diff --git a/Makefile b/Makefile
deleted file mode 100644
index 420284b..0000000
--- a/Makefile
+++ /dev/null
@@ -1,101 +0,0 @@
-ACCOUNT := noelmni
-SERVICE := deep-fcd
-IMAGE 	:= $(ACCOUNT)/$(SERVICE) # noelmni/deep-fcd
-TAG		:= latest
-UID		:= 2551
-GID		:= 618
-CASE_ID := sub-00055
-TMPDIR	:= /host/hamlet/local_raid/data/ravnoor/sandbox
-PRED_DIR	:= /host/hamlet/local_raid/data/ravnoor/sandbox/pytests
-BRAIN_MASKING := 1
-PREPROCESS		:= 1
-
-.PHONY: all clean
-
-build:
-	docker build -t $(ACCOUNT)/$(SERVICE):$(TAG) .
-
-clean-build:
-	docker build -t $(ACCOUNT)/$(SERVICE):$(TAG) . --no-cache
-
-test-pipeline:
-	./app/inference.py $(CASE_ID) t1.nii.gz flair.nii.gz $(TMPDIR) cuda0 $(BRAIN_MASKING) $(PREPROCESS)
-
-memray-profiling:
-	python3 -m memray run ./app/inference.py $(CASE_ID) t1_brain.nii.gz t2_brain.nii.gz $(TMPDIR) cuda0 0 0
-
-memray-profiling-cpu:
-	python3 -m memray run ./app/inference.py $(CASE_ID) t1_brain.nii.gz t2_brain.nii.gz $(TMPDIR) cpu 0 0
-
-test-preprocess:
-	./app/preprocess.sh $(CASE_ID) t1.nii.gz flair.nii.gz $(TMPDIR) $(BRAIN_MASKING) $(PREPROCESS)
-
-test-pipeline-docker:
-	docker run --rm -it --init \
-	--gpus=all	\
-	--user="$(UID):$(GID)" \
-	--volume="$(TMPDIR):/tmp" \
-	$(ACCOUNT)/$(SERVICE):$(TAG) \
-	/app/inference.py $(CASE_ID) T1.nii.gz FLAIR.nii.gz /tmp cuda0 $(BRAIN_MASKING) $(PREPROCESS)
-
-test-pipeline-docker_ci:
-	docker run --rm -it --init \
-	--gpus=all	\
-	--user="$(UID):$(GID)" \
-	--volume="$(TMPDIR):/tmp" \
-	--env CI_TESTING=1 \
-	--env CI_TESTING_GT=/tmp/$(CASE_ID)/label_final_MD.nii.gz \
-	$(ACCOUNT)/$(SERVICE):$(TAG) \
-	/app/inference.py $(CASE_ID) T1.nii.gz FLAIR.nii.gz /tmp cuda0 $(BRAIN_MASKING) $(PREPROCESS)
-
-test-pipeline-docker_testing:
-	docker run --rm -it --init \
-	--gpus=all	\
-	--user="$(UID):$(GID)" \
-	--volume="$(PRED_DIR):/tmp" \
-	--env CI_TESTING=1 \
-	--env CI_TESTING_PATIENT_ID=$(CASE_ID) \
-	--env CI_TESTING_PRED_DIR=/tmp \
-	$(ACCOUNT)/$(SERVICE):$(TAG) \
-		bash /tests/run_tests.sh
-
-test-reporting:
-	./app/utils/reporting.py $(CASE_ID) $(TMPDIR)/
-
-install-jupyter-kernel:
-	python -m ipykernel install --user --name deepFCD
-
-clean:
-	rm -rf $(TMPDIR)/$(CASE_ID)/{tmp,native,transforms}
-	rm -f $(TMPDIR)/$(CASE_ID)/{*_final,*denseCrf3d*,*_native,*_maskpred}.nii.gz
-
-docker-clean:
-	docker run --rm -it --init \
-	--volume="$(TMPDIR):/tmp" \
-	busybox:latest \
-	rm -rf /tmp/$(CASE_ID)/{tmp,native,transforms,noel_deepFCD_dropoutMC} && \
-	rm -f /tmp/$(CASE_ID)/{*_final,*denseCrf3d*,*_native,*_maskpred}.nii.gz
-
-prune:
-	docker image prune
-
-runner-build:
-	docker-compose -f ci/runner.docker-compose.yml build
-
-runner-ps:
-	docker-compose -f ci/runner.docker-compose.yml ps
-
-runner-up:
-	docker-compose -f ci/runner.docker-compose.yml up --remove-orphans -d
-
-runner-down:
-	docker-compose -f ci/runner.docker-compose.yml down
-
-runner-logs:
-	docker-compose -f ci/runner.docker-compose.yml logs -f
-
-runner-scale:
-	docker-compose -f ci/runner.docker-compose.yml up --scale runner=1 -d
-
-runner-bash:
-	docker-compose -f ci/runner.docker-compose.yml exec -it runner bash
\ No newline at end of file
diff --git a/justfile b/justfile
new file mode 100644
index 0000000..2f494ca
--- /dev/null
+++ b/justfile
@@ -0,0 +1,132 @@
+set export
+
+ACCOUNT := "noelmni"
+SERVICE := "deep-fcd"
+IMAGE := ACCOUNT + "/" + SERVICE
+TAG := "latest"
+UID := "2551"
+GID := "618"
+CASE_ID := "PLO_JUL"
+TMPDIR := "/host/hamlet/local_raid/data/ravnoor/sandbox"
+PRED_DIR := "/host/hamlet/local_raid/data/ravnoor/sandbox/pytests"
+BRAIN_MASKING := "1"
+PREPROCESS := "1"
+
+# build Docker image
+build:
+  docker build -t {{ACCOUNT}}/{{SERVICE}}:{{TAG}} .
+
+# build Docker image without cache
+clean-build:
+  docker build -t {{ACCOUNT}}/{{SERVICE}}:{{TAG}} . --no-cache
+
+create-locked-pyenv: 
+  micromamba run -n base conda-lock -f app/environment.yml -p linux-64 --lockfile app/conda-lock.yml
+
+install-pyenv: create-locked-pyenv
+  micromamba create --prefix ${MAMBA_ROOT_PREFIX}/envs/fcd -f app/conda-lock.yml --yes
+
+# run test pipeline
+test-pipeline:
+    ./app/inference.py {{CASE_ID}} T1.nii.gz FLAIR.nii.gz {{TMPDIR}} cuda0 {{BRAIN_MASKING}} {{PREPROCESS}}
+
+# run scalene profiling
+scalene-profiling:
+    python3 -m scalene --cpu --gpu --memory ./app/inference.py {{CASE_ID}} T1.nii.gz FLAIR.nii.gz {{TMPDIR}} cuda0 1 1
+
+# run memray profiling
+memray-profiling:
+    python3 -m memray run ./app/inference.py {{CASE_ID}} t1_brain.nii.gz t2_brain.nii.gz {{TMPDIR}} cuda0 0 0
+
+# run memray profiling on CPU
+memray-profiling-cpu:
+    python3 -m memray run ./app/inference.py {{CASE_ID}} t1_brain.nii.gz t2_brain.nii.gz {{TMPDIR}} cpu 0 0
+
+# test preprocessing
+test-preprocess:
+    ./app/preprocess.sh {{CASE_ID}} t1.nii.gz flair.nii.gz {{TMPDIR}} {{BRAIN_MASKING}} {{PREPROCESS}}
+
+# test pipeline in Docker
+test-pipeline-docker:
+    docker run --rm -it --init \
+    --gpus=all \
+    --user="{{UID}}:{{GID}}" \
+    --volume="{{TMPDIR}}:/tmp" \
+    {{ACCOUNT}}/{{SERVICE}}:{{TAG}} \
+    /app/inference.py {{CASE_ID}} T1.nii.gz FLAIR.nii.gz /tmp cuda0 {{BRAIN_MASKING}} {{PREPROCESS}}
+
+# test pipeline in Docker with CI testing
+test-pipeline-docker_ci:
+    docker run --rm -it --init \
+    --gpus=all \
+    --user="{{UID}}:{{GID}}" \
+    --volume="{{TMPDIR}}:/tmp" \
+    --env CI_TESTING=1 \
+    --env CI_TESTING_GT=/tmp/{{CASE_ID}}/label_final_MD.nii.gz \
+    {{ACCOUNT}}/{{SERVICE}}:{{TAG}} \
+    /app/inference.py {{CASE_ID}} T1.nii.gz FLAIR.nii.gz /tmp cuda0 {{BRAIN_MASKING}} {{PREPROCESS}}
+
+# test pipeline in Docker for testing
+test-pipeline-docker_testing:
+    docker run --rm -it --init \
+    --gpus=all \
+    --user="{{UID}}:{{GID}}" \
+    --volume="{{PRED_DIR}}:/tmp" \
+    --env CI_TESTING=1 \
+    --env CI_TESTING_PATIENT_ID={{CASE_ID}} \
+    --env CI_TESTING_PRED_DIR=/tmp \
+    {{ACCOUNT}}/{{SERVICE}}:{{TAG}} \
+    bash /tests/run_tests.sh
+
+# test reporting
+test-reporting:
+    ./app/utils/reporting.py {{CASE_ID}} {{TMPDIR}}/
+
+# install Jupyter kernel
+install-jupyter-kernel:
+    python -m ipykernel install --user --name deepFCD
+
+# clean up temporary files
+clean:
+    rm -rf {{TMPDIR}}/{{CASE_ID}}/{tmp,native,transforms}
+    rm -f {{TMPDIR}}/{{CASE_ID}}/{*_final,*denseCrf3d*,*_native,*_maskpred}.nii.gz
+
+# clean up Docker container
+docker-clean:
+    docker run --rm -it --init \
+    --volume="{{TMPDIR}}:/tmp" \
+    busybox:latest \
+    rm -rf /tmp/{{CASE_ID}}/{tmp,native,transforms,noel_deepFCD_dropoutMC} && \
+    rm -f /tmp/{{CASE_ID}}/{*_final,*denseCrf3d*,*_native,*_maskpred}.nii.gz
+
+# prune Docker images
+prune:
+    docker image prune
+
+# build runner
+runner-build:
+    docker-compose -f ci/runner.docker-compose.yml build
+
+# show runner processes
+runner-ps:
+    docker-compose -f ci/runner.docker-compose.yml ps
+
+# start runner
+runner-up:
+    docker-compose -f ci/runner.docker-compose.yml up --remove-orphans -d
+
+# stop runner
+runner-down:
+    docker-compose -f ci/runner.docker-compose.yml down
+
+# show runner logs
+runner-logs:
+    docker-compose -f ci/runner.docker-compose.yml logs -f
+
+# scale runner
+runner-scale:
+    docker-compose -f ci/runner.docker-compose.yml up --scale runner=1 -d
+
+# access runner bash
+runner-bash:
+    docker-compose -f ci/runner.docker-compose.yml exec -it runner bash