From 4ebcf363ba463ef98c2c02968117a59795e596aa Mon Sep 17 00:00:00 2001
From: Connor Laughland <71669181+conochur@users.noreply.github.com>
Date: Mon, 10 Aug 2026 12:10:34 -0700
Subject: [PATCH 1/2] Update README.md

added method to command line calls
---
 README.md | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index e6cf31b..31f6413 100644
--- a/README.md
+++ b/README.md
@@ -10,8 +10,9 @@ We are planning on occasional updating this tool with no fixed schedule. Communi
 `acpreprocessing.stitching_modules.convert_to_n5.tiff_to_ngff`
 - Sequentially reads image arrays from a tiff stack series for pixel-wise deskew (optional), for computing a downsampling pyramid to a user-defined depth, and for writing out the data volume into a next-generation file format (zarr v3).
 ```
-python zarrv3_to_zarr.py \
---input_file PATH_TO_INPUT_ZARR_FILE \
+
+python -m acpreprocessing.stitching_modules.convert_to_n5.tiff_to_ngff \
+--input_dir PATH_TO_TIFF_DIR \
 --output_file PATH_TO_OUTPUT_ZARR_FILE \
 --group_names LIST_OF_GROUP_NAMES \
 --group_attributes LIST_OF_GROUP_ATTRIBUTE_DICTS \
@@ -20,10 +21,10 @@ python zarrv3_to_zarr.py \
 ```
 
 **Point extraction**
-`acpreprocessing.stitching_modules.acstitch.extract_points`
 - Detects blob features within user-defined ROIs of a source tile and generates initial point correspondences with a target tile using the estimated tile offset.
 ```
-python extract_points.py \
+
+python -m acpreprocessing.stitching_modules.acstitch.extract_points \
 --p_tile PATH_TO_SOURCE_TILE \
 --q_tile PATH_TO_TARGET_TILE \
 --output_file PATH_TO_OUTPUT_POINTMATCH_FILE \
@@ -35,10 +36,10 @@ python extract_points.py \
 ```
 
 **Tile stitching**
-`acpreprocessing.stitching_modules.acstitch.stitch`
 - Generate point correspondences between tiles from template matching or SIFT features at user-defined resolution level (mip).
 ```
-python stitch_tiles.py \
+
+python -m acpreprocessing.stitching_modules.acstitch.stitch \
 --input_file PATH_TO_INPUT_POINTMATCH_FILE \
 --output_file PATH_TO_OUTPUT_POINTMATCH_FILE \
 --stitch_method STITCH_METHOD_ccorr_OR_sift \

From b4f6712c2e83274fffb4d6b2dc1d67fd5d1a370f Mon Sep 17 00:00:00 2001
From: Connor Laughland <71669181+conochur@users.noreply.github.com>
Date: Mon, 10 Aug 2026 12:10:53 -0700
Subject: [PATCH 2/2] Update README.md

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 31f6413..6740c14 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,6 @@ We are planning on occasional updating this tool with no fixed schedule. Communi
 ### Methods
 
 **Deskew and zarr conversion**
-`acpreprocessing.stitching_modules.convert_to_n5.tiff_to_ngff`
 - Sequentially reads image arrays from a tiff stack series for pixel-wise deskew (optional), for computing a downsampling pyramid to a user-defined depth, and for writing out the data volume into a next-generation file format (zarr v3).
 ```