Remove analysis module (#166)

* remove analysis module

* move scripts from /examples to /scripts

* clean up requirements

* pytest ignote scripts/

* move acquisition_settings to examples

* Update README.md

* update paper link

* add note on biahub installation

README.md

@@ -5,7 +5,7 @@ shrimPy (pronounced: ʃrɪm-pai) is a pythonic framework for high-throughput sma
 
 The acquisition engine synchronizes data collection using hardware triggering and carries out smart microscopy tasks such as autofocus and autoexposure.
 
-The acquired multidimensional raw datasets are processed by the reconstruction engine to generate registered multimodal data that can be used for analysis. Raw data are first converted to the [OME-Zarr](https://ngff.openmicroscopy.org/) format using [iohub](https://github.com/czbiohub-sf/iohub) to facilitate parallel processing and metadata management. Discrete data volumes then undergo deskewing of fluorescence channels, reconstruction of phase and orientation (using [recOrder](https://github.com/mehta-lab/recOrder)), registration and virtual staining (using [VisCy](https://github.com/mehta-lab/viscy)).
+The acquired multidimensional raw datasets are processed with the [biahub](https://github.com/czbiohub-sf/biahub) library to generate registered multimodal data that can be used for analysis. Raw data are first converted to the [OME-Zarr](https://ngff.openmicroscopy.org/) format using [iohub](https://github.com/czbiohub-sf/iohub) to facilitate parallel processing and metadata management. Discrete data volumes then undergo deskewing of fluorescence channels, reconstruction of phase and orientation (using [recOrder](https://github.com/mehta-lab/recOrder)), registration and virtual staining (using [VisCy](https://github.com/mehta-lab/viscy)).
 
 This version of the code still uses the legacy name `mantis`, which overlaps with the name of the microscope which is used to acquire data. In a future release we will transition the codebase to the name `shrimPy`.
 
@@ -26,8 +26,12 @@ conda activate mantis
 pip install .
 ```
 
+3. Optionally, install the [biahub](https://github.com/czbiohub-sf/biahub) image analysis library.
+
+   `biahub` is currently used when characterizing the microscope point spread function, and will be used for real-time image processing in the future.
+
 ## Setting up the mantis microscope
-The mantis microscope implements simultaneous label-free and light-sheet imaging as described in [Ivanov et al.](https://www.biorxiv.org/content/10.1101/2023.12.19.572435v1) The two imaging modalities are acquired on two independent arms of the microscope running separate instances of [Micro-Manager](https://micro-manager.org/) and [pycromanager](https://pycro-manager.readthedocs.io/). shrimPy was developed to enable robust long-term imaging with mantis and efficient analysis of resulting TB-scale datasets.
+The mantis microscope implements simultaneous label-free and light-sheet imaging as described in [Ivanov et al.](https://doi.org/10.1093/pnasnexus/pgae323) The two imaging modalities are acquired on two independent arms of the microscope running separate instances of [Micro-Manager](https://micro-manager.org/) and [pycromanager](https://pycro-manager.readthedocs.io/). shrimPy and [biahub](https://github.com/czbiohub-sf/biahub) were developed to enable robust long-term imaging with mantis and efficient analysis of the resulting TB-scale datasets on a high-performance compute cluster.
 
 The [Setup Guide](docs/setup_guide.md) outlines how the mantis microscope is configured.
 
@@ -47,7 +51,7 @@ Data are acquired using `mantis run-acquisition`, and a list of arguments can be
 mantis run-acquisition --help
 ```
 
-The mantis acquisition is configured using a YAML file. An example of a configuration file can be found [here](mantis/acquisition/settings/example_acquisition_settings.yaml).
+The mantis acquisition is configured using a YAML file. An example of a configuration file can be found [here](examples/acquisition_settings/example_acquisition_settings.yaml).
 
 This is an example of a command which will start an acquisition on the mantis microscope:
 
@@ -68,111 +72,7 @@ mantis run-acquisition \
 
 ## Data reconstruction
 
-Data reconstruction also uses a command line interface. All reconstruction calls take an input `-i` and an output `-o`, and most reconstruction calls use configuration files passed via a `-c` option.
-
-A typical set of CLI calls to go from raw data to registered volumes looks like:
-
-```sh
-# CONVERT TO ZARR
-iohub convert \
-    -i ./acq_name/acq_name_labelfree_1 \
-    -o ./acq_name_labelfree.zarr \
-iohub convert \
-    -i ./acq_name/acq_name_lightsheet_1 \
-    -o ./acq_name_lightsheet.zarr
-
-# DECONVOLVE FLUORESCENCE
-# estimate PSF parameters
-mantis estimate-psf \
-    -i ./beads.zarr \
-    -c ./psf_params.yml \
-    -o ./psf.zarr
-# deconvolve data
-mantis deconvolve \
-    -i ./acq_name_lightsheet.zarr \
-    -c ./deconvolve_params.yml \
-    --psf-dirpath ./psf.zarr
-    -o ./acq_name_lightsheet_deconvolved.zarr
-
-# DESKEW FLUORESCENCE
-# estimate deskew parameters
-mantis estimate-deskew \
-    -i ./acq_name_lightsheet.zarr/0/0/0 \
-    -o ./deskew.yml
-# apply deskew parameters
-mantis deskew \
-    -i ./acq_name_lightsheet.zarr/*/*/* \
-    -c ./deskew_params.yml \
-    -o ./acq_name_lightsheet_deskewed.zarr
-
-# RECONSTRUCT PHASE/BIREFRINGENCE
-recorder reconstruct \
-    -i ./acq_name_labelfree.zarr/*/*/* \
-    -c ./recon.yml \
-    -o ./acq_name_labelfree_reconstructed.zarr
-
-# STABILIZE
-# estimate stabilization parameters
-mantis estimate-stabilization \
-    -i ./acq_name_labelfree.zarr/*/*/* \
-    -o ./stabilization.yml \
-    --stabilize-xy \
-    --stabilize-z
-# stabilize data
-mantis stabilize \
-    -i ./acq_name_labelfree.zarr/*/*/* \
-    -c ./stabilization.yml \
-    -o ./acq_name_labelfree_stabilized.zarr/*/*/*
-
-# REGISTER
-# estimate registration parameters
-mantis estimate-registration \
-    -s ./acq_name_labelfree_reconstructed.zarr/0/0/0 \
-    -t ./acq_name_lightsheet_deskewed.zarr/0/0/0 \
-    -o ./register.yml
-# optimize registration parameters
-mantis optimize-registration \
-    -s ./acq_name_labelfree_reconstructed.zarr/0/0/0 \
-    -t ./acq_name_lightsheet_deskewed.zarr/0/0/0 \
-    -c ./register.yml \
-    -o ./register_optimized.yml
-# register data
-mantis register \
-    -s ./acq_name_labelfree_reconstructed.zarr/*/*/* \
-    -t ./acq_name_lightsheet_deskewed.zarr/*/*/* \
-    -c ./register_optimized.yml \
-    -o ./acq_name_registered.zarr
-
-# CONCATENATE CHANNELS
-mantis concatenate \
-    -c ./concatenate.yml \
-    -o ./acq_name_concatenated.zarr
-
-# STITCH
-# estimate stitching parameters
-mantis estimate-stitching \
-    -i ./acq_name.zarr/*/*/* \
-    -o ./stitching.yml \
-    --channel DAPI
-    --percent-overlap 0.05
-# stitch fields of view
-mantis stitch \
-    -i ./acq_name.zarr/*/*/* \
-    -c ./stitching.yml \
-    -o ./acq_name_stitched.zarr/*/*/*
-```
-
-## Additional utilities
-
-We have also developed the following CLI utilities to help with data acquisition and reconstruction
-
-```sh
-# Estimate fluorescence bleaching
-mantis estimate-bleaching --help
-
-# Generate an HTML report with PSF measurements
-mantis characterize-psf --help
-```
+Data reconstruction is accomplished with the [biahub](https://github.com/czbiohub-sf/biahub) library. Visit the link for the latest information on our reconstruction workflows.
 
 ## Data and metadata format