Version 0.5.0

.github/workflows/docker-publish.yml

@@ -31,25 +31,27 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Install the cosign tool except on PR
       # https://github.com/sigstore/cosign-installer
       - name: Install Cosign
         if: github.event_name != 'pull_request'
         uses: sigstore/cosign-installer@v3.1.1
         with:
-          cosign-release: 'v2.2.1'
+          cosign-release: 'v2.2.4'
 
-      # Workaround: https://github.com/docker/build-push-action/issues/461
-      - name: Setup Docker buildx
-        uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -59,24 +61,26 @@ jobs:
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        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@v2
-      
+        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
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@ac9327eae2b366085ac7f6a2d02df8aa8ead720a
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
         with:
           context: .
-          platforms: linux/amd64,linux/arm64
           push: ${{ github.event_name != 'pull_request' }}
+          platforms: linux/amd64,linux/arm64
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/python-publish.yml

@@ -0,0 +1,69 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      url: https://pypi.org/p/backsub/
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

.gitignore

@@ -0,0 +1,7 @@
+backsub/__pycache__
+dist/
+__pycache__
+.DS_Store
+backsub/testing.ipynb
+build/
+backsub.egg-info/

CHANGELOG.md

@@ -3,21 +3,42 @@
 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.##]
+
+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.
+
+### `Added`
+- `compression` parameter
+- two RAM profiles: (1) default, uses moderate RAM. (2) Uses approximately half of the default RAM at the cost of a slight loss in precision of the calculation of the downsized dimensions of the pyramidal output image. This means the dimensions of the pyramidal level will differ between profile 1 and 2. The high-resolution level is not affected by this.
+- organizes the tool in five scripts: (1) CLI, (2) ome-schema structure, (3) ome-schema writer, (4) background subtraction and writing of output image and (5) extraction of metadata from Lunaphore COMET images to create the marker table.
+- logger has been re-designed.
+- restructured README
+- `tile-size` parameter now defaults to 256 instead of 1024
+- support for different data types - primarily np.uint8 in addition to np.uint16
+
+### `Fixed`
+- output image file-size is reduced by applying lossless compression ("LZW" by default)
+
+### `Removed`
+- Palom and OpenCV as dependencies
+- old scripts, version history should be checked instead.
+- `chunksize` argument - chunking is done now only by the default dask.array behaviour
+
 ## v0.4.1 - [2023.11.21]
 
-Complete rework of Backsub to include Palom's pyramid writer (https://github.com/labsyspharm/palom).
-Added dask array chunking and delayed execution for subtraction that happenes while the output pyramidal `ome.tif` is being created.
-Added `CHANGELOG.md`.
+The script has been rewritten to perform channel subtraction in a RAM-efficient manner - updating is highly recommended. If the output file is much bigger than expected, adjust the `--tile-size` parameter to a smaller value (e.g `512`). Changing the `--chunk-size` parameter may affect performance (lower values increase execution time, higher values increase RAM usage).
 
 ### `Added`
-- `--chunk-size` parameter
+- `--chunk-size` parameter for dask array chunking and delayed execution for subtraction that happens while the output pyramidal OME-TIFF is being created.
 - Palom's pyramid writer
+- `CHANGELOG.md`
 
 ### `Fixed`
 - Fixed issue with RAM inefficiency - reworked Backsub.
 
 ### `Removed`
 - `--pyramid` tag introduced in v0.3.4, for smaller images, a smaller tile size should be specified now.
 
+## Versions v0.2.0 and older:
 
-I did not keep a changelog before version v0.4.1.
+The `markers.csv` file which gives details about the channels needs to contain the following columns: "Filter", "background" and "exposure". An exemplary [markers_old.csv](https://github.com/SchapiroLabor/Background_subtraction/files/9549686/markers.csv) file is given. The "Filter" column should specify the Filter used when acquiring images. If different stains are aquired with the same filter, the *exact same value* needs to be written (including background) as it is used for determining which background channel should be subtracted. The "background" column should contain logical `TRUE` values for channels which represent autofluorescence. The "exposure" column should contain the exposure time used for channel acquisition, and the measure unit should be consistent across the column. Exposure time is used for scaling the value of the background to be comparable to the processed channel. Usage of these versions is strongly disencouraged.

Dockerfile

@@ -1,13 +1,25 @@
-FROM continuumio/miniconda3
-
-COPY environment.yml .
-RUN apt-get update -qq && apt-get install -y \
-    build-essential \
-    ffmpeg \
-    libsm6 \
-    libxext6
-
-RUN conda env create -f environment.yml
-ENV PATH="/opt/conda/envs/backsub/bin:$PATH"
-WORKDIR /background_subtraction
-COPY . .
+FROM mambaorg/micromamba:1.5.10-noble
+
+# Copy conda environment file
+COPY --chown=$MAMBA_USER:$MAMBA_USER ./environment.yml /tmp/conda.yml
+
+# Install environment
+RUN micromamba install -y -n base -f /tmp/conda.yml \
+    && micromamba install -y -n base conda-forge::procps-ng \
+    && micromamba env export --name base --explicit > environment.lock \
+    && echo ">> CONDA_LOCK_START" \
+    && cat environment.lock \
+    && echo "<< CONDA_LOCK_END" \
+    && micromamba clean -a -y
+
+# Switch to root to copy everything
+USER root
+
+# Ensure micromamba binaries are in PATH
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
+
+# Copy the rest of the current directory into /app inside the container
+WORKDIR /app
+COPY . .
+
+RUN micromamba run -n base pip install .