cleaning up /docs

docs/README.md

@@ -1,15 +1,27 @@
-# Welcome to `recOrder`'s documentation
+# Welcome to `waveorder`'s documentation
 
-**I want to buy hardware for a polarized-light installation:** start with the [buyers guide](./buyers-guide.md).
+We have organized our documentation by user type and intended task.
 
-**I would like to install `recOrder` on my microscope:** start with the [microscope installation guide](./microscope-installation-guide.md).
+## Software users
 
-**I would like to use the `napari plugin`:** start with the [plugin guide](./napari-plugin-guide.md).
+**Reconstruct existing data:** start with the [reconstruction guide](./reconstruction-guide.md) and consult the [data schema](./data-schema.md) for `waveorder`'s data format.
 
-**I would like to reconstruct existing data:** start with the [reconstruction guide](./reconstruction-guide.md) and consult the [data schema](./data-schema.md) for `recOrder`'s format.
+**Reconstruct with a GUI:** start with the [plugin's reconstruction guide](./napari-plugin-guide.md#reconstruction-tab).
 
-**I would like to set up a development environment and test `recOrder`**: start with the [development guide](./development-guide.md).
+**Integrate `waveorder` into my software:** start with [`examples/`](./examples/)
 
-**I would like understand `recOrder`'s calibration routine**: read the [calibration guide](./calibration-guide.md).
+## Hardware users
 
-**I noticed an error in the documentation or code:** [open an issue](https://github.com/mehta-lab/recOrder/issues/new/choose) or [send us an email](mailto:shalin.mehta@czbiohub.org,talon.chandler@czbiohub.org). We appreciate your help!
+**Buy hardware for a polarized-light installation:** start with the [buyer's guide](./buyers-guide.md).
+
+**Install `waveorder` on my microscope:** start with the [microscope installation guide](./microscope-installation-guide.md).
+
+**Use the `napari plugin` to calibrate:** start with the [plugin guide](./napari-plugin-guide.md).
+
+**Understand `waveorder`'s calibration routine**: read the [calibration guide](./calibration-guide.md).
+
+## Software developers
+
+**Set up a development environment and test `waveorder`**: start with the [development guide](./development-guide.md).
+
+**Report an error in the documentation or code:** [open an issue](https://github.com/mehta-lab/waveorder/issues/new/choose) or [send us an email](mailto:shalin.mehta@czbiohub.org,talon.chandler@czbiohub.org). We appreciate your help!

docs/data-schema.md

@@ -1,35 +1,35 @@
 # Data schema
 
-This document defines the standard for data acquired with `recOrder`.
+This document defines the standard for data acquired with `waveorder`.
 
 ## Raw directory organization
 
 Currently, we structure raw data in the following hierarchy:
 
 ```text
 working_directory/                      # commonly YYYY_MM_DD_exp_name, but not enforced
-├── polarization_calibration_0.txt        
+├── polarization_calibration_0.txt
 │   ...
 ├── polarization_calibration_<i>.txt    # i calibration repeats
 │
 ├── bg_0
 │   ...
 ├── bg_<j>                              # j background repeats
-│   ├── background.zarr             
-│   ├── polarization_calibration.txt    # copied into each bg folder 
+│   ├── background.zarr
+│   ├── polarization_calibration.txt    # copied into each bg folder
 │   ├── reconstruction.zarr
 │   ├── reconstruction_settings.yml     # for use with `recorder reconstruct`
 │   └── transfer_function.zarr          # for use with `recorder apply-inv-tf`
 │
-├── <acq_name_0>_snap_0   
-├── <acq_name_0>_snap_1 
+├── <acq_name_0>_snap_0
+├── <acq_name_0>_snap_1
 │   ├── raw_data.zarr
 │   ├── reconstruction.zarr
 │   ├── reconstruction_settings.yml
 │   └── transfer_function.zarr
 │   ...
 ├── <acq_name_0>_snap_<k>               # k repeats with the first acquisition name
-│   ├── raw_data.zarr          
+│   ├── raw_data.zarr
 │   ├── reconstruction.zarr
 │   ├── reconstruction_settings.yml
 │   └── transfer_function.zarr
@@ -38,10 +38,10 @@ working_directory/                      # commonly YYYY_MM_DD_exp_name, but not
 ├── <acq_name_l>_snap_0                 # l different acquisition names
 │   ...
 ├── <acq_name_l>_snap_<m>               # m repeats for this acquisition name
-    ├── raw_data.zarr 
+    ├── raw_data.zarr
     ├── reconstruction.zarr
     ├── reconstruction_settings.yml
     └── transfer_function.zarr
 ```
 
-Each `.zarr` contains an [OME-NGFF v0.4](https://ngff.openmicroscopy.org/0.4/) in HCS format with a single field of view. 
+Each `.zarr` contains an [OME-NGFF v0.4](https://ngff.openmicroscopy.org/0.4/) in HCS format with a single field of view.