docker workflow and documentation fix

.github/workflows/docker-publish.yml

@@ -6,10 +6,11 @@ name: Docker
 # documentation.
 
 on:
-  release:
-    types: published
   pull_request:
     branches: [ "main" ]
+
+  release:
+    types: [ published ]
 
 env:
   # Use docker.io for Docker Hub if empty
@@ -33,14 +34,19 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      # Enable QEMU for cross-platform builds
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       # Install the cosign tool except on PR
       # https://github.com/sigstore/cosign-installer
-      - name: Install Cosign
+      - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@v3.1.1
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
         with:
           cosign-release: 'v2.2.4'
-          
+
       # Set up BuildKit Docker container builder to be able to build
       # multi-platform images and export cache
       # https://github.com/docker/setup-buildx-action
@@ -64,12 +70,6 @@ jobs:
         uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-      - name: Get the tag name
-        run: echo "TAG=${GITHUB_REF/refs\/tags\//}" >> $GITHUB_ENV
-
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
 
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
@@ -84,3 +84,18 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

CHANGELOG.md

@@ -3,7 +3,19 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v0.5.0 - [2025.11.##]
+## v0.5.1 - [2025.11.13]
+
+Minor fixes to automated workflows and documentation.
+
+### `Added`
+
+### `Fixed`
+- docker publish workflow
+- README image links and updated installation guide
+
+### `Removed`
+
+## v0.5.0 - [2025.11.13]
 
 Rework of Backsub to not have Palom as a dependency reducing the environment size and making it lightweight, and reducing the output file size, while keeping the time and memory usage efficiency.
 

README.md

@@ -5,7 +5,7 @@ Backsub performs pixel-by-pixel background subtraction between marker and backgr
 
 Example of pixel-wise autofluorescence subtraction with Backsub:
 <p align="left">
-  <img src="example/application_example.png" alt="Background subtraction example" width="750">
+  <img src="https://raw.githubusercontent.com/SchapiroLabor/Background_subtraction/main/example/application_example.png" alt="Background subtraction example" width="750">
 </p>
 
 ## Introduction
@@ -19,47 +19,69 @@ The primary use case is autofluorescence subtraction for multichannel and multic
 
 Background subtraction is performed using the following formula:
 
-$Marker_{corrected} = Marker_{raw} - Background \times \frac{Exposure_{Marker}}{Exposure_{Background}}$
+Marker_corrected = Marker_raw − Background × (Exposure_Marker / Exposure_Background)
 
 ## Installation
 
-Backsub can be run either in a preconfigured Docker container or in a local conda environment.
+Backsub can be installed directly from PyPI, or run in a preconfigured Docker container. For development or container builds, a fixed-version Conda environment is provided.
 
-### Option 1: Docker
+### Option 1: Install from PyPI
 
-Pull the latest container from the GitHub Container Registry:
+Backsub is available from [PyPI](https://pypi.org/project/backsub/)
+```bash
+pip install backsub
+```
+After installation, you can run the tool directly in the command line
+```bash
+backsub --help
+```
+Example:
+```bash
+backsub \
+    -r /path/to/input_image.tif \
+    -o /path/to/corrected_image.ome.tif \
+    -m /path/to/markers.csv \
+    -mo /path/to/markers_corrected.csv
 ```
+
+### Option 2: Docker
+
+Pull the latest container from the GitHub Container Registry:
+```bash
 docker pull ghcr.io/schapirolabor/background_subtraction:latest
 ```
 You can then run Backsub directly, mounting your input and output directories:
-```
+```bash
 docker run --rm -v $(pwd):/data ghcr.io/schapirolabor/background_subtraction:latest \
-    python background_sub.py \
+    backsub \
     -r /data/input_image.tif \
     -o /data/corrected_image.ome.tif \
     -m /data/markers.csv \
     -mo /data/markers_corrected.csv
 ```
-Note that all required dependencies are already included inside the container.
 
 If you want to build the container yourself, clone the repository first, then build it from the provided Dockerfile:
 ```
 git clone https://github.com/SchapiroLabor/Background_subtraction.git
 cd Background_subtraction
-docker build -t background_subtraction:latest .
+docker build -t backsub:latest .
 ```
-### Option 2: Conda
 
-Clone the repository and create the Conda environment:
-```
+### Option 3: Development / Conda environment
+
+For development or reproducible research setups:
+```bash
 git clone https://github.com/SchapiroLabor/Background_subtraction.git
 cd Background_subtraction
 conda env create -f environment.yml
 conda activate backsub_env
+
+pip install -e .
 ```
-You can now run Backsub locally (note that you need to point to the tool's script):
-```
-python backsub/background_sub.py -h
+
+Run with
+```bash
+python -m backsub.background_sub --help
 ```
 
 ## Execution and usage
@@ -155,4 +177,6 @@ This project is licensed under the terms of the [MIT License](https://github.com
 
 If you use Backsub in your work, please cite it as:
 
-> Bestak, K., Perez, V., & Wuennemann, F. (2025). Backsub: pixel-by-pixel channel subtraction tool for multiplexed immunofluorescence data.
+> Bestak, K., Perez, V., & Wuennemann, F. (2025).  
+> **Backsub: a pixel-by-pixel channel subtraction tool for multiplexed immunofluorescence data.**
+> Available at: [https://github.com/SchapiroLabor/Background_subtraction](https://github.com/SchapiroLabor/Background_subtraction)

backsub/_version.py

@@ -1,2 +1,2 @@
 # backsub/_version.py
-__version__ = "0.5.0"
+__version__ = "0.5.1"