Clarify that image_preprocessing is only for punctate structures

.pre-commit-config.yaml

@@ -88,12 +88,13 @@ repos:
 
   # md formatting
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.14
+    rev: 0.7.16
     hooks:
       - id: mdformat
         args: ["--number"]
         additional_dependencies:
           - mdformat-gfm
+          - mdformat-gfm-alerts
           - mdformat-tables
           - mdformat_frontmatter
           # - mdformat-toc

docs/PREPROCESSING.md

@@ -2,32 +2,36 @@
 
 Preprocessing is divided into three steps that use two different virtual environments.
 
-1. Alignment, masking, and registration (`image_preprocessing` virtual environment)
+1. Punctate structures: Alignment, masking, and registration (`image_preprocessing` virtual environment)
 2. Punctate structures: Generate pointclouds (main virtual environment)
 3. Polymorphic structures: Generate SDFs (main virtual environment)
 
 # Configure input data
 
 1. Datasets are hosted on quilt. Download raw data at the following links
 
-* [cellPACK synthetic dataset](https://open.quiltdata.com/b/allencell/tree/aics/morphology_appropriate_representation_learning/cellPACK_single_cell_punctate_structure/)
-* [DNA replication foci dataset](https://open.quiltdata.com/b/allencell/packages/aics/nuclear_project_dataset_4)
-* [WTC-11 hIPSc single cell image dataset v1](https://staging.allencellquilt.org/b/allencell/tree/aics/hipsc_single_cell_image_dataset/)
-* [Nucleolar drug perturbation dataset](https://open.quiltdata.com/b/allencell/tree/aics/NPM1_single_cell_drug_perturbations/)
+- [cellPACK synthetic dataset](https://open.quiltdata.com/b/allencell/tree/aics/morphology_appropriate_representation_learning/cellPACK_single_cell_punctate_structure/)
+- [DNA replication foci dataset](https://open.quiltdata.com/b/allencell/packages/aics/nuclear_project_dataset_4)
+- [WTC-11 hIPSc single cell image dataset v1](https://staging.allencellquilt.org/b/allencell/tree/aics/hipsc_single_cell_image_dataset/)
+- [Nucleolar drug perturbation dataset](https://open.quiltdata.com/b/allencell/tree/aics/NPM1_single_cell_drug_perturbations/)
 
-> [!NOTE]  
-> Ensure to download all the data in the same folder where the repo was cloned!
+> [!NOTE]
+> Ensure to download all the data in the `benchmarking_representations` folder.
 
-# Alignment, masking, and registration
-1. Edit the data paths in the file `/subpackages/image_preprocessing/config/config.yaml` to point to your copies of the data.
+# Punctate structures: Alignment, masking, and registration
+
+1. Edit the data paths in the file `subpackages/image_preprocessing/config/config.yaml` to point to your copies of the data.
 2. Follow the [installation and usage instructions](/subpackages/image_preprocessing/README.md) to create the `image_preprocessing` virtual environment and run the Snakefile.
 
 # Switch to main virtual environment
+
 1. Deactivate the `image_preprocessing` virtual environment (if applicable).
 2. Follow the [installation instructions](./USAGE.md) (everything before "Usage") for the main virtual environment.
 
 # Punctate structures: Generate pointclouds
-Edit the data paths in the following file to match the location of your copy of the data, then run it.
+
+Edit the data paths in the following file to match the location of the outputs of the alignment, masking, and registration step, then run it.
+
 ```
 src
 └── br
@@ -38,7 +42,9 @@ src
 ```
 
 # Polymorphic structures: Generate SDFs
+
 Edit the data paths in the following files to match the location of your copy of the data, then run both.
+
 ```
 src
 └── br

subpackages/image_preprocessing/README.md

@@ -5,20 +5,28 @@ Code for alignment, masking, and registration of 3D single cell images.
 # Installation
 
 Move to this `image_preprocessing` directory.
+
 ```bash
 cd subpackages/image_preprocessing
 ```
 
 Install dependencies.
+
 ```bash
 conda create --name preprocessing_env python=3.10
 conda activate preprocessing_env
 pip install -r requirements.txt
 pip install -e .
 ```
 
+# Configuration
+
+Edit the data paths in the file `subpackages/image_preprocessing/config/config.yaml` to point to your copies of the data.
+
 # Usage
+
 Once data is downloaded and config files are set up, run preprocessing scripts.
+
 ```bash
 snakemake -s Snakefile --cores all
-```
+```