Add section on cryo-et portal to doc

Author: constantinpape

doc/start_page.md

@@ -124,3 +124,10 @@ Domain adaptation is implemented in `synapse_net.training.domain_adaptation`. Yo
 
 We also provide functionality for 'regular' neural network training. In this case, you have to provide data **and** manual annotations for the structure(s) you want to segment.
 This functionality is implemented in `synapse_net.training.supervised_training`. You can find an example script that shows how to use it [here](https://github.com/computational-cell-analytics/synapse-net/blob/main/examples/network_training.py).
+
+## Segmentation for the CryoET Data Portal
+
+We have published segmentation results for tomograms of synapses stored in the [CryoET Data Portal](https://cryoetdataportal.czscience.com/). So far we have made the following depositions:
+- [CZCDP-10330](https://cryoetdataportal.czscience.com/depositions/10330): Contains synaptic vesicle segmentations for over 50 tomograms of synaptosomes. The segmentations were made with a model domain adapted to the synaptosome tomograms.
+
+The scripts for the submissions can be found in [scripts/cryo/cryo-et-portal](https://github.com/computational-cell-analytics/synapse-net/tree/main/scripts/cryo/cryo-et-portal).

scripts/cryo/cryo-et-portal/.gitignore

@@ -0,0 +1,4 @@
+credentials.portal
+sync_with_s3.sh
+segmentations/
+upload_CZCDP-10330/

scripts/cryo/cryo-et-portal/README.md

@@ -0,0 +1,6 @@
+# Segmentation for the CryoET Data Portal
+
+Scripts to prepare submissions for the [CryoET Data Portal](https://cryoetdataportal.czscience.com).
+
+We have created the following submissions for the portal:
+- [CZCDP-10330](https://cryoetdataportal.czscience.com/depositions/10330): synaptic vesicles segmented in tomograms of synaptosomes.

scripts/cryo/cryo-et-portal/reformat_submission.py

@@ -0,0 +1,29 @@
+import os
+from glob import glob
+from pathlib import Path
+from shutil import move
+
+import cryoet_data_portal as cdp
+from tqdm import tqdm
+
+
+def main():
+    input_folder = "segmentations"
+    output_root = "upload_CZCDP-10330"
+
+    client = cdp.Client()
+
+    tomograms = sorted(glob(os.path.join("segmentations/*.ome.zarr")))
+    for input_file in tqdm(tomograms, desc="Formatting submission"):
+        tomo_id = Path(input_file).stem
+        tomo_id = int(Path(tomo_id).stem)
+
+        tomo = cdp.Tomogram.get_by_id(client, tomo_id)
+        output_folder = os.path.join(output_root, str(tomo.run.dataset_id))
+        os.makedirs(output_folder, exist_ok=True)
+        output_file = os.path.join(output_folder, f"{tomo.run.name}.zarr")
+        move(input_file, output_file)
+
+
+if __name__ == "__main__":
+    main()