diff --git a/dockerfiles/RunCellpose_CellposeOmnipose/Dockerfile b/dockerfiles/RunCellpose_CellposeOmnipose/Dockerfile new file mode 100644 index 00000000..79cd0ff5 --- /dev/null +++ b/dockerfiles/RunCellpose_CellposeOmnipose/Dockerfile @@ -0,0 +1,8 @@ +FROM pytorch/pytorch:1.13.0-cuda11.6-cudnn8-runtime + +RUN pip install cellpose==1.0.2 +RUN pip install omnipose + +# hotfix for the now-deprecated `peakdetect` package +# latest omnipose on github fixes this by no longer using `peakdetect` library, but not on pypi +RUN sed -i 's/from\ scipy\ import\ fft/from\ scipy.fftpack import\ fft/g' /opt/conda/lib/python3.9/site-packages/peakdetect/peakdetect.py diff --git a/dockerfiles/RunCellpose_CellposeOmnipose/Makefile b/dockerfiles/RunCellpose_CellposeOmnipose/Makefile new file mode 100644 index 00000000..5546139f --- /dev/null +++ b/dockerfiles/RunCellpose_CellposeOmnipose/Makefile @@ -0,0 +1,23 @@ +NAME ?= runcellpose_omnipose_no_pretrained +TAG ?= 1.0.2 +REPO ?= cellprofiler +IMG := $(REPO)/$(NAME):$(TAG) + +.PHONEY: build +build: + docker build -t $(IMG) . + +.PHONY: run +run: + docker run \ + -it --rm \ + $(IMG) \ + bash + +.PHONY: deploy +deploy: + docker image push $(IMG) + +.PHONY: clean_docker +clean_docker: + docker rmi $(IMG) diff --git a/setup.py b/setup.py index 4508d1fd..abce419d 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ install_deps = [ "cellprofiler", "cellprofiler-core", - ] + ] cellpose_deps = [ "cellpose>=1.0.2"