diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 653769fbca..27e95f4656 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -62,6 +62,13 @@ jobs:
         pip install --editable .[evaluate]
         python -c "import openproblems"
 
+    - name: Download docker images
+      run: |
+        for image in $(find ./docker -mindepth 1 -type d -exec basename {} \;); do
+          docker pull singlecellopenproblems/${image} &
+        done
+        wait
+
     - name: Update Docker images
       if: |
         !(
diff --git a/docker/openproblems-python-batch-integration/Dockerfile b/docker/openproblems-python-batch-integration/Dockerfile
new file mode 100644
index 0000000000..697905d79c
--- /dev/null
+++ b/docker/openproblems-python-batch-integration/Dockerfile
@@ -0,0 +1,24 @@
+FROM singlecellopenproblems/openproblems-r-base:latest
+
+USER root
+WORKDIR /
+
+ARG NB_USER="sagemaker-user"
+ARG NB_UID="1000"
+ARG NB_GID="100"
+
+RUN sed -i '$ d' /etc/apt/sources.list
+RUN \
+apt-get update --allow-releaseinfo-change && \
+apt-get -y install --no-install-recommends gcc git python3-llvmlite && \
+apt-get autoremove -y && \
+rm -rf /var/lib/apt/lists/*
+
+# Install Python packages
+COPY ./docker/openproblems-python-batch-integration/requirements.txt ./requirements.txt
+RUN pip install --no-cache-dir -r requirements.txt
+# force reinstall annoy addresses https://github.com/spotify/annoy/issues/513
+RUN pip install --no-cache-dir --force annoy==1.17.0
+
+USER $NB_UID
+WORKDIR /home/$NB_USER
diff --git a/docker/openproblems-python-batch-integration/README.md b/docker/openproblems-python-batch-integration/README.md
new file mode 100644
index 0000000000..02a18e1c20
--- /dev/null
+++ b/docker/openproblems-python-batch-integration/README.md
@@ -0,0 +1,15 @@
+# openproblems-python-extras Docker image
+
+Base image: singlecellopenproblems/openproblems-r-base
+
+OS: Debian Stretch
+
+Python: 3.8
+
+Python packages:
+
+* scIB
+* mnnpy
+* scanorama
+* bbknn
+* scVI
diff --git a/docker/openproblems-python-batch-integration/requirements.txt b/docker/openproblems-python-batch-integration/requirements.txt
new file mode 100644
index 0000000000..9c92302df9
--- /dev/null
+++ b/docker/openproblems-python-batch-integration/requirements.txt
@@ -0,0 +1,6 @@
+annoy==1.17.1
+bbknn==1.5.*
+git+https://github.com/scottgigante-immunai/mnnpy@eb4c551  # branch: patch-2
+git+https://github.com/theislab/scib@77ab015
+scanorama==1.7.0
+scvi-tools~=0.16  # pinned in #313
diff --git a/docker/openproblems-python-bedtools/Dockerfile b/docker/openproblems-python-bedtools/Dockerfile
deleted file mode 100644
index d2ad393378..0000000000
--- a/docker/openproblems-python-bedtools/Dockerfile
+++ /dev/null
@@ -1,28 +0,0 @@
-FROM singlecellopenproblems/openproblems:latest
-
-ARG NB_USER="sagemaker-user"
-ARG NB_UID="1000"
-ARG NB_GID="100"
-
-USER root
-WORKDIR /
-
-# Install pybedtools dependency
-ARG BUILD_PACKAGES=""
-ARG PACKAGE_VERSION=2.27.1
-RUN apt-get update && \
-    apt-get install --yes git openssl build-essential zlib1g-dev && \
-    cd /tmp && \
-    git clone https://github.com/arq5x/bedtools2.git && \
-    cd bedtools2 && \
-    git checkout v$PACKAGE_VERSION && \
-    make && \
-    mv bin/* /usr/local/bin && \
-    cd /
-
-# install dependencies and openproblems
-COPY ./docker/openproblems-python-bedtools/requirements.txt ./requirements.txt
-RUN pip install --no-cache-dir -r requirements.txt
-
-USER $NB_UID
-WORKDIR /home/$NB_USER
diff --git a/docker/openproblems-python-bedtools/README.md b/docker/openproblems-python-bedtools/README.md
deleted file mode 100644
index d7b9935395..0000000000
--- a/docker/openproblems-python-bedtools/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# openproblems-python-extras Docker image
-
-Base image: singlecellopenproblems/openproblems
-
-OS: Debian Stretch
-
-Python: 3.8
-
-Python packages:
-
-* pybedtools
-* pyensembl
diff --git a/docker/openproblems-python-bedtools/requirements.txt b/docker/openproblems-python-bedtools/requirements.txt
deleted file mode 100644
index 5f308af4ed..0000000000
--- a/docker/openproblems-python-bedtools/requirements.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-pybedtools==0.9.*
-pyensembl==2.0.*
diff --git a/docker/openproblems-python-extras/requirements.txt b/docker/openproblems-python-extras/requirements.txt
index 7d6aee63d5..c51a5d771a 100644
--- a/docker/openproblems-python-extras/requirements.txt
+++ b/docker/openproblems-python-extras/requirements.txt
@@ -1,7 +1,17 @@
 cmake==3.24.1.1
+git+https://github.com/BayraktarLab/cell2location.git@7e7aa231cc61ff460da14402fa3b9a1fa3ec69ac
+git+https://github.com/czbiohub/molecular-cross-validation@04d9df0
 git+https://github.com/jorvis/Multicore-TSNE@6832575
 git+https://github.com/KrishnaswamyLab/harmonic-alignment@v0.1#subdirectory=python
+git+https://github.com/michalk8/neuralee@8946abf  # contains gradient error fix
 git+https://github.com/scottgigante-immunai/knn-smoothing@python_package
 magic-impute==3.0.*
 phate==1.0.*
+pybedtools==0.9.*
+pyensembl==2.0.*
+scalex==1.0.2
+scvi-tools==0.16.*
+tangram-sc==1.0.*
+tensorflow-cpu==2.9.*
+torch==1.12.*
 xgboost==1.6.*
diff --git a/docker/openproblems-python-pytorch/requirements.txt b/docker/openproblems-python-pytorch/requirements.txt
deleted file mode 100644
index 56bd2a53dc..0000000000
--- a/docker/openproblems-python-pytorch/requirements.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-git+https://github.com/BayraktarLab/cell2location.git@7e7aa231cc61ff460da14402fa3b9a1fa3ec69ac
-git+https://github.com/czbiohub/molecular-cross-validation@04d9df0
-git+https://github.com/michalk8/neuralee@8946abf  # contains gradient error fix
-jax==0.3.23
-jaxlib==0.3.22
-scalex==1.0.2
-scikit-misc==0.1.*
-scvi-tools~=0.17  # pinned in #313
-tangram-sc==1.0.*
-torch==1.12.*
-xgboost==1.6.*
diff --git a/docker/openproblems-python-pytorch/Dockerfile b/docker/openproblems-python-scvi/Dockerfile
similarity index 65%
rename from docker/openproblems-python-pytorch/Dockerfile
rename to docker/openproblems-python-scvi/Dockerfile
index 0f5b8521a3..f7edd2e4dc 100644
--- a/docker/openproblems-python-pytorch/Dockerfile
+++ b/docker/openproblems-python-scvi/Dockerfile
@@ -7,8 +7,8 @@ ARG NB_GID="100"
 USER root
 WORKDIR /
 
-# install dependencies and openproblems
-COPY ./docker/openproblems-python-pytorch/requirements.txt ./requirements.txt
+# Install Python packages
+COPY ./docker/openproblems-python-scvi/requirements.txt ./requirements.txt
 RUN pip install --no-cache-dir -r requirements.txt
 
 USER $NB_UID
diff --git a/docker/openproblems-python-pytorch/README.md b/docker/openproblems-python-scvi/README.md
similarity index 64%
rename from docker/openproblems-python-pytorch/README.md
rename to docker/openproblems-python-scvi/README.md
index d566a8efd5..546cec9bc0 100644
--- a/docker/openproblems-python-pytorch/README.md
+++ b/docker/openproblems-python-scvi/README.md
@@ -9,9 +9,3 @@ Python: 3.8
 Python packages:
 
 * scvi-tools
-* tangram
-* torch
-* neuralee
-* xgboost
-* molecular-cross-validation
-* cell2location
diff --git a/docker/openproblems-python-scvi/requirements.txt b/docker/openproblems-python-scvi/requirements.txt
new file mode 100644
index 0000000000..87aa041993
--- /dev/null
+++ b/docker/openproblems-python-scvi/requirements.txt
@@ -0,0 +1,5 @@
+jax==0.3.23
+jaxlib==0.3.22
+scikit-misc==0.1.*
+scvi-tools~=0.17  # pinned in #313
+xgboost==1.6.*
diff --git a/docker/openproblems-python-tensorflow/Dockerfile b/docker/openproblems-python-tensorflow/Dockerfile
deleted file mode 100644
index 0a996f9221..0000000000
--- a/docker/openproblems-python-tensorflow/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM singlecellopenproblems/openproblems:latest
-
-ARG NB_USER="sagemaker-user"
-ARG NB_UID="1000"
-ARG NB_GID="100"
-
-USER root
-WORKDIR /
-
-# install dependencies and openproblems
-COPY ./docker/openproblems-python-tensorflow/requirements.txt ./requirements.txt
-RUN pip install --no-cache-dir -r requirements.txt
-
-USER $NB_UID
-WORKDIR /home/$NB_USER
diff --git a/docker/openproblems-python-tensorflow/requirements.txt b/docker/openproblems-python-tensorflow/requirements.txt
deleted file mode 100644
index f2a476acf9..0000000000
--- a/docker/openproblems-python-tensorflow/requirements.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-git+https://github.com/Avsecz/kopt@6a5c890  # master
-git+https://github.com/scottgigante-immunai/dca@1f4edbc  # patch-1 contains tf version bump
-protobuf==3.20.*
-tensorflow==2.9.0
diff --git a/docker/openproblems-python-tf2.4/Dockerfile b/docker/openproblems-python-tf2.4/Dockerfile
new file mode 100644
index 0000000000..dcdabaf28d
--- /dev/null
+++ b/docker/openproblems-python-tf2.4/Dockerfile
@@ -0,0 +1,18 @@
+FROM singlecellopenproblems/openproblems:latest
+
+ARG NB_USER="sagemaker-user"
+ARG NB_UID="1000"
+ARG NB_GID="100"
+
+USER root
+WORKDIR /
+
+# Install Python packages
+COPY ./docker/openproblems-python-tf2.4/requirements.txt ./requirements.txt
+RUN pip install --no-cache-dir -r requirements.txt
+
+# tensorflow downgrades numpy and h5py (and therefore anndata)
+RUN pip install --no-cache-dir -e /usr/src/singlecellopenproblems
+
+USER $NB_UID
+WORKDIR /home/$NB_USER
diff --git a/docker/openproblems-python-tensorflow/README.md b/docker/openproblems-python-tf2.4/README.md
similarity index 56%
rename from docker/openproblems-python-tensorflow/README.md
rename to docker/openproblems-python-tf2.4/README.md
index 3f4c4dbf67..f08a69ea20 100644
--- a/docker/openproblems-python-tensorflow/README.md
+++ b/docker/openproblems-python-tf2.4/README.md
@@ -1,4 +1,4 @@
-# openproblems-python-tensorflow Docker image
+# openproblems-python-tf2.4 Docker image
 
 Base image: singlecellopenproblems/openproblems
 
@@ -8,5 +8,6 @@ Python: 3.8
 
 Python packages:
 
-* tensorflow
+* keras >=2.4,<2.6
+* tensorflow >=2.4,<2.5
 * dca
diff --git a/docker/openproblems-python-tf2.4/requirements.txt b/docker/openproblems-python-tf2.4/requirements.txt
new file mode 100644
index 0000000000..31a56c2ea2
--- /dev/null
+++ b/docker/openproblems-python-tf2.4/requirements.txt
@@ -0,0 +1,4 @@
+dca==0.3.*
+keras>=2.4,<2.11
+pyyaml==6.0  # pinned in #431
+tensorflow-cpu==2.4.*  # pinned in dca
diff --git a/docker/openproblems-r-base/README.md b/docker/openproblems-r-base/README.md
index ebca77780d..785a9ace1b 100644
--- a/docker/openproblems-r-base/README.md
+++ b/docker/openproblems-r-base/README.md
@@ -28,4 +28,4 @@ R packages:
 Python packages:
 
 * rpy2
-* anndata2ri>=1.1
+* anndata2ri>=1.0.6
diff --git a/docker/openproblems-r-extras/r_requirements.txt b/docker/openproblems-r-extras/r_requirements.txt
index 0b8da4bde9..efd4ceeba6 100644
--- a/docker/openproblems-r-extras/r_requirements.txt
+++ b/docker/openproblems-r-extras/r_requirements.txt
@@ -46,7 +46,6 @@ shiny@1.4.0.2
 sparsesvd@0.2
 systemfonts@1.0.4
 textshaping@0.3.6
-theislab/kBET@a10ffea # master
 tibble@3.1.7
 tidymodels@0.1.2
 tidyverse@1.3.0
diff --git a/docker/openproblems-r-extras/requirements.txt b/docker/openproblems-r-extras/requirements.txt
index 1795471bae..9d03431a90 100644
--- a/docker/openproblems-r-extras/requirements.txt
+++ b/docker/openproblems-r-extras/requirements.txt
@@ -1,3 +1,3 @@
 git+https://github.com/KrishnaswamyLab/harmonic-alignment@v0.1#subdirectory=python
-git+https://github.com/theislab/scib@f0be826
+git+https://github.com/theislab/scib@v1.0.2
 xgboost==1.6.*
diff --git a/docker/openproblems-r-pytorch/README.md b/docker/openproblems-r-pytorch/README.md
index 33d3e5a30c..03ccbc07d4 100644
--- a/docker/openproblems-r-pytorch/README.md
+++ b/docker/openproblems-r-pytorch/README.md
@@ -8,12 +8,12 @@ Python: 3.8
 
 R: 4.0
 
+R packages:
+
+* batchelor
+* sparsesvd
+* dplyr
+
 Python packages:
 
-* harmony-pytorch
-* torch
-* bbknn
-* mnnpy
-* scib
-* scanorama
-* scvi-tools
+* harmonic-alignment
diff --git a/docker/openproblems-r-pytorch/requirements.txt b/docker/openproblems-r-pytorch/requirements.txt
index c9dfe890a9..e7c8df42b7 100644
--- a/docker/openproblems-r-pytorch/requirements.txt
+++ b/docker/openproblems-r-pytorch/requirements.txt
@@ -1,8 +1,3 @@
-annoy==1.17.1
-bbknn==1.5.*
-git+https://github.com/scottgigante-immunai/mnnpy@eb4c551  # branch: patch-2
-git+https://github.com/theislab/scib@f0be826
+git+https://github.com/theislab/scib@v1.0.2
 harmony-pytorch==0.1.*
-scanorama==1.7.0
-scvi-tools~=0.16  # pinned in #313
 torch==1.13.*
diff --git a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py
index e83d47bb54..322891b202 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py
@@ -21,7 +21,7 @@
 @metric(
     metric_name="Cell Cycle Score",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def cc_score(adata, test=False):
     from ._utils import _get_split
diff --git a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/iso_label_sil.py b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/iso_label_sil.py
index c1f8c4be2d..c3575de5b8 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/iso_label_sil.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/iso_label_sil.py
@@ -15,7 +15,7 @@
 @metric(
     metric_name="Isolated label Silhouette",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def isolated_labels_sil(adata):
     from scib.metrics import isolated_labels
diff --git a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py
index 7efca62ffe..886f26078b 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py
@@ -18,7 +18,7 @@
 @metric(
     metric_name="PC Regression",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def pcr(adata):
     from ._utils import _get_split
diff --git a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py
index 9f28cd1284..c02e5e42aa 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py
@@ -24,7 +24,7 @@
 @metric(
     metric_name="Batch ASW",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def silhouette_batch(adata):
     from scib.metrics import silhouette_batch
diff --git a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py
index bb2bece193..36991e1d67 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py
@@ -12,7 +12,7 @@
 @metric(
     metric_name="Silhouette",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def silhouette(adata):
     from scib.metrics import silhouette
diff --git a/openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py b/openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py
index bb7f90cae8..d40b36b740 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py
@@ -21,7 +21,7 @@
 @metric(
     metric_name="HVG conservation",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 def hvg_conservation(adata):
     from scib.metrics import hvg_overlap
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py
index 97570dccd8..017ca8f766 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py
@@ -10,7 +10,7 @@
     paper_url="https://academic.oup.com/bioinformatics/article/36/3/964/5545955",
     paper_year=2020,
     code_url="https://github.com/Teichlab/bbknn",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py
index 96e53538d3..3043a552e1 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py
@@ -10,7 +10,7 @@
     paper_url="https://academic.oup.com/biostatistics/article/8/1/118/252073",
     paper_year=2007,
     code_url="https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py
index 0146f5b6e3..99dab39203 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py
@@ -10,7 +10,7 @@
     paper_url="https://www.nature.com/articles/nbt.4091",
     paper_year=2018,
     code_url="https://github.com/chriscainx/mnnpy",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py
index 461ea04a94..36843b81ed 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py
@@ -11,7 +11,7 @@
     paper_url="https://doi.org/10.1038/s41467-022-33758-z",
     paper_year=2022,
     code_url="https://github.com/jsxlei/SCALEX",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py
index a5efc04b35..d6e80162b5 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py
@@ -10,7 +10,7 @@
     paper_url="https://www.nature.com/articles/s41587-019-0113-3",
     paper_year=2019,
     code_url="https://github.com/brianhie/scanorama",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py
index 8f98a3c931..d5bf463974 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py
@@ -11,7 +11,7 @@
     paper_url="https://doi.org/10.15252/msb.20209620",
     paper_year=2021,
     code_url="https://github.com/YosefLab/scvi-tools",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py
index 35f1cd7ac5..9e9a82a9f2 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py
@@ -10,7 +10,7 @@
     paper_url="https://www.nature.com/articles/s41592-018-0229-2",
     paper_year=2018,
     code_url="https://github.com/YosefLab/scvi-tools",
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 
 
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py
index 0d082fff44..13e7eb8ce1 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py
@@ -16,7 +16,7 @@
 @metric(
     metric_name="ARI",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 def ari(adata):
     from scib.metrics import ari
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/graph_connectivity.py b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/graph_connectivity.py
index 52dd7c44b2..3a9732d0e2 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/graph_connectivity.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/graph_connectivity.py
@@ -22,7 +22,7 @@
 @metric(
     metric_name="Graph connectivity",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def graph_connectivity(adata):
     import scib.metrics
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_f1.py b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_f1.py
index 71cd7ca209..df86b043d9 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_f1.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_f1.py
@@ -27,7 +27,7 @@
 @metric(
     metric_name="Isolated label F1",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",  # only if required
 )
 def isolated_labels_f1(adata):
     from scib.metrics import isolated_labels
diff --git a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py
index 3356507b2e..bbcdc7cd9d 100644
--- a/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py
+++ b/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py
@@ -15,7 +15,7 @@
 @metric(
     metric_name="NMI",
     maximize=True,
-    image="openproblems-r-pytorch",
+    image="openproblems-python-batch-integration",
 )
 def nmi(adata):
     from scib.metrics.clustering import opt_louvain  # isort:skip
diff --git a/openproblems/tasks/_cell_cell_communication/_common/methods/liana.py b/openproblems/tasks/_cell_cell_communication/_common/methods/liana.py
index a528c9c9e3..dc2bba944c 100644
--- a/openproblems/tasks/_cell_cell_communication/_common/methods/liana.py
+++ b/openproblems/tasks/_cell_cell_communication/_common/methods/liana.py
@@ -43,10 +43,6 @@ def _liana(
     adata.layers["logcounts"] = adata.layers["log_cpm"]
     del adata.layers["log_cpm"]
 
-    # remove dataframe before R conversion
-    target = adata.uns["ccc_target"]
-    del adata.uns["ccc_target"]
-
     # Run LIANA
     liana_res = _r_liana(
         adata,
@@ -57,9 +53,6 @@ def _liana(
         **kwargs,
     )
 
-    # return target to uns
-    adata.uns["ccc_target"] = target
-
     # Format results
     liana_res["score"] = liana_res[score_col]
     adata.uns["ccc_pred"] = liana_res
diff --git a/openproblems/tasks/denoising/datasets/pancreas.py b/openproblems/tasks/denoising/datasets/pancreas.py
index bd039ad88e..c18ddbeee1 100644
--- a/openproblems/tasks/denoising/datasets/pancreas.py
+++ b/openproblems/tasks/denoising/datasets/pancreas.py
@@ -11,7 +11,7 @@
     "across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, "
     "and SMARTER-seq). Here we just use the inDrop1 batch, which includes"
     "1937 cells × 15502 genes.",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def pancreas(test=False):
     adata = load_pancreas(test=test, keep_techs=["inDrop1"])
diff --git a/openproblems/tasks/denoising/datasets/pbmc.py b/openproblems/tasks/denoising/datasets/pbmc.py
index 440ebe8a3b..fcf0fc782b 100644
--- a/openproblems/tasks/denoising/datasets/pbmc.py
+++ b/openproblems/tasks/denoising/datasets/pbmc.py
@@ -11,7 +11,7 @@
         "1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. "
         "Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics."
     ),
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def pbmc(test=False):
     adata = load_tenx_1k_pbmc(test=test)
diff --git a/openproblems/tasks/denoising/datasets/tabula_muris_senis.py b/openproblems/tasks/denoising/datasets/tabula_muris_senis.py
index 9524cc4e95..a5c62f953e 100644
--- a/openproblems/tasks/denoising/datasets/tabula_muris_senis.py
+++ b/openproblems/tasks/denoising/datasets/tabula_muris_senis.py
@@ -10,7 +10,7 @@
     dataset_summary="All lung cells from Tabula Muris Senis, a 500k cell-atlas from 18 "
     "organs and tissues across the mouse lifespan. Here we use just 10x data from lung."
     " 24540 cells × 16160 genes across 3 time points.",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def tabula_muris_senis_lung_random(test=False):
     adata = load_tabula_muris_senis(
diff --git a/openproblems/tasks/denoising/methods/dca.py b/openproblems/tasks/denoising/methods/dca.py
index 458f9ecb05..fddfb85d51 100644
--- a/openproblems/tasks/denoising/methods/dca.py
+++ b/openproblems/tasks/denoising/methods/dca.py
@@ -30,7 +30,7 @@ def _dca(adata, test=False, epochs=None):
     paper_url="https://www.nature.com/articles/s41467-018-07931-2",
     paper_year=2019,
     code_url="https://github.com/theislab/dca",
-    image="openproblems-python-tensorflow",
+    image="openproblems-python-tf2.4",
 )
 def dca(adata, test=False, epochs=None):
     return _dca(adata, test=test, epochs=epochs)
diff --git a/openproblems/tasks/denoising/metrics/poisson.py b/openproblems/tasks/denoising/metrics/poisson.py
index 93db71eee2..ebd2a73378 100644
--- a/openproblems/tasks/denoising/metrics/poisson.py
+++ b/openproblems/tasks/denoising/metrics/poisson.py
@@ -1,7 +1,7 @@
 from ....tools.decorators import metric
 
 
-@metric(metric_name="Poisson loss", maximize=False, image="openproblems-python-pytorch")
+@metric(metric_name="Poisson loss", maximize=False, image="openproblems-python-extras")
 def poisson(adata):
     from molecular_cross_validation.mcv_sweep import poisson_nll_loss
 
diff --git a/openproblems/tasks/dimensionality_reduction/methods/neuralee.py b/openproblems/tasks/dimensionality_reduction/methods/neuralee.py
index 420132dbf2..41f55dbb65 100644
--- a/openproblems/tasks/dimensionality_reduction/methods/neuralee.py
+++ b/openproblems/tasks/dimensionality_reduction/methods/neuralee.py
@@ -18,7 +18,7 @@
     paper_url="https://www.frontiersin.org/articles/10.3389/fgene.2020.00786/full",
     paper_year=2020,
     code_url="https://github.com/HiBearME/NeuralEE",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 
 
diff --git a/openproblems/tasks/label_projection/methods/scvi_tools.py b/openproblems/tasks/label_projection/methods/scvi_tools.py
index 1cec698b27..6212f8cd69 100644
--- a/openproblems/tasks/label_projection/methods/scvi_tools.py
+++ b/openproblems/tasks/label_projection/methods/scvi_tools.py
@@ -10,7 +10,7 @@
     paper_url="https://doi.org/10.15252/msb.20209620",
     paper_year=2021,
     code_url="https://github.com/YosefLab/scvi-tools",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-scvi",
 )
 
 _scanvi_scarches_method = functools.partial(
@@ -19,7 +19,7 @@
     paper_url="https://doi.org/10.1101/2020.07.16.205997",
     paper_year=2021,
     code_url="https://github.com/YosefLab/scvi-tools",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-scvi",
 )
 
 
diff --git a/openproblems/tasks/regulatory_effect_prediction/methods/beta.py b/openproblems/tasks/regulatory_effect_prediction/methods/beta.py
index 1eeff4992e..e5dffb6fa7 100644
--- a/openproblems/tasks/regulatory_effect_prediction/methods/beta.py
+++ b/openproblems/tasks/regulatory_effect_prediction/methods/beta.py
@@ -235,7 +235,7 @@ def _beta(adata, test=False, top_genes=None, threshold=1):
     paper_year=2013,
     code_version="1.0",
     code_url="http://cistrome.org/BETA",
-    image="openproblems-python-bedtools",
+    image="openproblems-python-extras",
 )
 def beta(adata, test=False, top_genes=None, threshold=1):
     adata = _beta(adata, test=test, top_genes=top_genes, threshold=threshold)
diff --git a/openproblems/tasks/spatial_decomposition/datasets/destvi/generate.py b/openproblems/tasks/spatial_decomposition/datasets/destvi/generate.py
index e446b07687..86005d07f2 100644
--- a/openproblems/tasks/spatial_decomposition/datasets/destvi/generate.py
+++ b/openproblems/tasks/spatial_decomposition/datasets/destvi/generate.py
@@ -11,7 +11,7 @@
     "from the destVI manuscripts leveraging sparsePCA. Number of cells and "
     "cell types present in each spatial spot is computed via combination of "
     "kernel-based parametrization of a categorical distribution and the NB model.",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def destvi(test=False):
     from .utils import generate_synthetic_dataset
diff --git a/openproblems/tasks/spatial_decomposition/methods/cell2location.py b/openproblems/tasks/spatial_decomposition/methods/cell2location.py
index 168472cbbb..2caf9d4956 100644
--- a/openproblems/tasks/spatial_decomposition/methods/cell2location.py
+++ b/openproblems/tasks/spatial_decomposition/methods/cell2location.py
@@ -12,7 +12,7 @@
     paper_url="https://doi.org/10.1038/s41587-021-01139-4",
     paper_year=2022,
     code_url="https://github.com/BayraktarLab/cell2location",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 
 
diff --git a/openproblems/tasks/spatial_decomposition/methods/destvi.py b/openproblems/tasks/spatial_decomposition/methods/destvi.py
index 4338a465fd..9330ba1d92 100644
--- a/openproblems/tasks/spatial_decomposition/methods/destvi.py
+++ b/openproblems/tasks/spatial_decomposition/methods/destvi.py
@@ -11,7 +11,7 @@
     paper_url="https://doi.org/10.1038/s41587-022-01272-8",
     paper_year=2022,
     code_url="https://github.com/YosefLab/scvi-tools",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def destvi(
     adata,
diff --git a/openproblems/tasks/spatial_decomposition/methods/stereoscope.py b/openproblems/tasks/spatial_decomposition/methods/stereoscope.py
index f9c025319e..c2695e4253 100644
--- a/openproblems/tasks/spatial_decomposition/methods/stereoscope.py
+++ b/openproblems/tasks/spatial_decomposition/methods/stereoscope.py
@@ -10,7 +10,7 @@
     paper_url="https://doi.org/10.1038/s41587-022-01272-8",
     paper_year=2020,
     code_url="https://github.com/scverse/scvi-tools",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def stereoscope(adata, test=False, max_epochs_sc=None, max_epochs_sp=None):
     from scvi.external import RNAStereoscope
diff --git a/openproblems/tasks/spatial_decomposition/methods/tangram.py b/openproblems/tasks/spatial_decomposition/methods/tangram.py
index c05eb0339f..329676c4aa 100644
--- a/openproblems/tasks/spatial_decomposition/methods/tangram.py
+++ b/openproblems/tasks/spatial_decomposition/methods/tangram.py
@@ -10,7 +10,7 @@
     paper_url="https://doi.org/10.1038/s41592-021-01264-7",
     paper_year=2021,
     code_url="https://github.com/broadinstitute/Tangram",
-    image="openproblems-python-pytorch",
+    image="openproblems-python-extras",
 )
 def tangram(adata, test=False, num_epochs=None, n_markers=None):
     # analysis based on:
diff --git a/pytest.ini b/pytest.ini
index 273a414dbc..447d92b2a1 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -10,5 +10,4 @@ filterwarnings =
     ignore:X\.dtype being converted to np\.float32 from float64:FutureWarning
     ignore:is_categorical is deprecated and will be removed in a future version:FutureWarning
     ignore:The use of (converter|py2rpy|rpy2py) in module rpy2.robjects.conversion is deprecated.:DeprecationWarning
-    ignore:`Model\.state_updates` will be removed in a future version\.:UserWarning
     always:Container failed with AssertionError\. Retrying [0-9]* more time:RuntimeWarning
diff --git a/setup.py b/setup.py
index 89ead383cd..a6a1c213f4 100644
--- a/setup.py
+++ b/setup.py
@@ -4,14 +4,14 @@
 import os
 
 install_requires = [
-    "numpy>=1.19.2,<1.24",
-    "scikit-learn<=1.1.*",
+    "numpy>=1.22,<1.24",
+    "scikit-learn==1.1.*",
     "anndata==0.8.*",
     "scprep>=1.2.1",
-    "scipy>=1.7,<1.10",
+    "scipy>=1.8,<1.10",
     "scanpy>=1.6",
-    "louvain==0.8.*",
-    "python-igraph==0.10.*",
+    "louvain==0.7.*",
+    "python-igraph<0.10",
     "decorator<5.0",  # pinned in #324
     "memory-profiler==0.60",
     "colorama==0.4.*",
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 6f02c7fe2b..c8378a3cea 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -27,7 +27,6 @@ rule docker_refresh:
     input: tools.refresh_images
 
 rule refresh_docker_image:
-    threads: 0
     priority: 50
     input:
         dockerfile = "{}/{{image}}/refresh.Dockerfile".format(tools.IMAGES_DIR),
@@ -79,7 +78,6 @@ rule update_docker_image:
         "touch {output}"
 
 rule build_docker_image:
-    threads: 0.5
     input:
         dockerfile = "{}/{{image}}/Dockerfile".format(tools.IMAGES_DIR),
         requirements = tools.docker_build_requirements,
@@ -110,7 +108,6 @@ rule login_docker:
         "docker login --username=singlecellopenproblems --password=$(cat {input})"
 
 rule push_docker_image:
-    threads: 0
     input:
         build = "{}/{{image}}/.docker_update".format(tools.IMAGES_DIR),
         login = ".docker_login",
@@ -120,7 +117,6 @@ rule push_docker_image:
         "docker push --quiet singlecellopenproblems/{wildcards.image}"
 
 rule pull_docker_image:
-    threads: 0
     output:
         temp(touch("{}/{{image}}/.docker_pull".format(tools.IMAGES_DIR)))
     shell:
diff --git a/workflow/snakemake_tools.py b/workflow/snakemake_tools.py
index 02d327dc55..8c9b92e42b 100644
--- a/workflow/snakemake_tools.py
+++ b/workflow/snakemake_tools.py
@@ -264,7 +264,6 @@ def docker_image_label(image, label):
     return output
 
 
-@functools.lru_cache(None)
 def docker_imagespec_changed(image, dockerfile):
     """Check if the Dockerfile has changed
 
@@ -274,17 +273,6 @@ def docker_imagespec_changed(image, dockerfile):
     If working with a github actions-built image, check if there is any diff
     between the Dockerfile and base/main
     """
-    base_image = _docker_base(image)
-    if base_image is not None:
-        base_docker_path = os.path.join(IMAGES_DIR, base_image)
-        base_dockerfile = os.path.join(base_docker_path, "Dockerfile")
-        if docker_imagespec_changed(base_image, base_dockerfile):
-            print(
-                "{}: base image spec changed".format(image),
-                file=sys.stderr,
-            )
-            return True
-
     if not docker_image_exists(image):
         # will be downloaded from dockerhub
         build_type = "github_actions"