updating readme, adding/renaming contributing and contributors

CITATION.cff

@@ -0,0 +1,148 @@
+# This file describes how to cite the quantem software (schema: https://citation-file-format.github.io).
+# It is maintained by hand. Unlike Zenodo's auto-generated author list, this file will not
+# pick up new contributors on its own: update `authors`, `version`, and `date-released`
+# with each release.
+message: >-
+  If you use quantem in your research, please cite this software using the metadata below,
+  along with any relevant method papers listed in the README.
+title: "quantem: quantitative electron microscopy analysis toolkit"
+abstract: >-
+  quantem is a quantitative electron microscopy data analysis toolkit built on PyTorch, 
+  providing tools for analyzing many kinds of transmission electron microscopy data.
+type: software
+authors:
+  - given-names: "Arthur R. C."
+    family-names: McCray
+    orcid: "0000-0001-6077-4698"
+    affiliation: "Stanford University"  
+  - given-names: Colin
+    family-names: Ophus
+    orcid: "0000-0003-2348-8558"  
+    affiliation: "Stanford University"  
+  - given-names: "Stephanie M."
+    family-names: Ribet
+    orcid: "0000-0002-7117-066X"  
+    affiliation: "Lawrence Berkeley National Laboratory"  
+  - given-names: Georgios
+    family-names: Varnavides
+    orcid: "0000-0001-8338-3323"  
+    affiliation: "Delft University of Technology"  
+  - given-names: Cedric
+    family-names: Lim
+    orcid: "0009-0000-1319-5175"  
+    affiliation: "Stanford University"  
+  - given-names: Karen
+    family-names: Ehrhardt
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: Matthew
+    family-names: Feickert
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: Carter
+    family-names: Francis
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: "Sangjoon Bob"
+    family-names: Lee
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: Darshan
+    family-names: Mali
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: Nicholas
+    family-names: Marchese
+    # orcid: ""  
+    # affiliation: ""  
+  - given-names: Will
+    family-names: Millsaps
+    # orcid: ""  
+    # affiliation: ""  
+doi: 10.5281/zenodo.18642593  # concept DOI (always resolves to the latest release)
+license: MIT
+repository-code: "https://github.com/electronmicroscopy/quantem"
+url: "https://github.com/electronmicroscopy/quantem"
+keywords:
+  - electron microscopy
+  - 4D-STEM
+  - ptychography
+  - tomography
+  - TEM
+  - STEM
+  - PyTorch
+references:
+  - type: article
+    title: "Deep generative priors for robust and efficient electron ptychography"
+    authors:
+      - given-names: "Arthur R. C."
+        family-names: McCray
+      - given-names: "Stephanie M."
+        family-names: Ribet
+      - given-names: Georgios
+        family-names: Varnavides
+      - given-names: Colin
+        family-names: Ophus
+    year: 2025
+    url: "https://arxiv.org/abs/2511.07795"
+    notes: "arXiv:2511.07795"
+  - type: article
+    title: "Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights"
+    authors:
+      - given-names: Georgios
+        family-names: Varnavides
+      - given-names: "Julie Marie"
+        family-names: Bekkevold
+      - given-names: "Stephanie M."
+        family-names: Ribet
+      - given-names: "Mary C."
+        family-names: Scott
+      - given-names: Lewys
+        family-names: Jones
+      - given-names: Colin
+        family-names: Ophus
+    journal: "Microscopy and Microanalysis"
+    volume: 32
+    issue: 2
+    year: 2026
+    doi: 10.1093/mam/ozaf139
+  - type: article
+    title: >-
+      Missing Wedge Inpainting and Joint Alignment in Electron Tomography through
+      Implicit Neural Representations
+    authors:
+      - given-names: Cedric
+        family-names: Lim
+      - given-names: Corneel
+        family-names: Casert
+      - given-names: "Arthur R. C."
+        family-names: McCray
+      - given-names: Serin
+        family-names: Lee
+      - given-names: Andrew
+        family-names: Barnum
+      - given-names: Jennifer
+        family-names: Dionne
+      - given-names: Colin
+        family-names: Ophus
+    year: 2025
+    url: "https://arxiv.org/abs/2512.08113"
+    notes: "arXiv:2512.08113"
+  - type: article
+    title: >-
+      Multi-angle Precession Electron Diffraction (MAPED): A Versatile Approach to
+      4D-STEM Precession
+    authors:
+      - given-names: "Stephanie M."
+        family-names: Ribet
+      - given-names: Rohan
+        family-names: Dhall
+      - given-names: Colin
+        family-names: Ophus
+      - given-names: "Karen C."
+        family-names: Bustillo
+    journal: "Microscopy and Microanalysis"
+    volume: 31
+    issue: 6
+    year: 2025
+    doi: 10.1093/mam/ozaf103

CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing to quantem
+
+Thanks for your interest in improving quantem! Bug reports, feature requests, and pull requests are all welcome.
+
+## Contribution workflow
+
+- Open an [issue](https://github.com/electronmicroscopy/quantem/issues) to report a bug or discuss a feature before starting larger work.
+- Fork the repository and create a feature branch off the appropriate base branch (`dev` for most work or ask a maintainer if you are unsure).
+- Make your changes, keeping them formatted and linted (see below), and add tests where it makes sense.
+- Push to your fork and open a pull request against `electronmicroscopy/quantem`.
+
+## Development setup
+
+We use [uv](https://docs.astral.sh/uv/) to manage the package.
+
+Getting started:
+
+- [install uv](https://docs.astral.sh/uv/getting-started/installation/)
+- `git clone` the repo and `cd` into the directory
+- run `uv sync` to install all the dependencies in an editable environment
+- run `uv sync --all-packages` to also install `quantem.widget` (optional)
+
+For widget developers (requires [Node.js](https://nodejs.org/)):
+
+- `cd widget && npm install` to install JS dependencies
+- `npm run build` to build the widget
+- `npm run dev` to watch for changes during development
+
+The following will set up the pre-commit and [ruff](https://github.com/astral-sh/ruff) for linting and formatting. These commands only need to be run once when first setting up your dev environment: 
+
+- `uv tool install pre-commit` 
+- `uv tool install ruff`
+- `pre-commit install`
+
+Once these have been installed, the `.pre-commit-config.yaml` file will be run when trying to `git commit`. Errors that cannot be auto-fixed  will be listed and you will have to resolve them before committing. In many cases you will get a warning that the formatting and auto-fixes have been applied; you can stage the changes for commit with `git add -u` and the pre-commit should allow you to commit your changes.
+
+Dependency management:
+
+- use `uv add package_name` to add dependencies
+- use `uv remove package_name` to remove dependencies
+- use `uv add dev_package_name --dev` to add a dev dependency, i.e. that devs need (e.g. pytest) but you don't want shipped to users
+- use `uv pip install testing_package_name` to install a package you think you might need, but don't want to add to dependencies just yet
+
+Running python/scripts in environment:
+
+- use `uv run python`, `uv run jupyterlab` etc. to automatically activate the environment and run your command
+- alternatively use `source .venv/bin/activate` to explicitly activate environment and use `python`, `jupyterlab` etc. as usual
+  - note that if you're using an IDE like VS Code, it probably activates the environment automatically
+

CONTRIBUTORS.md

@@ -1,38 +1,47 @@
-# Developer Instructions
+# Contributors
 
-We use [uv](https://docs.astral.sh/uv/) to manage the package.
+``quantem`` is developed by researchers and students across the electron microscopy community. 
+Thank you to everyone who has contributed code, ideas, bug reports, and tutorials.
 
-Getting started:
+Contributions are broken down by module: 
 
-- [install uv](https://docs.astral.sh/uv/getting-started/installation/)
-- `git clone` the repo and `cd` into the directory
-- run `uv sync` to install all the dependencies in an editable environment
-- run `uv sync --all-packages` to also install `quantem.widget` (optional)
+## Core
+- [Georgios Varnavides](https://github.com/gvarnavi)
+- [Arthur McCray](https://github.com/arthurmccray)
+- [Colin Ophus](https://github.com/cophus)
+- [Stephanie Ribet](https://github.com/smribet)
+- [Cedric Lim](https://github.com/cedriclim1)
+- [Matthew Feickert](https://github.com/matthewfeickert)
 
-For widget developers (requires [Node.js](https://nodejs.org/)):
+## Diffraction
+- [Karen Ehrhardt](https://github.com/ehrhardtkm)
+- [Colin Ophus](https://github.com/cophus)
+- [Nicholas Marchese](https://github.com/NJMarchese)
 
-- `cd widget && npm install` to install JS dependencies
-- `npm run build` to build the widget
-- `npm run dev` to watch for changes during development
+## Diffractive Imaging
+- [Arthur McCray](https://github.com/arthurmccray)
+- [Georgios Varnavides](https://github.com/gvarnavi)
+- [Stephanie Ribet](https://github.com/smribet)
+- [Sangjoon Bob Lee](https://github.com/bobleesj)
 
-The following will set up the pre-commit and [ruff](https://github.com/astral-sh/ruff) for linting and formatting. These commands only need to be run once when first setting up your dev environment: 
+## Imaging
+- [Colin Ophus](https://github.com/cophus)
+- [Sangjoon Bob Lee](https://github.com/bobleesj)
+- [Will Millsaps](https://github.com/wwmills)
+- [Darshan Mali](https://github.com/darshan-mali)
 
-- `uv tool install pre-commit` 
-- `uv tool install ruff`
-- `pre-commit install`
+## Spectroscopy
+- [Colin Ophus](https://github.com/cophus)
+- [Stephanie Ribet](https://github.com/smribet)
 
-Once these have been installed, the `.pre-commit-config.yaml` file will be run when trying to `git commit`. Errors that cannot be auto-fixed  will be listed and you will have to resolve them before committing. In many cases you will get a warning that the formatting and auto-fixes have been applied; you can stage the changes for commit with `git add -u` and the pre-commit should allow you to commit your changes.
+## Tomography 
+- [Cedric Lim](https://github.com/cedriclim1)
+- [Arthur McCray](https://github.com/arthurmccray)
 
-Dependency management:
+For the complete, always-up-to-date list of everyone who has contributed, 
+see the [GitHub contributors graph](https://github.com/electronmicroscopy/quantem/graphs/contributors).
 
-- use `uv add package_name` to add dependencies
-- use `uv remove package_name` to remove dependencies
-- use `uv add dev_package_name --dev` to add a dev dependency, i.e. that devs need (e.g. pytest) but you don't want shipped to users
-- use `uv pip install testing_package_name` to install a package you think you might need, but don't want to add to dependencies just yet
+---
 
-Running python/scripts in environment:
-
-- use `uv run python`, `uv run jupyterlab` etc. to automatically activate the environment and run your command
-- alternatively use `source .venv/bin/activate` to explicitly activate environment and use `python`, `jupyterlab` etc. as usual
-  - note that if you're using an IDE like VS Code, it probably activates the environment automatically
-
+This list is maintained by hand and grouped by contribution history. If your name is missing, 
+listed incorrectly, or you would like it shown differently, please open a pull request or issue.

README.md

@@ -1,14 +1,59 @@
+<img src="media/quantem_logo_53.png" alt="quantem_logo" width="200"/>
+
 # quantem
 
-This is the home repository for the quantitative electron microscopy (quantem) data analysis toolkit.
+[![PyPI version](https://img.shields.io/pypi/v/quantem.svg)](https://pypi.org/project/quantem/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18642593-blue)](https://doi.org/10.5281/zenodo.18642593)
+
+``quantem`` is a quantitative electron microscopy data analysis toolkit built on [PyTorch](https://pytorch.org/). It brings together tools for reconstructing or analyzing a wide range of transmission electron microscopy (TEM) techniques, including nanobeam diffraction, phase retrieval, real-space imaging and tomography, spectroscopy, and related analyses within a consistent, GPU-accelerated API.
+
+## Capabilities
+
+- **Ptychographic phase retrieval**: ML-enabled iterative reconstruction ([McCray et al., 2025](https://arxiv.org/abs/2511.07795)) and direct methods ([Varnavides et al., 2026](https://doi.org/10.1093/mam/ozaf139)).
+- **Tomography**: fast and accurate HAADF tomography using implicit representations ([Lim et al., 2025](https://arxiv.org/abs/2512.08113)).
+- **Imaging**: drift correction and lattice analysis for (S)TEM images.
+- **Data structures & I/O**: a unified `Dataset` hierarchy that reads common electron-microscopy formats and serializes to [Zarr](https://zarr.dev/).
+- **Visualization**: publication-quality figures with perceptually-uniform colormaps.
+- **GPU-accelerated & ML-ready**: a PyTorch backend with neural object representations and multi-GPU / multi-node reconstruction.
+- **Spectroscopy**: GPU-accelerated spectra fitting for EDS and EELS, under development.
+- **Diffraction**: multi-angle precession electron diffraction (MAPED), under development ([Ribet et al., 2025](https://doi.org/10.1093/mam/ozaf103)).
+
+## Installation
+
+quantem is available on the [Python Package Index](https://pypi.org/project/quantem/) and requires Python 3.11+:
+
+```bash
+pip install quantem
+```
+
+This installs PyTorch as a dependency. For CUDA-specific PyTorch builds, follow the [official PyTorch install guide](https://pytorch.org/get-started/locally/) for your platform first.
+
+To install from source or set up a development environment, see [CONTRIBUTING.md](CONTRIBUTING.md). A local install can also be used to access the newest development features of individual modules that exist on feature branches prior to PRs. 
+
+### GPU acceleration
+
+For custom CUDA kernels that accelerate tomography, ptychography, and io behind a torch-native API, see the companion [quantem-cuda](https://github.com/electronmicroscopy/quantem-cuda) package (optional, more coming soon).
+
+## Getting started
+
+The [quantem-tutorials](https://github.com/electronmicroscopy/quantem-tutorials) repository contains Jupyter notebooks that walk through the main workflows for each module.
+
+## Citing
+
+If you use quantem in your research, please cite this repository as well as the relevant paper(s) for any module(s) that you used:
+
+- **quantem (software)**: please cite the version you used. Ready to use citations can be copied from the [Zenodo record](https://doi.org/10.5281/zenodo.18642593), or from the "Cite this repository" button on [GitHub](https://github.com/electronmicroscopy/quantem).
 
-## Installation Instructions
+- **Iterative ptychography**: McCray, A. R. C., Ribet, S. M., Varnavides, G., & Ophus, C. (2025). *Deep generative priors for robust and efficient electron ptychography.* arXiv:2511.07795. https://arxiv.org/abs/2511.07795
+- **Direct ptychography**: Varnavides, G., Bekkevold, J. M., Ribet, S. M., Scott, M. C., Jones, L., & Ophus, C. (2026). *Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights.* Microscopy and Microanalysis, 32(2), ozaf139. https://doi.org/10.1093/mam/ozaf139
+- **Electron tomography (implicit neural representations)**: Lim, C., Casert, C., McCray, A. R. C., Lee, S., Barnum, A., Dionne, J., & Ophus, C. (2025). *Missing Wedge Inpainting and Joint Alignment in Electron Tomography through Implicit Neural Representations.* arXiv:2512.08113. https://arxiv.org/abs/2512.08113
+- **Multi-angle precession electron diffraction (MAPED)**: Ribet, S. M., Dhall, R., Ophus, C., & Bustillo, K. C. (2025). *Multi-angle Precession Electron Diffraction (MAPED): A Versatile Approach to 4D-STEM Precession.* Microscopy and Microanalysis, 31(6), ozaf103. https://doi.org/10.1093/mam/ozaf103
 
-The package is available on the Python Package Index (PyPi), as [quantem](https://pypi.org/project/quantem/).
 
-You can install it using `pip install quantem`.
+## Contributing
 
-For a developer install, please refer to [CONTRIBUTORS.md](CONTRIBUTORS.md).
+Contributions are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for the development setup and workflow, and [CONTRIBUTORS.md](CONTRIBUTORS.md) for the people who have built quantem.
 
 ## License