Merge pull request #234 from CellProfiler/cellpose_with_omnipose

Make dockerfile for cellpose with omnipose

Author: bethac07

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

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)

setup.py

@@ -8,7 +8,7 @@
     install_deps = [
         "cellprofiler",
         "cellprofiler-core",
-                ]
+    ]
 
     cellpose_deps = [
         "cellpose>=1.0.2,<3.0"