Concatenate with OME-Zarr v0.5 and sharding

biahub/concatenate.py

@@ -365,7 +365,7 @@ def concatenate(
     # Estimate resources
     batch_size = settings.shards_ratio[0] if settings.shards_ratio else 1
     num_cpus, gb_ram_per_cpu = estimate_resources(
-        shape=(T // batch_size, C, Z, Y, X), ram_multiplier=4 * batch_size, max_num_cpus=48
+        shape=(T // batch_size, C, Z, Y, X), ram_multiplier=4 * batch_size, max_num_cpus=16
     )
     # Prepare SLURM arguments
     slurm_args = {

pyproject.toml

@@ -47,11 +47,16 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-# note that dev dependencies are only pinned to major versions
-segmentation = ["cellpose"]
-sharding = ["tensorstore"]
+segment = ["cellpose"]
+
+track = ["ultrack @ git+https://github.com/royerlab/ultrack.git@v0.6.3"]
+
+shard = ["tensorstore"]
+
 build = ["build", "twine"]
-all = ["biahub[segmentation,sharding,build]"]
+
+all = ["biahub[segment,track,shard,build]"]
+
 dev = [
   "biahub[all]",
   "black==25.1",