.
- · Not a plagiarism or similarity checker. iThenticate and Turnitin own that.
- · Not a systematic-review screening platform. Covidence, Rayyan, and DistillerSR own that.
- · Not a statistical or notebook environment. R, Stata, SPSS, Jupyter, and RStudio own that.
- · Not certified for any specific IRB protocol, HIPAA Business Associate role, GDPR processor agreement, FERPA obligation, or institutional data-classification policy. Local processing reduces certain risk categories; compliance remains your and your institution's responsibility.
- · Not a substitute for verifying your own anonymization, redaction, and metadata removal before submission or sharing.
- · Not a Linux or iPad app today. Mac and Windows desktop only.
Frequently asked questions
Is FileHop a replacement for Zotero or Mendeley?
No. FileHop is a file workspace — it sits beside your reference manager. Zotero (or Mendeley, EndNote, Papers, Citavi, Paperpile) owns your citations, library, and BibTeX. FileHop handles the file work that happens around each paper: annotate, redact transcripts, anonymize a manuscript draft, prepare figures for submission, combine a dossier for an advisor (local OCR coming soon).
Can I use FileHop for unpublished manuscripts under peer review?
FileHop processes your files on your computer — they do not transit our servers for the file-handling tasks (annotate, redact, anonymize, convert, compress, merge). That reduces your exposure to third-party server risk for unpublished work relative to free online converters or cloud LLMs. Peer-review confidentiality, however, is your responsibility — FileHop cannot certify it for you. For reviewer copies in particular, the publisher's confidentiality requirements always govern.
Does the OCR run locally or in the cloud?
Local OCR is coming soon. When it ships it will run on-device by default as a downloadable model, so page images and extracted text never leave your machine. A cloud option will be available as an opt-in fallback for machines that cannot run the local model; it will be off by default and ask for explicit consent per task.
Will FileHop's OCR handle large research archives?
That is the goal. The forthcoming local OCR is designed for batch work on image-only PDFs, multipage TIFF, and scanned figures — running entirely on your machine. It is not yet available; this section describes the planned capability, not a shipped feature.
Will the OCR read handwriting, math, and tables?
Handwriting, math expressions, and table layouts are target use cases for the forthcoming local OCR. Until it ships, FileHop does not perform OCR — plan accordingly for archives that need text extraction today.
Does FileHop's redaction actually destroy the underlying text?
Yes. FileHop's redaction permanently removes text glyphs, image pixels, contained vector paths, and inline images inside the redaction region, then re-walks the output to confirm nothing redactable survives. It fails closed when content cannot be redacted faithfully. For anonymizing qualitative-research transcripts (participant names, locations, identifiers) or removing author-identifying paragraphs from a double-blind manuscript draft, this is the correct behavior. As a belt-and-braces precaution for the most sensitive material, you can also rasterize the page after redaction.
Will FileHop fully anonymize my manuscript for double-blind submission?
FileHop handles the file-layer hygiene: PDF metadata strip (author, title, timestamps, modification history), batch EXIF strip on every embedded figure, and destructive redaction of any author-identifying paragraphs you mark. The full workflow is: write in Word as usual, convert to PDF through FileHop, strip the PDF's metadata, batch-strip EXIF on the figure files, then visually review for self-references, 'Smith et al. (in prep)', distinctive grant numbers, or institutional affiliations in figure footers. FileHop does not in-place scrub the .docx — convert to PDF first, then strip the PDF metadata. The interpretive review (deciding what counts as identifying in your specific submission) is yours.
Is this OK for IRB-restricted interview transcripts?
FileHop keeps your transcripts on your computer for the file-handling work (annotate, redact, organize, combine). Local audio transcription is coming soon and, when it ships, the audio will also stay on your computer — reducing exposure to third-party transcription APIs and cloud LLMs, a risk category several IRBs have raised in recent years. None of this by itself satisfies your protocol's requirements; your IRB approval, data-classification policy, and institutional review continue to govern. Confirm with your IRB before changing your transcription workflow.
Does FileHop do citation extraction or BibTeX export?
No. Your reference manager handles that — Zotero's PDF-metadata retrieval, Mendeley, EndNote, Papers, Citavi, or Paperpile. FileHop is the file workspace that sits beside the reference manager; the bibliography stays in the reference manager.
How is FileHop different from Adobe Acrobat?
FileHop is a desktop-only app that runs locally without a cloud account; Acrobat is increasingly cloud-anchored and requires a per-seat subscription. FileHop is not a complete Acrobat replacement — Acrobat has features FileHop does not (e.g., certificate-backed e-signature, mature accessibility tooling). For the daily file work most researchers actually do (annotate papers, anonymize drafts, redact transcripts, prepare figures, compress for submission), FileHop covers it — and forthcoming local OCR will keep IRB-restricted material on your machine rather than in a cloud service. See our Adobe Acrobat alternative comparison for details.
Will it work on my Mac, Windows, or Linux machine?
Mac and Windows — including Apple Silicon. No Linux build today. No iPad or iOS app today. If those matter for your workflow, factor that in.
Can I try FileHop before committing?
Yes — FileHop has a free tier you can install and use without a subscription. Download it from the link above. The privacy story is architectural, not policy-based — the same install you try is the same install that processes files locally.
Bring the file work back to your desk
FileHop is free to install and runs locally on Mac and Windows. Your unpublished work, IRB-restricted material, and peer-review copies stay on disk.
Download FileHop Free