feabas-workbench 0.3.2__tar.gz

feabas_workbench-0.3.2/LICENSE

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feabas_workbench-0.3.2/NOTICE

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+FEABAS Workbench
+Copyright 2026 Georg Kislinger
+German Center for Neurodegenerative Diseases (DZNE) and Technical University of Munich (TUM)
+https://github.com/georgkislinger/feabas-workbench
+ORCID: https://orcid.org/0000-0002-6559-7421
+
+This product is licensed under the Apache License, Version 2.0 (see LICENSE).
+Redistributions of this software, or of substantial portions of it, in source or
+binary form, must retain this NOTICE file.
+
+This product is a front end for, and bundles the driver scripts, tools and default
+configuration files of, FEABAS 3.0.5:
+    Copyright (c) 2022 Yuelong Wu, Center for Brain Science, Harvard University
+    Licensed under the MIT License (see feabas_workbench/vendor/feabas_3_0_5/LICENSE
+    and THIRD_PARTY_NOTICES.md).

feabas_workbench-0.3.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: feabas-workbench
+Version: 0.3.2
+Summary: Desktop workbench around FEABAS: data prep, preprocessing, stitching, masks, structure-guided alignment and export for serial-section EM
+Author-email: Georg Kislinger <georg.kislinger@dzne.de>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/georgkislinger/feabas-workbench
+Project-URL: User guide, https://github.com/georgkislinger/feabas-workbench/blob/main/docs/USER_GUIDE.md
+Project-URL: Issues, https://github.com/georgkislinger/feabas-workbench/issues
+Project-URL: FEABAS, https://github.com/YuelongWu/feabas
+Project-URL: FEABAS paper, https://doi.org/10.64898/2026.06.07.730510
+Project-URL: Changelog, https://github.com/georgkislinger/feabas-workbench/blob/main/CHANGELOG.md
+Keywords: electron-microscopy,connectomics,stitching,alignment,FEABAS,serial-section
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Environment :: Win32 (MS Windows)
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+License-File: THIRD_PARTY_NOTICES.md
+Requires-Dist: PySide6>=6.5
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: PyYAML>=6.0
+Requires-Dist: Pillow>=10
+Requires-Dist: tifffile
+Requires-Dist: imagecodecs
+Requires-Dist: h5py
+Requires-Dist: psutil
+Requires-Dist: opencv-python-headless
+Requires-Dist: tensorstore
+Provides-Extra: dl
+Requires-Dist: torch; extra == "dl"
+Requires-Dist: torchvision; extra == "dl"
+Requires-Dist: segmentation-models-pytorch; extra == "dl"
+Requires-Dist: ultralytics; extra == "dl"
+Requires-Dist: careamics==0.3.2; extra == "dl"
+Requires-Dist: scikit-image; extra == "dl"
+Provides-Extra: viewer
+Requires-Dist: tensorstore; extra == "viewer"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pyinstaller; extra == "dev"
+Dynamic: license-file
+
+<h1 align="center">FEABAS Workbench</h1>
+
+<p align="center">
+  A desktop app for stitching and aligning serial-section EM volumes with
+  <a href="https://github.com/YuelongWu/feabas">FEABAS</a> – for people who do not want to touch YAML files or a terminal.
+</p>
+
+<p align="center">
+  <a href="https://github.com/georgkislinger/feabas-workbench/actions/workflows/ci.yml"><img alt="CI" src="https://github.com/georgkislinger/feabas-workbench/actions/workflows/ci.yml/badge.svg"></a>
+  <img alt="Python 3.10+" src="https://img.shields.io/badge/python-3.10%2B-blue">
+  <img alt="Windows | Linux" src="https://img.shields.io/badge/platform-Windows%20%7C%20Linux-lightgrey">
+  <img alt="FEABAS 3.0.5" src="https://img.shields.io/badge/FEABAS-3.0.5-8a2be2">
+  <a href="https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/LICENSE"><img alt="Apache-2.0 license" src="https://img.shields.io/badge/license-Apache--2.0-green"></a>
+</p>
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/window3_stitching.png" alt="Stitching window" width="880">
+</p>
+
+[FEABAS](https://github.com/YuelongWu/feabas) – *Finite-Element Assisted Brain Assembly System*, by Yuelong Wu and Jeff W. Lichtman
+(Harvard; MIT licence) and described in [Wu & Lichtman, 2026](https://doi.org/10.64898/2026.06.07.730510) – is a state-of-the-art
+pipeline for stitching and elastically aligning serial-section electron-microscopy data. It is driven
+from the command line by YAML files. The workbench
+wraps it in seven windows, one per stage, and adds the parts the command line leaves to you: reading tile
+positions out of microscope metadata, building the masks, test runs on subsets, quality overlays, rolling
+back, and exporting to a viewer.
+
+FEABAS itself is not modified: its driver scripts (3.0.5) are vendored and run as subprocesses in your
+FEABAS environment with the project folder as working directory.
+
+## What it does
+
+| Window | What happens there |
+|---|---|
+| **0 Setup** | Finds or installs the Python environments (FEABAS; PyTorch + CAREamics + ultralytics + segmentation-models-pytorch), checks the GPU, remembers where Fiji and VASTlite are. |
+| **1 Project & data** | Points at the raw tiles, guesses how filenames encode row/column/section (Thermo Maps, Zeiss Atlas, sequential numbers, custom pattern), reads pixel size and stage positions from the TIFF metadata, previews the layout, writes FEABAS's `stitch_coord` files. |
+| **2 Preprocessing** | Optional histogram matching to a template and CAREamics Noise2Void / N2V2 / StructN2V denoising trained on tiles you pick. |
+| **3 Stitching** | Tile matching, montage optimisation and rendering with the settings that matter up front; test runs on a few sections and tiles in a sandbox; a full-resolution viewer for seams; every other setting in a documented tree editor. |
+| **4 Masks** | Thumbnails, tissue-vs-background masks (tile footprint, a black/white frame peeled from the outside in, fixed margins, or texture/intensity — each method shows only its own settings), fold detection with the bundled U-Net (or one you train here), import of masks made elsewhere, composition into FEABAS's material mask, split lines for broken sections, hand editing in Fiji. |
+| **5 Alignment** | Coarse (thumbnail) and fine (finite-element) alignment with its own compare distance, sandbox test runs, red/green and checkerboard overlays, and — optional, switched on in Setup — **structure-guided alignment**: a YOLO-seg model finds nuclei / mitochondria / vessels and the alignment is driven from them. |
+| **6 Export & view** | Full-resolution PNG tiles or a Neuroglancer precomputed volume, mipmaps, VASTlite export (`.vsvi`, hard-linked, instant), OME-Zarr, open in VASTlite / Fiji / Neuroglancer. |
+
+Across all of them: pipeline state is read from the files on disk (done / partly done / stale / errors /
+blocked), **clear a step and everything after it**, **snapshots** to roll back to, a log with FEABAS's
+own messages, cancellable jobs, and subset runs (`--start/--stop/--step`) for spreading work over machines.
+
+## What the result looks like
+
+The example dataset used during development: 10 serial sections, 8 × 5 tiles of 6144 × 4096 px at
+10 nm as written by a Thermo Fisher microscope, through the whole pipeline with default settings.
+
+<table>
+  <tr>
+    <td align="center"><img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/result_stitched_section.jpg" width="420" alt="Stitched section"><br><sub>One stitched section, 32 768 × 32 768 px, from 40 tiles.</sub></td>
+    <td align="center"><img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/result_aligned_overlay.jpg" width="420" alt="Aligned sections overlay"><br><sub>Two consecutive aligned sections in red and green: yellow where they coincide.</sub></td>
+  </tr>
+</table>
+
+<details>
+<summary>More windows</summary>
+<p align="center">
+  <img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/window1_project.png" width="700" alt="Project & data window"><br>
+  <img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/window4_masks.png" width="700" alt="Masks window"><br>
+  <img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/window5_alignment.png" width="700" alt="Alignment window"><br>
+  <img src="https://raw.githubusercontent.com/georgkislinger/feabas-workbench/v0.3.2/docs/img/window6_export.png" width="700" alt="Export window">
+</p>
+</details>
+
+## Install
+
+The heavy parts – FEABAS and PyTorch – go into separate environments that the app creates for you from
+its **Setup** page afterwards (internet needed; the deep-learning one is several GB; without conda the
+Setup page downloads micromamba for that). So this only concerns the GUI. Pick the row that matches your
+machine:
+
+| You have | Do this |
+|---|---|
+| **a Windows PC with nothing on it** (no Python, no conda) | Download `FEABAS-Workbench-<version>-windows-x64.zip` from the [Releases page](https://github.com/georgkislinger/feabas-workbench/releases), unpack it, start `FEABAS-Workbench\FEABAS-Workbench.exe` (SmartScreen warns once: *More info → Run anyway*). Or get the source (below) and double-click `tools\install.bat`: with no package manager on the PC it downloads a standalone micromamba and continues. |
+| **micromamba / Miniforge / Miniconda / Anaconda** | Get the source (**Code → Download ZIP**, or `git clone`), unpack, then Windows: double-click `tools\install.bat` · Linux/macOS: `bash tools/install.sh`. The script finds the package manager, creates the `feabas-workbench` env, installs the app and hard-wires `start_gui.bat` / `start_gui.sh` to it. |
+| **plain Python ≥ 3.10**, no conda | `pip install feabas-workbench` into any environment of yours ([PyPI](https://pypi.org/project/feabas-workbench/); the same wheel is attached to every GitHub release). Or, in the unpacked source: `python -m venv .venv` then `.venv\Scripts\python -m pip install -e .` (Linux: `.venv/bin/python`). |
+
+Start with **`start_gui.bat`** (Windows) or **`./start_gui.sh`** (Linux/macOS) – both find the
+environment on their own – or, after a pip install, with `feabas-workbench` (`feabas-workbench-cli`
+keeps a console window, for tracebacks). Then open **Setup**: *Detect
+environments* finds existing FEABAS / PyTorch environments, otherwise *Install fw-feabas* and *Install
+fw-dl* create them.
+
+> **Tip:** Linux desktops have the Qt libraries already. On a minimal server install add
+> `sudo apt install libegl1 libopengl0 libxkbcommon0 libdbus-1-3 libxcb-cursor0 libfontconfig1`.
+
+**Try it without data:** `python -m feabas_workbench.core.synthetic D:\demo` makes a small synthetic
+serial-section dataset with a ready project; open it in the workbench, or run the whole pipeline on it
+with `python tools/run_demo_pipeline.py D:\demo --feabas-python <fw-feabas python>` (this is what CI does).
+
+The full version with every option, and every window and setting explained – what it does, when to
+change it, what it makes stale – is the **[user guide](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/docs/USER_GUIDE.md)**. The same text as a page
+with a contents rail and search is [`docs/user_guide.html`](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/docs/user_guide.html): open it in a browser
+from your download.
+
+## A typical run
+
+1. **Project & data** – *New project* (an empty folder on a big disk) → tile folder → *Guess rule* →
+   *Read from image metadata* → *Scan tiles* → check the preview → *Write stitch_coord files*.
+2. **Stitching** – set workers and render driver → *Run all*. For a new dataset, first *Test on subset*
+   with one section and a few tiles, look at the seams, then run for real.
+3. **Masks** – *Make thumbnails* (about 500–2000 px; the suggested mip does that) → tissue rule →
+   *Detect folds* → *Compose*. Check a few sections with the overlay; paint split lines through broken sections.
+4. **Alignment** – *Match thumbnails* → *Optimize coarse stack* → *Render coarse stack* → check red/green →
+   *Generate meshes* → *Fine matching* → *Optimize stack*.
+5. **Export & view** – render PNG tiles + mipmaps → *Export* (VAST) → *Open in VASTlite*; or render the
+   precomputed volume and open it in Neuroglancer.
+
+For the plain case, **Pipeline → Run the standard pipeline…** (Ctrl+R) queues steps 2–4 in one go and
+stops at the first failure.
+
+When something upstream changes, the affected steps show **stale**; *Clear…* on the earliest affected step
+lists what will be deleted, then re-run. Make a snapshot first if the previous state was valuable.
+
+### Structure-guided alignment
+
+Off by default (Setup → Interface shows the tab). With a YOLO-seg model (bring `.pt` weights, or train on a YOLO-format dataset from the
+Alignment window): *Detect structures* on thumbnails, then *Match structures* – centroids of the same
+structures in neighbouring sections become coarse matches, either added to FEABAS's feature matches with a
+weight or used instead of them where they succeed. For fine alignment, *restrict* turns tissue outside the
+structures into a low-stiffness material, or *Re-weight fine matches* damps the matches outside them.
+The idea: let the user say what the alignment should be driven from – nuclei, mitochondria, vessels –
+instead of features they cannot see.
+
+<details>
+<summary>Layout of a project folder</summary>
+
+```
+project/
+  workbench_project.json     workbench state (source folder, naming rule, voxel size, settings)
+  configs/                   general_configs.yaml (points FEABAS here), default_*.yaml, your overrides
+  stitch/stitch_coord/       one TSV per section (input to FEABAS)
+  stitch/, stitched_sections/, thumbnail_align/, align/, aligned_stack/, logs/   FEABAS outputs
+  preprocessed/{histmatch,denoised}/   preprocessed tiles mirroring the raw folder
+  masks/{tissue,folds,structures}/     intermediate masks; manifest.json marks hand-edited ones
+  models/{n2v,folds,yolo}/             trained models
+  tests/<name>/              sandbox working directories for subset test runs
+  snapshots/<stamp>/         rollback copies of matches/meshes/transforms/configs
+  exports/                   VAST / OME-Zarr exports
+```
+
+The project folder *is* the FEABAS working directory. Your raw tiles stay where they are.
+</details>
+
+## Development
+
+```bash
+python -m pytest tests -q                                    # core tests + offscreen GUI smoke test
+python -m feabas_workbench --project X --screenshot out/     # render every window offscreen
+python -m build                                              # wheel + sdist
+pyinstaller tools/feabas_workbench.spec                      # GUI-only executable (environments stay external)
+```
+
+`feabas-workbench --selfcheck report.json` verifies an installation (vendored FEABAS, checkpoint, worker
+staging) without opening a window.
+
+CI, on every commit: lint (ruff, pyflakes level), the tests, the offscreen render of every window on a
+synthetic project and the wheel build on Ubuntu and Windows for Python 3.11 and 3.12; the **whole
+FEABAS pipeline** on a synthetic 4-section dataset on Linux (`tools/run_demo_pipeline.py`, and once more
+through the GUI's job queue with `tools/run_demo_pipeline_gui.py`); and the frozen Windows build with
+its self-check. A `v*` tag builds the wheel, sdist and Windows zip, publishes the GitHub Release and
+uploads the wheel and sdist to PyPI (trusted publishing, no stored token; the README goes through
+`tools/absolutize_readme.py` first because PyPI does not resolve relative links).
+
+Code map: `feabas_workbench/core` (Qt-free: project, tiles, configs, steps, jobs, pipeline, masks, images,
+test runs, environments, synthetic data), `feabas_workbench/workers` (subprocess workers: histogram matching, N2V, fold U-Net, YOLO,
+structure matching, match re-weighting, export), `feabas_workbench/ui` (PySide6 pages and widgets),
+`feabas_workbench/vendor/feabas_3_0_5` (FEABAS driver scripts, tools and default configs),
+`feabas_workbench/resources` (the bundled fold U-Net weights: an fp16 export with every model weight, so it
+detects and can be fine-tuned; only the original training run's optimizer state is not included, which
+only matters for resuming that run — the full 280 MB checkpoint is not bundled).
+
+## Credits and license
+
+This is a front end for **[FEABAS](https://github.com/YuelongWu/feabas)** by Yuelong Wu (Center for
+Brain Science, Harvard University), which does the actual stitching and alignment; the method is
+described in Wu & Lichtman (2026), [doi:10.64898/2026.06.07.730510](https://doi.org/10.64898/2026.06.07.730510). FEABAS is MIT-licensed;
+its driver scripts and default configuration files are vendored here unchanged, with their license, under
+`feabas_workbench/vendor/feabas_3_0_5/` (see [THIRD_PARTY_NOTICES.md](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/THIRD_PARTY_NOTICES.md)).
+
+The workbench is released under the [Apache License 2.0](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/LICENSE). Its [NOTICE](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/NOTICE) file carries the
+author attribution; anyone who redistributes the workbench, or substantial parts of it, has to keep it.
+
+## How to cite
+
+Cite FEABAS for the stitching and alignment – that is where the science is:
+
+> Wu, Y. & Lichtman, J. W. (2026). *FEABAS: A Stitching and Alignment Tool for Serial EM Data.*
+> bioRxiv. https://doi.org/10.64898/2026.06.07.730510
+
+and, if the workbench was useful in your work, the workbench too (GitHub's *Cite this repository*
+button uses [CITATION.cff](https://github.com/georgkislinger/feabas-workbench/blob/v0.3.2/CITATION.cff)):
+
+> Kislinger, G. (2026). *FEABAS Workbench* (version 0.3.2) [Computer software].
+> https://github.com/georgkislinger/feabas-workbench — ORCID 0000-0002-6559-7421