diff --git a/Dockerfile.dataset_submissions b/Dockerfile.dataset_submissions
index 75bc557f3168..89ecf4b464b5 100644
--- a/Dockerfile.dataset_submissions
+++ b/Dockerfile.dataset_submissions
@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.9
+FROM public.ecr.aws/lambda/python:3.12
 
 # Update AWS root Certificates
 ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem
diff --git a/Dockerfile.upload_failures b/Dockerfile.upload_failures
index 7c8c70496df7..6a7dd3b2e357 100644
--- a/Dockerfile.upload_failures
+++ b/Dockerfile.upload_failures
@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.8
+FROM public.ecr.aws/lambda/python:3.12
 
 # Update AWS root Certificates
 ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem
diff --git a/Dockerfile.upload_success b/Dockerfile.upload_success
index a0da68b1991d..43566c4f274a 100644
--- a/Dockerfile.upload_success
+++ b/Dockerfile.upload_success
@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.8
+FROM public.ecr.aws/lambda/python:3.12
 
 # Update AWS root Certificates
 ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem
diff --git a/python_dependencies/processing/requirements.txt b/python_dependencies/processing/requirements.txt
index 3001fe45b984..e46793bec85b 100644
--- a/python_dependencies/processing/requirements.txt
+++ b/python_dependencies/processing/requirements.txt
@@ -1,24 +1,24 @@
-anndata==0.10.8
+anndata==0.10.9
 awscli
 boto3>=1.11.17
 botocore>=1.14.17
 cellxgene-schema
 dataclasses-json
-ddtrace==2.1.4
-numba==0.59.1
-numpy<2
+ddtrace==2.14.2
+numba==0.60.0
+numpy<3
 pandas>2,<3
 psutil>=5.9.0
 psycopg2-binary==2.*
 pyarrow>=1.0
 pydantic>=1.9.0
 python-json-logger
-pyvips==2.2.2
+pyvips==2.2.3
 requests>=2.22.0
 rpy2==3.5.16
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
-s3fs==0.4.2
-scanpy==1.9.8
+s3fs==2024.9.0
+scanpy==1.10.3
 SQLAlchemy==2.*
 tenacity
-tiledb==0.25.0  # Portal's tiledb version should always be the same or older than Explorer's
+tiledb==0.32.3  # Portal's tiledb version should always be the same or older than Explorer's