From 6c718941a09d57e273125efe956eac048887341e Mon Sep 17 00:00:00 2001
From: AlbertDominguez <adomi@stanford.edu>
Date: Fri, 2 Feb 2024 18:31:49 +0100
Subject: [PATCH] Initial release

---
 .github/workflows/test_and_deploy.yml         |  79 ++++
 .gitignore                                    |  20 +
 .napari/DESCRIPTION.md                        |  92 +++++
 .pre-commit-config.yaml                       |  21 ++
 LICENSE                                       |  28 ++
 MANIFEST.in                                   |   6 +
 README.md                                     |  38 ++
 artwork/spotiflow_logo.png                    | Bin 0 -> 11822 bytes
 docs/index.md                                 |   3 +
 mkdocs.yml                                    |  11 +
 napari_spotiflow/__init__.py                  |  13 +
 napari_spotiflow/_dock_widget.py              | 350 ++++++++++++++++++
 napari_spotiflow/_io_hooks.py                 |  97 +++++
 napari_spotiflow/_sample_data.py              |   9 +
 napari_spotiflow/napari.yaml                  |  30 ++
 .../resources/spotiflow_transp_small.png      | Bin 0 -> 4629 bytes
 pyproject.toml                                |   5 +
 requirements.txt                              |   5 +
 setup.cfg                                     |  46 +++
 tests/data/test1.csv                          |   8 +
 tests/data/test2.csv                          |   8 +
 tests/example.py                              |  31 ++
 tests/test_reader.py                          |  16 +
 tests/test_widget.py                          |   9 +
 tox.ini                                       |  38 ++
 25 files changed, 963 insertions(+)
 create mode 100644 .github/workflows/test_and_deploy.yml
 create mode 100644 .gitignore
 create mode 100644 .napari/DESCRIPTION.md
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 LICENSE
 create mode 100644 MANIFEST.in
 create mode 100644 README.md
 create mode 100644 artwork/spotiflow_logo.png
 create mode 100644 docs/index.md
 create mode 100644 mkdocs.yml
 create mode 100644 napari_spotiflow/__init__.py
 create mode 100644 napari_spotiflow/_dock_widget.py
 create mode 100644 napari_spotiflow/_io_hooks.py
 create mode 100644 napari_spotiflow/_sample_data.py
 create mode 100644 napari_spotiflow/napari.yaml
 create mode 100644 napari_spotiflow/resources/spotiflow_transp_small.png
 create mode 100644 pyproject.toml
 create mode 100644 requirements.txt
 create mode 100644 setup.cfg
 create mode 100644 tests/data/test1.csv
 create mode 100644 tests/data/test2.csv
 create mode 100644 tests/example.py
 create mode 100644 tests/test_reader.py
 create mode 100644 tests/test_widget.py
 create mode 100644 tox.ini

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
new file mode 100644
index 0000000..7885307
--- /dev/null
+++ b/.github/workflows/test_and_deploy.yml
@@ -0,0 +1,79 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  push:
+    branches:
+      - wheels
+  release:
+    types:
+      - published
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.9, "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # these libraries enable testing on Qt on linux
+      - uses: tlambert03/setup-qt-libs@v1
+
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+          if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      # and
+      # tox-conda: https://github.com/tox-dev/tox-conda
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools tox tox-gh-actions
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with tox
+        uses: aganders3/headless-gui@v1
+        with:
+          run: python -m tox
+        env:
+          PLATFORM: ${{ matrix.platform }}
+
+  deploy:
+    needs: [test]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published' # upload to pypi only on release
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U setuptools setuptools_scm wheel twine build
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          python -m build .
+          twine upload dist/*
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..4214462
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,20 @@
+*/__pycache__/
+*.py[cod]
+.idea
+
+.DS_Store
+.ipynb_checkpoints
+.pytest_cache
+*.egg-info/
+build/
+dist/
+htmlcov/
+.coverage*
+
+*.npz
+*.tif*
+*.hdf5
+*.h5
+*.zip
+*.so
+*.tfevents.*
diff --git a/.napari/DESCRIPTION.md b/.napari/DESCRIPTION.md
new file mode 100644
index 0000000..9183c54
--- /dev/null
+++ b/.napari/DESCRIPTION.md
@@ -0,0 +1,92 @@
+
+
+<!-- This file is designed to provide you with a starting template for documenting
+the functionality of your plugin. Its content will be rendered on your plugin's
+napari hub page.
+
+The sections below are given as a guide for the flow of information only, and
+are in no way prescriptive. You should feel free to merge, remove, add and 
+rename sections at will to make this document work best for your plugin. 
+
+# Description
+
+This should be a detailed description of the context of your plugin and its 
+intended purpose.
+
+If you have videos or screenshots of your plugin in action, you should include them
+here as well, to make them front and center for new users. 
+
+You should use absolute links to these assets, so that we can easily display them 
+on the hub. The easiest way to include a video is to use a GIF, for example hosted
+on imgur. You can then reference this GIF as an image.
+
+![Example GIF hosted on Imgur](https://i.imgur.com/A5phCX4.gif)
+
+Note that GIFs larger than 5MB won't be rendered by GitHub - we will however,
+render them on the napari hub.
+
+The other alternative, if you prefer to keep a video, is to use GitHub's video
+embedding feature.
+
+1. Push your `DESCRIPTION.md` to GitHub on your repository (this can also be done
+as part of a Pull Request)
+2. Edit `.napari/DESCRIPTION.md` **on GitHub**.
+3. Drag and drop your video into its desired location. It will be uploaded and
+hosted on GitHub for you, but will not be placed in your repository.
+4. We will take the resolved link to the video and render it on the hub.
+
+Here is an example of an mp4 video embedded this way.
+
+https://user-images.githubusercontent.com/17995243/120088305-6c093380-c132-11eb-822d-620e81eb5f0e.mp4
+
+# Intended Audience & Supported Data
+
+This section should describe the target audience for this plugin (any knowledge,
+skills and experience required), as well as a description of the types of data
+supported by this plugin.
+
+Try to make the data description as explicit as possible, so that users know the
+format your plugin expects. This applies both to reader plugins reading file formats
+and to function/dock widget plugins accepting layers and/or layer data.
+For example, if you know your plugin only works with 3D integer data in "tyx" order,
+make sure to mention this.
+
+If you know of researchers, groups or labs using your plugin, or if it has been cited
+anywhere, feel free to also include this information here.
+
+# Quickstart
+
+This section should go through step-by-step examples of how your plugin should be used.
+Where your plugin provides multiple dock widgets or functions, you should split these
+out into separate subsections for easy browsing. Include screenshots and videos
+wherever possible to elucidate your descriptions. 
+
+Ideally, this section should start with minimal examples for those who just want a
+quick overview of the plugin's functionality, but you should definitely link out to
+more complex and in-depth tutorials highlighting any intricacies of your plugin, and
+more detailed documentation if you have it.
+
+# Additional Install Steps (uncommon)
+We will be providing installation instructions on the hub, which will be sufficient
+for the majority of plugins. They will include instructions to pip install, and
+to install via napari itself.
+
+Most plugins can be installed out-of-the-box by just specifying the package requirements
+over in `setup.cfg`. However, if your plugin has any more complex dependencies, or 
+requires any additional preparation before (or after) installation, you should add 
+this information here.
+
+# Getting Help
+
+This section should point users to your preferred support tools, whether this be raising
+an issue on GitHub, asking a question on image.sc, or using some other method of contact.
+If you distinguish between usage support and bug/feature support, you should state that
+here.
+
+# How to Cite
+
+Many plugins may be used in the course of published (or publishable) research, as well as
+during conference talks and other public facing events. If you'd like to be cited in
+a particular format, or have a DOI you'd like used, you should provide that information here. -->
+
+The developer has not yet provided a napari-hub specific description.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..21a62d0
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.254
+    hooks:
+    - id: ruff
+      args: [--fix, --fix-only, --exit-non-zero-on-fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+    - id: black
+  - repo: https://github.com/mwouts/jupytext
+    rev: v1.14.0
+    hooks:
+    - id: jupytext
+      args: [--from, ipynb, --to, "py:percent"]
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..7f32bb8
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,28 @@
+
+Copyright (c) 2023, Albert Dominguez Mantes, Martin Weigert
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of napari-spotiflow nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..0439384
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,6 @@
+include LICENSE
+include README.md
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..79205f9
--- /dev/null
+++ b/README.md
@@ -0,0 +1,38 @@
+[![License: BSD-3](https://img.shields.io/badge/License-BSD3-blue.svg)](https://www.gnu.org/licenses/bsd3)
+[![PyPI](https://img.shields.io/pypi/v/napari-spotiflow.svg?color=green)](https://pypi.org/project/napari-spotiflow)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-spotiflow.svg?color=green)](https://python.org)
+[![tests](https://github.com/weigertlab/napari-spotiflow/workflows/tests/badge.svg)](https://github.com/weigertlab/napari-spotiflow/actions)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-spotiflow)](https://napari-hub.org/plugins/napari-spotiflow)
+
+![Logo](artwork/spotiflow_logo.png)
+---
+
+# napari-spotiflow
+
+Napari plugin for *Spotiflow*, a deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method for fluorescence microscopy. For the main repo, see [here](https://github.com/weigertlab/spotiflow). 
+
+  
+https://github.com/weigertlab/napari-spotiflow/assets/11042162/99c09826-bda7-46bc-a9a8-6e0c52b3f9f1
+
+
+----------------------------------
+
+# Usage 
+
+1. Open 2d raw image (or open one of our samples eg `File > Open Sample > napari-spotiflow > HybISS`)
+2. Start Plugin `Plugins > napari-spotiflow`
+3. Select model (pretrained or custom trained) and optionally adjust other parameter
+4. Click `run`
+
+## Supported input formats
+- [x] 2D (YX or YXC)
+- [x] 2D+t (TYX or TYXC)
+
+## Installation
+
+Clone the repo and install it in an environment with `napari` and `spotiflow`.
+
+```
+git clone git@github.com:weigertlab/napari-spotiflow.git
+pip install -e napari-spotiflow
+```
diff --git a/artwork/spotiflow_logo.png b/artwork/spotiflow_logo.png
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diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..130505f
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,3 @@
+# Welcome to napari-spotiflow
+
+Napari plugin for Spotiflow
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..d5e0f7b
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,11 @@
+site_name: napari-spotiflow
+site_description: Napari plugin for Spotiflow
+site_author: Albert Dominguez Mantes, Martin Weigert
+
+theme: readthedocs
+
+
+repo_url: https://github.com/weigertlab/napari-spotiflow
+
+pages:
+- Home: index.md
diff --git a/napari_spotiflow/__init__.py b/napari_spotiflow/__init__.py
new file mode 100644
index 0000000..fccf822
--- /dev/null
+++ b/napari_spotiflow/__init__.py
@@ -0,0 +1,13 @@
+__version__ = "0.0.2"
+
+_point_layer2d_default_kwargs = dict(size=8,
+                                     symbol='ring',
+                                     opacity=1,
+                                     face_color=[1.,.5,.2],
+                                     edge_color=[1.,.5,.2])
+
+
+# def sample_data_2d():
+#     from spotiflow.data import hybiss_data_2d
+#     
+#     return [(hybiss_data_2d(), {"name": "HybISS data (2d)"})]
diff --git a/napari_spotiflow/_dock_widget.py b/napari_spotiflow/_dock_widget.py
new file mode 100644
index 0000000..5fae90c
--- /dev/null
+++ b/napari_spotiflow/_dock_widget.py
@@ -0,0 +1,350 @@
+from magicgui import magicgui
+from magicgui import widgets as mw
+from magicgui.application import use_app
+
+import functools
+import time
+import numpy as np
+
+from pathlib import Path
+from warnings import warn
+
+import napari
+from typing import List, Union
+from enum import Enum
+from psygnal import Signal
+
+
+def abspath(root, relpath):
+    from pathlib import Path
+    root = Path(root)
+    if root.is_dir():
+        path = root/relpath
+    else:
+        path = root.parent/relpath
+    return str(path.absolute())
+
+
+def change_handler(*widgets, init=True):
+    """Implementation from https://github.com/stardist/stardist-napari/blob/main/stardist_napari/_dock_widget.py
+    """
+    def decorator_change_handler(handler):
+        @functools.wraps(handler)
+        def wrapper(*args):
+            source = Signal.sender()
+            emitter = Signal.current_emitter()
+            return handler(*args)
+
+        for widget in widgets:
+            widget.changed.connect(wrapper)
+            if init:
+                widget.changed(widget.value)
+        return wrapper
+
+    return decorator_change_handler
+
+
+def plugin_wrapper():
+    # delay imports until plugin is requested by user
+    import torch
+    from spotiflow.model import Spotiflow
+    from spotiflow.utils import normalize
+    from spotiflow.model.pretrained import list_registered
+    from napari_spotiflow import _point_layer2d_default_kwargs
+
+    def get_data(image):
+        image = image.data[0] if image.multiscale else image.data
+        return np.asarray(image)
+
+    models_reg = list_registered()
+
+    if 'general' in models_reg:
+        models_reg = ['general'] + sorted([m for m in models_reg if m != 'general'])
+    else:
+        models_reg = sorted(models_reg)
+
+    model_configs = dict()
+    model_selected = None
+
+    CUSTOM_MODEL = 'CUSTOM_MODEL'
+    model_type_choices = [('Pre-trained', Spotiflow), ('Custom', CUSTOM_MODEL)]
+    peak_mode_choices = ["fast", "skimage"]
+
+
+    @functools.lru_cache(maxsize=None)
+    def get_model(model_type, model, device):
+        kwargs = dict(inference_mode=True, map_location=device)
+        
+        if model_type == CUSTOM_MODEL:
+            return Spotiflow.from_folder(model, **kwargs)
+        else:
+            return model_type.from_pretrained(model, **kwargs)
+        
+    # -------------------------------------------------------------------------
+
+
+    DEFAULTS = dict (
+        model_type     = Spotiflow,
+        model2d        = 'general',
+        norm_image     = True,
+        perc_low       =  1.0,
+        perc_high      = 99.8,
+        use_optimized  = True,
+        prob_thresh    = 0.5,
+        n_tiles        = '1,1',
+        cnn_output     = False,
+        peak_mode      = 'fast',
+        exclude_border = False,
+        scale          = 1.0,
+        min_distance   = 2,
+        auto_n_tiles   = True,
+        subpix         = True,
+    )
+
+    # -------------------------------------------------------------------------
+
+    logo = abspath(__file__, 'resources/spotiflow_transp_small.png')
+
+    @magicgui (
+        label_head      = dict(widget_type='Label', label=f'<h1><img src="{logo}"></h1>'),
+        image           = dict(label='Input Image'),
+        label_nn        = dict(widget_type='Label', label='<br><b>Neural Network Prediction:</b>'),
+        model_type      = dict(widget_type='RadioButtons', label='Model Type', orientation='horizontal', choices=model_type_choices, value=DEFAULTS['model_type']),
+        model2d         = dict(widget_type='ComboBox', visible=True, label='Pre-trained Model', choices=models_reg, value=DEFAULTS['model2d']),
+        model_folder    = dict(widget_type='FileEdit', visible=True, label='Custom Model', mode='d'),
+        mode            = dict(widget_type='RadioButtons', label='Mode', orientation='horizontal', choices=['2D', '2D+t'], value='2D'),
+        norm_image      = dict(widget_type='CheckBox', text='Normalize Image', value=DEFAULTS['norm_image']),
+        scale           = dict(widget_type='FloatSpinBox', label='Scale factor',                min=0.5, max=2, step=0.1,  value=DEFAULTS['scale']),
+        subpix          = dict(widget_type='CheckBox', text='Subpixel prediction', value=DEFAULTS['subpix']),
+        label_nms       = dict(widget_type='Label', label='<br><b>NMS Postprocessing:</b>'),
+        perc_low        = dict(widget_type='FloatSpinBox', label='Percentile low',              min=0.0, max=100.0, step=0.1,  value=DEFAULTS['perc_low']),
+        perc_high       = dict(widget_type='FloatSpinBox', label='Percentile high',             min=0.0, max=100.0, step=0.1,  value=DEFAULTS['perc_high']),
+        use_optimized   = dict(widget_type='CheckBox', text='Use optimized probability threshold', value=DEFAULTS['use_optimized']),
+        prob_thresh     = dict(widget_type='FloatSpinBox', label='Probability/Score Threshold', min=0.0, max=  1.0, step=0.05, value=DEFAULTS['prob_thresh']),
+        peak_mode       = dict(widget_type='RadioButtons', label='Peak extraction mode', orientation='horizontal', choices=peak_mode_choices, value=DEFAULTS['peak_mode']),
+        exclude_border  = dict(widget_type='CheckBox', text='Exclude border', value=DEFAULTS['exclude_border']),
+        min_distance    = dict(widget_type='SpinBox', label='Minimum distance', min=1, max=5, step=1, value=DEFAULTS['min_distance']),
+        auto_n_tiles    = dict(widget_type='Checkbox', text='Automatically infer tiling', value=DEFAULTS['auto_n_tiles']),
+        n_tiles         = dict(widget_type='LiteralEvalLineEdit', label='Number of Tiles', value=DEFAULTS['n_tiles']),
+        label_adv       = dict(widget_type='Label', label='<br><b>Advanced Options:</b>'),
+        cnn_output      = dict(widget_type='CheckBox', text='Show CNN Output', value=DEFAULTS['cnn_output']),
+        progress_bar    = dict(label=' ', min=0, max=0, visible=False),
+        layout          = 'vertical',
+        persist         = True,
+        call_button     = True,
+    )
+    def plugin (
+        viewer: napari.Viewer,
+        label_head,
+        image: napari.layers.Image,
+        label_nn,
+        model_type,
+        model2d,
+        model_folder,
+        mode: str,
+        norm_image,
+        perc_low,
+        perc_high,
+        scale,
+        subpix,
+        label_nms,
+        use_optimized,
+        prob_thresh,
+        peak_mode,
+        exclude_border,
+        min_distance,
+        label_adv,
+        auto_n_tiles,
+        n_tiles,
+        cnn_output,
+        progress_bar: mw.ProgressBar,
+    ) -> List[napari.types.LayerDataTuple]:
+        DEVICE_STR = "cuda" if torch.cuda.is_available() else "mps" if torch.backends.mps.is_available() else "cpu"
+        
+        model = get_model(
+            model_type,
+            {
+                Spotiflow: model2d,
+                CUSTOM_MODEL: model_folder,
+            }[model_type],
+            DEVICE_STR
+        )
+           
+        model.to(torch.device(DEVICE_STR))
+        try:
+            model = torch.compile(model)
+        except RuntimeError as _:
+            warn("Could not compile the model module. Will run without compiling, which can be slightly slower.")
+        except Exception as e:
+            raise e
+
+        layers = []
+    
+        assert image is not None, "Please add an image layer to the viewer!"
+        x = get_data(image)
+
+        if mode == "2D":
+            assert x.ndim in {2,3}, "Image must be YX or CYX!" # TODO: parametrize axis order
+
+            if x.ndim==3:
+                x = x.transpose(1,2,0)
+
+            if x.ndim==3 and len(n_tiles)==2:
+                n_tiles = n_tiles + (1,)
+
+            if norm_image:
+                print("Normalizing image...")
+                x = normalize(x, perc_low, perc_high)
+
+        elif mode == "2D+t":
+            assert x.ndim in {3,4}, "Movie must be TYX or TCYX!" # TODO: parametrize axis order
+
+            if x.ndim==4 and len(n_tiles)==2:
+                n_tiles = n_tiles + (1,)
+            if norm_image:
+                print("Normalizing frames...")
+                x = np.stack([normalize(_x, perc_low, perc_high) for _x in x])
+
+        app = use_app()
+        def progress(size):
+            def _progress(it, **kwargs):
+                progress_bar.label = 'Spotiflow Prediction'
+                progress_bar.range = (0, size)
+                progress_bar.value = 0
+                progress_bar.show()
+                app.process_events()
+                for item in it:
+                    yield item
+                    progress_bar.increment(1)
+                    app.process_events()
+                app.process_events()
+            return _progress
+        actual_prob_thresh = prob_thresh if not use_optimized else None
+        if mode == "2D":
+            actual_n_tiles = tuple(max(1,s//1024) for s in x.shape) if auto_n_tiles else n_tiles
+            pred_points, details = model.predict(x,
+                                                prob_thresh=actual_prob_thresh,
+                                                n_tiles=actual_n_tiles,
+                                                peak_mode=peak_mode,
+                                                exclude_border=exclude_border,
+                                                min_distance=min_distance,
+                                                scale=scale,
+                                                verbose=True,
+                                                progress_bar_wrapper=progress(np.prod(actual_n_tiles)),
+                                                device=DEVICE_STR,
+                                                subpix=subpix,
+                                                )
+
+            if cnn_output:
+                details_prob_heatmap = details.heatmap
+                details_flow = details.flow
+
+        elif mode == "2D+t":
+            actual_n_tiles = tuple(max(1,s//1024) for s in x.shape[1:]) if auto_n_tiles else n_tiles
+            pred_points_t, details_t = tuple(zip(*tuple(model.predict(_x,
+                                                prob_thresh=actual_prob_thresh,
+                                                n_tiles=actual_n_tiles,
+                                                peak_mode=peak_mode,
+                                                exclude_border=exclude_border,
+                                                min_distance=min_distance,
+                                                scale=scale,
+                                                verbose=True,
+                                                device=DEVICE_STR,
+                                                subpix=subpix,
+                                                ) for _x in progress(x.shape[0])(x))))
+
+            pred_points = tuple(np.concatenate([[i], p])
+                                for i,ps in enumerate(pred_points_t) for p in ps)
+            if cnn_output:
+                details_prob_heatmap = np.stack([det.heatmap for det in details_t], axis=0)
+                details_flow = np.stack([det.flow for det in details_t], axis=0)
+                                           
+        if cnn_output:
+            layers.append((.5*(1+details_flow), dict(name=f'Stereographic flow ({image.name})',
+                                           ), 'image'))
+            layers.append((details_prob_heatmap, dict(name=f'Gaussian heatmap ({image.name})',
+                                           colormap='magma'), 'image'))
+        points_layer_name = f'Spots ({image.name})'
+        for l in viewer.layers:
+            if l.name == points_layer_name:
+                viewer.layers.remove(l)
+    
+        layers.append((pred_points, dict(name=f'Spots ({image.name})',
+                                             **_point_layer2d_default_kwargs), 'points'))
+
+        
+        progress_bar.hide()
+
+        return layers
+
+    # # -------------------------------------------------------------------------
+    
+    plugin.n_tiles.value = DEFAULTS['n_tiles']
+    plugin.label_head.value = '<small></small>'
+
+    # make labels prettier (https://doc.qt.io/qt-5/qsizepolicy.html#Policy-enum)
+    for w in (plugin.label_head, plugin.label_nn, plugin.label_nms, plugin.label_adv):
+        w.native.setSizePolicy(1|2, 0)
+
+    # -------------------------------------------------------------------------
+
+    widget_for_modeltype = {
+        Spotiflow: plugin.model2d,
+        CUSTOM_MODEL: plugin.model_folder,
+    }
+
+    def widgets_inactive(*widgets, active):
+        for widget in widgets:
+            widget.visible = active
+
+    def widgets_valid(*widgets, valid):
+        for widget in widgets:
+            widget.native.setStyleSheet("" if valid else "background-color: lightcoral")
+
+    def select_model(key):
+        nonlocal model_selected
+        model_selected = key
+        config = model_configs.get(key)
+        print(config)
+
+    # allow some widgets to shrink because their size depends on user input
+    plugin.image.native.setMinimumWidth(240)
+    plugin.model2d.native.setMinimumWidth(240)
+
+    plugin.label_head.native.setOpenExternalLinks(True)
+
+    layout = plugin.native.layout()
+    layout.insertStretch(layout.count()-2)
+
+    @change_handler(plugin.use_optimized)
+    def _thr_change(active: bool):
+        widgets_inactive(
+            plugin.prob_thresh,
+            active=not active
+        )
+        
+    @change_handler(plugin.model_type, init=False)
+    def _model_type_change(model_type: Union[str, type]):
+        selected = widget_for_modeltype[model_type]
+        for w in set((plugin.model2d, plugin.model_folder)) - {selected}:
+            w.hide()
+        selected.show()
+        # trigger _model_change
+        selected.changed(selected.value)        
+    
+    @change_handler(plugin.norm_image)
+    def _norm_image_change(active: bool):
+        widgets_inactive(
+            plugin.perc_low, plugin.perc_high, active=active
+        )
+    
+    @change_handler(plugin.auto_n_tiles)
+    def _auto_n_tiles_change(active: bool):
+        widgets_inactive(
+            plugin.n_tiles,
+            active=not active
+        )
+
+    return plugin
+
+
diff --git a/napari_spotiflow/_io_hooks.py b/napari_spotiflow/_io_hooks.py
new file mode 100644
index 0000000..a5d0f97
--- /dev/null
+++ b/napari_spotiflow/_io_hooks.py
@@ -0,0 +1,97 @@
+"""
+
+Simple csv reader populating a custom points layer 
+
+"""
+import logging
+from pathlib import Path
+from typing import Union
+
+import numpy as np
+import pandas as pd
+from napari_builtins.io import napari_get_reader as default_napari_get_reader
+
+COLUMNS = ('z', 'y', 'x')
+
+
+COLUMNS_NAME_MAP_2D = {
+    'axis-0' : 'y',
+    'axis-1' : 'x',
+}
+
+COLUMNS_NAME_MAP_3D = {
+    'axis-0' : 'z',
+    'axis-1' : 'y',
+    'axis-2' : 'x',
+}
+
+
+def _load_and_parse_csv(path, **kwargs):
+    df = pd.read_csv(path, **kwargs)
+    df.columns = df.columns.str.lower()
+    df.columns = df.columns.str.strip()
+    if 'axis-2' in df.columns:
+        df = df.rename(columns = lambda n: COLUMNS_NAME_MAP_3D.get(n,n))
+    else:
+        df = df.rename(columns = lambda n: COLUMNS_NAME_MAP_2D.get(n,n))
+
+    return df
+
+def _validate_dataframe(df):
+    return set(COLUMNS[-2:]).issubset(set(df.columns))
+
+def _validate_path(path: Union[str, Path]):
+    """ checks whether path is a valid csv """
+    if isinstance(path, str):
+        path = Path(path)
+    check = isinstance(path, Path) and \
+        path.suffix == ".csv" and \
+        _validate_dataframe(_load_and_parse_csv(path))
+    
+    if not check:
+        logging.warn(f'napari-spotiflow: failed to validate {path}')
+
+    return check 
+
+        
+
+
+def napari_get_reader(path):
+    print(f"opening {path} with napari-spotiflow")
+    if _validate_path(path):
+        return reader_function
+    else:
+        return default_napari_get_reader
+
+
+def reader_function(path):
+    from napari_spotiflow import _point_layer2d_default_kwargs
+        
+    if not _validate_path(path):
+        return None 
+
+    df = _load_and_parse_csv(path)
+
+    # if 3d
+    if set(COLUMNS).issubset(set(df.columns)):
+        # data = df[list(columns)].to_numpy()
+        data = df[['z','y','x']].to_numpy()
+    else:
+        # data = df[list(columns[-2:])].to_numpy()
+        data = df[['y','x']].to_numpy()
+        
+    kwargs = dict(_point_layer2d_default_kwargs)
+
+    return [(data, kwargs, 'points')]
+
+
+
+def napari_write_points(path, data, meta):
+    if data.shape[-1]==2:
+        df = pd.DataFrame(data[:,::-1], columns=['x','y'])
+    elif data.shape[-1]==3:
+        df = pd.DataFrame(data[:,::-1], columns=['x','y','z'])
+    else:
+        return None    
+    df.to_csv(path, index=False)
+    return path
diff --git a/napari_spotiflow/_sample_data.py b/napari_spotiflow/_sample_data.py
new file mode 100644
index 0000000..d65b0b4
--- /dev/null
+++ b/napari_spotiflow/_sample_data.py
@@ -0,0 +1,9 @@
+def _test_image_hybiss_2d():
+    from spotiflow import sample_data
+
+    return [(sample_data.test_image_hybiss_2d(), {"name": "hybiss_2d"})]
+
+
+def _test_image_terra_2d():
+    from spotiflow import sample_data
+    return [(sample_data.test_image_terra_2d(), {"name": "terra_2d"})]
diff --git a/napari_spotiflow/napari.yaml b/napari_spotiflow/napari.yaml
new file mode 100644
index 0000000..dc30f07
--- /dev/null
+++ b/napari_spotiflow/napari.yaml
@@ -0,0 +1,30 @@
+name: napari-spotiflow
+display_name: napari-spotiflow
+contributions:
+  commands:
+    - id: napari-spotiflow.reader
+      python_name: napari_spotiflow._io_hooks:napari_get_reader
+      title: open csv data with napari-spotiflow   
+    - id: napari-spotiflow.widget
+      python_name: napari_spotiflow._dock_widget:plugin_wrapper
+      title: Spotiflow
+    - id: napari-spotiflow.data.hybiss_2d
+      title: HybISS (2D) sample
+      python_name: napari_spotiflow._sample_data:_test_image_hybiss_2d
+    - id: napari-spotiflow.data.terra_2d
+      title: Terra (2D) sample
+      python_name: napari_spotiflow._sample_data:_test_image_terra_2d
+  sample_data:
+    - key: hybiss
+      display_name: HybISS
+      command: napari-spotiflow.data.hybiss_2d
+    - key: terra
+      display_name: Terra
+      command: napari-spotiflow.data.terra_2d
+  readers:
+    - command: napari-spotiflow.reader
+      accepts_directories: false
+      filename_patterns: ["*.csv"]
+  widgets:
+    - command: napari-spotiflow.widget
+      display_name: Spotiflow widget
\ No newline at end of file
diff --git a/napari_spotiflow/resources/spotiflow_transp_small.png b/napari_spotiflow/resources/spotiflow_transp_small.png
new file mode 100644
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..c2315ce
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..8e62ec1
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,5 @@
+# The requirements listed here are for development. 
+# Requirements of your napari plugin should be listed in setup.cfg
+# See also: https://caremad.io/posts/2013/07/setup-vs-requirement/
+
+-e .
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..3da7c4b
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,46 @@
+[metadata]
+name = napari-spotiflow
+version = 0.1.0
+author = Albert Dominguez Mantes, Martin Weigert
+author_email = albert.dominguezmantes@epfl.ch, martin.weigert@epfl.ch
+url = https://github.com/weigertlab/napari-spotiflow
+license = BSD-3-Clause
+description = Napari plugin for Spotiflow
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers =
+    Development Status :: 4 - Beta
+    Intended Audience :: Developers
+    Framework :: napari
+    Topic :: Software Development :: Testing
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Operating System :: OS Independent
+    License :: OSI Approved :: BSD License
+
+project_urls =
+    Bug Tracker = https://github.com/weigertlab/napari-spotiflow/issues
+    Documentation = https://github.com/weigertlab/napari-spotiflow#README.md
+    Source Code = https://github.com/weigertlab/napari-spotiflow
+    User Support = https://github.com/weigertlab/napari-spotiflow/issues
+
+[options]
+packages = find:
+python_requires = >=3.9, <3.12
+
+install_requires =
+    spotiflow
+    npe2
+    napari
+
+[options.package_data]
+napari-spotiflow = 
+    napari.yaml
+    resources/*
+
+[options.entry_points] 
+napari.manifest = 
+    napari-spotiflow = napari_spotiflow:napari.yaml
diff --git a/tests/data/test1.csv b/tests/data/test1.csv
new file mode 100644
index 0000000..e667fce
--- /dev/null
+++ b/tests/data/test1.csv
@@ -0,0 +1,8 @@
+index,axis-0,axis-1
+0.0,56.67851654278793,84.35855659341217
+1.0,59.85682811629277,66.24218062443461
+2.0,108.48499519091675,23.33497438211933
+3.0,53.182373811932614,40.49785687904544
+4.0,41.10478983261424,56.07158358921913
+5.0,47.46141297962391,28.42027289972707
+6.0,14.406972615173618,35.4125583614377
diff --git a/tests/data/test2.csv b/tests/data/test2.csv
new file mode 100644
index 0000000..a338185
--- /dev/null
+++ b/tests/data/test2.csv
@@ -0,0 +1,8 @@
+y,x
+56.67851654278793,84.35855659341217
+59.85682811629277,66.24218062443461
+108.48499519091675,23.33497438211933
+53.182373811932614,40.49785687904544
+41.10478983261424,56.07158358921913
+47.46141297962391,28.42027289972707
+14.406972615173618,35.4125583614377
diff --git a/tests/example.py b/tests/example.py
new file mode 100644
index 0000000..9ed4316
--- /dev/null
+++ b/tests/example.py
@@ -0,0 +1,31 @@
+import sys
+import numpy as np
+import napari
+
+from csbdeep.utils import normalize
+import numpy as np
+from tqdm import tqdm 
+import argparse
+from spotiflow.model import SpotNet
+from spotiflow.data import hybiss_data_2d
+
+def example_2d():
+    x =  hybiss_data_2d()
+    viewer =  napari.Viewer()
+    viewer.add_image(x)
+    viewer.window.add_plugin_dock_widget('napari-spotiflow')
+
+
+def example_2d_time():
+    x =  hybiss_data_2d()
+    x = np.tile(x, (4,1,1))
+    viewer =  napari.Viewer()
+    viewer.add_image(x)
+    viewer.window.add_plugin_dock_widget('napari-spotiflow')
+    
+if __name__ == '__main__':
+
+    viewer = example_2d()
+
+    napari.run()
+    
diff --git a/tests/test_reader.py b/tests/test_reader.py
new file mode 100644
index 0000000..1bbce12
--- /dev/null
+++ b/tests/test_reader.py
@@ -0,0 +1,16 @@
+import pytest
+from pathlib import Path
+from napari_spotiflow._io_hooks import reader_function
+
+
+def test_reader():
+    paths = sorted(Path('data').glob('*.csv'))
+    layers = tuple(reader_function(path) for path in paths)
+
+    assert not any([lay is None for lay in layers])
+    return layers
+
+
+if __name__ == '__main__':
+
+    layers = test_reader()
diff --git a/tests/test_widget.py b/tests/test_widget.py
new file mode 100644
index 0000000..de36a0c
--- /dev/null
+++ b/tests/test_widget.py
@@ -0,0 +1,9 @@
+import napari
+from napari_spotiflow._dock_widget import plugin_wrapper
+
+if __name__ == "__main__":
+    dock = plugin_wrapper()
+    
+    v = napari.Viewer()
+    v.window.add_dock_widget(dock, area="right")
+    napari.run()
\ No newline at end of file
diff --git a/tox.ini b/tox.ini
new file mode 100644
index 0000000..84de77c
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,38 @@
+# For more information about tox, see https://tox.readthedocs.io/en/latest/
+[tox]
+envlist = py{39,310,311}-{linux,macos,windows}
+
+[gh-actions]
+python =
+    3.9: py39
+    3.10: py310
+    3.11: py311
+    
+[gh-actions:env]
+PLATFORM =
+    ubuntu-latest: linux
+    macos-latest: macos
+    windows-latest: windows
+
+[testenv]
+platform = 
+    macos: darwin
+    linux: linux
+    windows: win32
+passenv = 
+    CI
+    GITHUB_ACTIONS
+    DISPLAY
+    XAUTHORITY
+    NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
+    PYVISTA_OFF_SCREEN
+deps = 
+    pytest  # https://docs.pytest.org/en/latest/contents.html
+    pytest-xvfb ; sys_platform == 'linux'
+    # you can remove these if you don't use them
+    napari
+    magicgui
+    pytest-qt
+    qtpy
+    pyqt5
+commands = pytest -v --color=yes