Update README and sample contribution

README.md

@@ -4,28 +4,36 @@
 [![Python package index](https://img.shields.io/pypi/v/recOrder-napari.svg)](https://pypi.org/project/recOrder-napari)
 [![Development Status](https://img.shields.io/pypi/status/napari.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
 
-`recOrder` is a napari plugin and command-line tool for quantitative label-free microscopy that depends on a computational optics library, [`waveorder`](https://github.com/mehta-lab/waveorder), and an I/O library, [`iohub`](https://github.com/czbiohub-sf/iohub).  
+`recOrder` is a collection of computational imaging methods. It currently provides QLIPP (quantitative label-free imaging with phase and polarization), phase from defocus, and fluorescence deconvolution. 
 
-In this repository you will find python tools and a napari plugin that allow the user to calibrate microscope hardware, acquire multi-modal data, reconstruct density and anisotropy, and visualize the results.
+[![Unveiling the invisible](./docs/images/comms_video_screenshot.png)](https://www.youtube.com/watch?v=JEZAaPeZhck)
 
-The acquisition, calibration, background correction, reconstruction, and applications of QLIPP (quantitative label-free imaging with phase and polarization)  are described in the following [E-Life Paper](https://elifesciences.org/articles/55502):
+Acquisition, calibration, background correction, reconstruction, and applications of QLIPP are described in the following [E-Life Paper](https://elifesciences.org/articles/55502):
 
 ```bibtex
 Syuan-Ming Guo, Li-Hao Yeh, Jenny Folkesson, Ivan E Ivanov, Anitha P Krishnan, Matthew G Keefe, Ezzat Hashemi, David Shin, Bryant B Chhun, Nathan H Cho, Manuel D Leonetti, May H Han, Tomasz J Nowakowski, Shalin B Mehta, "Revealing architectural order with quantitative label-free imaging and deep learning," eLife 2020;9:e55502 DOI: 10.7554/eLife.55502 (2020).
 ```
 
-`recOrder` is to be used alongside a conventional widefield microscope fitted with a universal polarizer (Panel A below).  The universal polarizer allows for the collection of label-free information including the intrinsic anisotropy of the sample and its relative phase (density). These measurements are collected by acquiring data under calibrated, polarization-diverse illumination followed by a computational reconstruction. The overall structure of `recOrder` is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin.
+These are the kinds of data you can acquire with `recOrder` and QLIPP:
 
-![Flow Chart](https://github.com/mehta-lab/recOrder/blob/main/docs/images/recOrder_Fig1_Overview.png?raw=true)
+https://user-images.githubusercontent.com/9554101/271128301-cc71da57-df6f-401b-a955-796750a96d88.mov
 
-## Dataset
+https://user-images.githubusercontent.com/9554101/271128510-aa2180af-607f-4c0c-912c-c18dc4f29432.mp4
 
-[Slides](https://doi.org/10.5281/zenodo.5135889) and a [dataset](https://doi.org/10.5281/zenodo.5178487) shared during a workshop on QLIPP and recOrder can be found on Zenodo.
+## What do I need to use `recOrder`
+`recOrder` is to be used alongside a conventional widefield microscope. For QLIPP, the microscope must be fitted with an analyzer and a universal polarizer: 
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5178487.svg)](https://doi.org/10.5281/zenodo.5178487)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5135889.svg)](https://doi.org/10.5281/zenodo.5135889)
+https://user-images.githubusercontent.com/9554101/273073475-70afb05a-1eb7-4019-9c42-af3e07bef723.mp4
+
+For phase-from-defocus or fluorescence deconvolution methods, the universal polarizer is optional.
+
+The overall structure of `recOrder` is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin and the command-line interface (CLI) that allows users to perform reconstructions.
+
+![Flow Chart](https://github.com/mehta-lab/recOrder/blob/main/docs/images/recOrder_Fig1_Overview.png?raw=true)
 
-## Quick Start
+
+
+## Software Quick Start
 
 (Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:
 
@@ -48,3 +56,10 @@ napari -w recOrder-napari
 
 For more help, see [`recOrder`'s documentation](https://github.com/mehta-lab/recOrder/tree/main/docs). To install `recOrder` 
 on a microscope, see the [microscope installation guide](https://github.com/mehta-lab/recOrder/blob/main/docs/microscope-installation-guide.md).
+
+## Dataset
+
+[Slides](https://doi.org/10.5281/zenodo.5135889) and a [dataset](https://doi.org/10.5281/zenodo.5178487) shared during a workshop on QLIPP and recOrder can be found on Zenodo, and the napari plugin's sample contributions (`File > Open Sample > recOrder-napari` in napari).
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5178487.svg)](https://doi.org/10.5281/zenodo.5178487)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5135889.svg)](https://doi.org/10.5281/zenodo.5135889)

recOrder/napari.yaml

@@ -14,6 +14,9 @@ contributions:
   - id: recOrder-napari.polarization_target_reconstruction
     title: Polarization Target Data
     python_name: recOrder.scripts.samples:read_polarization_target_reconstruction
+  - id: recOrder-napari.zebrafish_embryo_reconstruction
+    title: Zebrafish Embryo Reconstruction
+    python_name: recOrder.scripts.samples:read_zebrafish_embryo_reconstruction
   readers:
   - command: recOrder-napari.get_reader
     accepts_directories: true
@@ -24,8 +27,11 @@ contributions:
   sample_data:
   - command: recOrder-napari.polarization_target_data
     key: polarization-target-data
-    display_name: Polarization Target Data
+    display_name: Polarization Target Data (10 MB)
   - command: recOrder-napari.polarization_target_reconstruction
     key: polarization-target-reconstruction
-    display_name: Polarization Target Reconstruction
+    display_name: Polarization Target Reconstruction (10 MB)
+  - command: recOrder-napari.zebrafish_embryo_reconstruction
+    key: zebrafish-embryo-reconstruction
+    display_name: Zebrafish Embryo Reconstruction (92 MB)
 

recOrder/scripts/samples.py

@@ -1,29 +1,59 @@
 import shutil
 from pathlib import Path
 
+from typing import Literal
 from iohub import open_ome_zarr
+from iohub.ngff import Plate
 from napari.utils.notifications import show_warning
 from platformdirs import user_data_dir
 from wget import download
 
 
-def download_and_unzip() -> tuple[Path]:
+def _build_layer_list(dataset: Plate, layer_names: list[str]):
+    layer_list = []
+    for channel_name in layer_names:
+        channel_index = dataset.channel_names.index(channel_name)
+        position = dataset["0/0/0"]
+        data = (position["0"][:, channel_index],)
+        layer_dict = {"name": channel_name, "scale": position.scale[3:]}
+        layer_list.append((data, layer_dict))
+
+    return layer_list
+
+
+def download_and_unzip(data_type: Literal["target", "embryo"]) -> tuple[Path]:
     """Downloads sample data .zip from zenodo, unzips, and returns Paths to the .zarr datasets.
 
     Skips the download if the files already exist.
 
     Uses platformdirs.user_data_dir to store data.
     """
-    temp_dirpath = Path(user_data_dir("recOrder-sample-v1.4"))
+
+    # Delete old data
+    old_data_dirs = ["recOrder-sample-v1.4"]
+    for old_data_dir in old_data_dirs:
+        old_data_path = Path(user_data_dir(old_data_dir))
+        if old_data_path.exists():
+            shutil.rmtree(str(old_data_path))
+
+    temp_dirpath = Path(user_data_dir("recOrder-sample-v1.5"))
     temp_dirpath.mkdir(exist_ok=True, parents=True)
-    data_dirpath = temp_dirpath / "sample_contribution"
+
+    if data_type == "target":
+        data_dirpath = temp_dirpath / "sample_contribution"
+        data_size = "10 MB"
+        data_url = "https://zenodo.org/record/8386856/files/sample_contribution.zip?download=1"
+    elif data_type == "embryo":
+        data_dirpath = temp_dirpath / "sample_contribution_embryo"
+        data_size = "92 MB"
+        data_url = "https://zenodo.org/record/8386856/files/sample_contribution_embryo.zip?download=1"
 
     if not data_dirpath.with_suffix(".zip").exists():
         show_warning(
-            "Downloading 10 MB sample contribution. This might take a moment..."
+            f"Downloading {data_size} sample contribution. This might take a moment..."
         )
-        data_url = "https://zenodo.org/record/8280720/files/sample_contribution.zip?download=1"
         download(data_url, out=str(temp_dirpath))
+
     if not data_dirpath.exists():
         shutil.unpack_archive(
             data_dirpath.with_suffix(".zip"), extract_dir=temp_dirpath
@@ -36,32 +66,20 @@ def download_and_unzip() -> tuple[Path]:
 
 def read_polarization_target_data():
     """Returns the polarization data sample contribution"""
-    data_path, _ = download_and_unzip()
-
+    data_path, _ = download_and_unzip("target")
     dataset = open_ome_zarr(data_path)
-    layer_list = []
-    for channel_index, channel_name in enumerate(dataset.channel_names):
-        position = dataset["0/0/0"]
-        data = (position["0"][0, channel_index],)
-        layer_dict = {"name": channel_name, "scale": position.scale[3:]}
-        layer_list.append((data, layer_dict))
-
-    return layer_list
+    return _build_layer_list(dataset, dataset.channel_names)
 
 
 def read_polarization_target_reconstruction():
     """Returns the polarization target reconstruction sample contribution"""
-
-    _, recon_path = download_and_unzip()
+    _, recon_path = download_and_unzip("target")
     dataset = open_ome_zarr(recon_path)
+    return _build_layer_list(dataset, ["Phase3D", "Retardance", "Orientation"])
 
-    layer_list = []
-    for channel_index, channel_name in enumerate(
-        ["Retardance", "Orientation"]
-    ):
-        position = dataset["0/0/0"]
-        data = (position["0"][0, channel_index],)
-        layer_dict = {"name": channel_name, "scale": position.scale[3:]}
-        layer_list.append((data, layer_dict))
 
-    return layer_list
+def read_zebrafish_embryo_reconstruction():
+    """Returns the embryo reconstruction sample contribution"""
+    _, recon_path = download_and_unzip("embryo")
+    dataset = open_ome_zarr(recon_path)
+    return _build_layer_list(dataset, ["Retardance", "Orientation"])