diff --git a/docs/README.md b/docs/README.md index 63bb918f..526d6ff0 100644 --- a/docs/README.md +++ b/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! \ No newline at end of file +**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! diff --git a/docs/data-schema.md b/docs/data-schema.md index 67b4194c..b400bf6d 100644 --- a/docs/data-schema.md +++ b/docs/data-schema.md @@ -1,6 +1,6 @@ # 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 @@ -8,28 +8,28 @@ 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_.txt # i calibration repeats │ ├── bg_0 │ ... ├── bg_ # 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` │ -├── _snap_0 -├── _snap_1 +├── _snap_0 +├── _snap_1 │   ├── raw_data.zarr │   ├── reconstruction.zarr │   ├── reconstruction_settings.yml │   └── transfer_function.zarr │ ... ├── _snap_ # 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 ├── _snap_0 # l different acquisition names │ ... ├── _snap_ # 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. \ No newline at end of file +Each `.zarr` contains an [OME-NGFF v0.4](https://ngff.openmicroscopy.org/0.4/) in HCS format with a single field of view.