mehta-lab · talonchandler · Jul 25, 2023 · Mar 7, 2023 · Mar 9, 2023 · Apr 18, 2023
diff --git a/docs/valuable-prs/2023-02-27.110.pr.open.md b/docs/valuable-prs/2023-02-27.110.pr.open.md
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_forward.py
diff --git a/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py b/examples/3D_PODT_phase_simulation/3D_PODT_Phase_recon.py
diff --git a/examples/README.md b/examples/README.md
@@ -1,12 +1,7 @@
-This folder of examples consists of:
+`waveorder` is undergoing a significant refactor, and this `examples/` folder serves as a good place to understand the current state of the repository.
 
-1) A set of simulations that will run as is. Any of the files in these folders 
-can be run with `python <script-name>.py`, and these files are included in 
-`waveorder`'s automated testing.  
-- `/2D_QLIPP_simulation/`
-- `/3D_PODT_Phase_simulation/`
-- `/PTI_simulation/`
+The `models/` folder demonstrates the latest functionality of `waveorder`. These scripts will run as is in an environment with `waveorder` and `napari` installed. Each script demonstrates a simulation and reconstruction with a **model**: a specific set of assumptions about the sample and the data being acquired. 
 
-2) A set of data-dependent reconstructions in `/experimental_reconstructions/`. 
-These files serve as a form of documentation for the types of reconstructions
-that `waveorder` can perform. 
+The `maintenance/` folder demonstrates the functionality of `waveorder` that we plan to move to `models/`. These scripts can be run as is, and they are being maintained with tests.
+
+The `documentation/` folder consists of examples that demonstrate reconstruction with real data. These examples require access to the complete datasets, so they are not being actively maintained and serve primarily as documentation.
diff --git a/...nt_Recon3D_anisotropic_target_small.ipynb → ...nt_Recon3D_anisotropic_target_small.ipynb b/...nt_Recon3D_anisotropic_target_small.ipynb → ...nt_Recon3D_anisotropic_target_small.ipynb
diff --git a/...ent/PTI_full_FOV_anisotropic_target.ipynb → ...ent/PTI_full_FOV_anisotropic_target.ipynb b/...ent/PTI_full_FOV_anisotropic_target.ipynb → ...ent/PTI_full_FOV_anisotropic_target.ipynb
diff --git a/...eriment/PTI_full_FOV_cardiac_muscle.ipynb → ...eriment/PTI_full_FOV_cardiac_muscle.ipynb b/...eriment/PTI_full_FOV_cardiac_muscle.ipynb → ...eriment/PTI_full_FOV_cardiac_muscle.ipynb
diff --git a/...I_full_FOV_cardiomyocyte_infected_1.ipynb → ...I_full_FOV_cardiomyocyte_infected_1.ipynb b/...I_full_FOV_cardiomyocyte_infected_1.ipynb → ...I_full_FOV_cardiomyocyte_infected_1.ipynb
diff --git a/...I_full_FOV_cardiomyocyte_infected_2.ipynb → ...I_full_FOV_cardiomyocyte_infected_2.ipynb b/...I_full_FOV_cardiomyocyte_infected_2.ipynb → ...I_full_FOV_cardiomyocyte_infected_2.ipynb
diff --git a/...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb → ...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb b/...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb → ...ent/PTI_full_FOV_cardiomyocyte_mock.ipynb
diff --git a/...xperiment/PTI_full_FOV_human_uterus.ipynb → ...xperiment/PTI_full_FOV_human_uterus.ipynb b/...xperiment/PTI_full_FOV_human_uterus.ipynb → ...xperiment/PTI_full_FOV_human_uterus.ipynb
diff --git a/...riment/PTI_full_FOV_mouse_brain_aco.ipynb → ...riment/PTI_full_FOV_mouse_brain_aco.ipynb b/...riment/PTI_full_FOV_mouse_brain_aco.ipynb → ...riment/PTI_full_FOV_mouse_brain_aco.ipynb
diff --git a/...xperiment/2D_QLIPP_recon_experiment.ipynb → ...xperiment/2D_QLIPP_recon_experiment.ipynb b/...xperiment/2D_QLIPP_recon_experiment.ipynb → ...xperiment/2D_QLIPP_recon_experiment.ipynb
diff --git a/...xperiment/3D_QLIPP_recon_experiment.ipynb → ...xperiment/3D_QLIPP_recon_experiment.ipynb b/...xperiment/3D_QLIPP_recon_experiment.ipynb → ...xperiment/3D_QLIPP_recon_experiment.ipynb
diff --git a/examples/documentation/README.md b/examples/documentation/README.md
@@ -0,0 +1 @@
+This folder of `documentation` examples consists of a set of data-dependent reconstructions in `/experimental_reconstructions/`. 
diff --git a/...e_deconvolution/fluorescence_deconv.ipynb → ...e_deconvolution/fluorescence_deconv.ipynb b/...e_deconvolution/fluorescence_deconv.ipynb → ...e_deconvolution/fluorescence_deconv.ipynb