diff --git a/micro-sam/1.1.1/Dockerfile b/micro-sam/1.1.1/Dockerfile new file mode 100644 index 00000000..431eb470 --- /dev/null +++ b/micro-sam/1.1.1/Dockerfile @@ -0,0 +1,44 @@ +# Base Image +FROM mambaorg/micromamba:1.5.10-noble + +# Matadata +LABEL base.image="mambaorg/micromamba:1.5.10-noble" +LABEL version="1" +LABEL software="micro-sam" +LABEL software.version="1.1.1" +LABEL about.summary="Tools for segmentation and tracking in microscopy build on top of Segment Anything." +LABEL about.home="https://github.com/computational-cell-analytics/micro-sam" +LABEL about.documentation="https://computational-cell-analytics.github.io/micro-sam/micro_sam.html" +LABEL about.license="MIT License" +LABEL about.license_file="https://github.com/computational-cell-analytics/micro-sam/blob/master/LICENSE" +LABEL about.tags="Bioinformatics, Image Analysis, Microscopy, Segmentation" + +# Maintainer +LABEL maintainer="Anwai Archit " +LABEL maintainer="Carolin Schwitalla " + + +# Copy conda.yml and install dependencies +COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml + +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 + +# Set the environment path +ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH" + +USER root + +# clone the repository and install the package +RUN pip install git+https://github.com/computational-cell-analytics/micro-sam.git@9b055c3 + + + + + + \ No newline at end of file diff --git a/micro-sam/1.1.1/conda.yml b/micro-sam/1.1.1/conda.yml new file mode 100644 index 00000000..604548d2 --- /dev/null +++ b/micro-sam/1.1.1/conda.yml @@ -0,0 +1,25 @@ +name: sam +channels: + - pytorch + - conda-forge +dependencies: + - cpuonly + # This pin is necessary because later nifty versions have import errors on windows. + - nifty =1.2.1=*_4 + - imagecodecs + - natsort + - pip + - zarr + - pooch + - protobuf <5 + - python-xxhash + - python-elf >=0.4.8 + - pytorch >=2.4 + - segment-anything + - torchvision + - torch_em >=0.7.0 + - tqdm + - timm + - git + - pip: + - git+https://github.com/ChaoningZhang/MobileSAM.git \ No newline at end of file