Add readme and fix dependencies

Author: constantinpape

environment.yaml

@@ -6,6 +6,7 @@ channels:
 
 dependencies:
   - cpuonly
+  - cluster_tools
   - scikit-image
   - pybdv
   - pytorch

scripts/ome_challenge/README.md

@@ -0,0 +1,6 @@
+# OME-Challenge
+
+Scripts for converting flamingo data for the [OME-NGFF-Challenge](https://forum.image.sc/t/ome2024-ngff-challenge/97363):
+- `convert_data.py`: to convert the data from the flamingo tif format to ome-zarr-v3 (via ome-zarr-v2 and the challenge converter tool)
+- `create_metadata.py`: to add additional top-level metadata to keep track of the different tiles, timepoints etc.
+- `upload_data.py`: to upload the data to s3 (needs credentials not stored in this repository)