463: publish the segmented synthetic Invasion Assay example

README.md

@@ -22,8 +22,8 @@ beside the data, so after loading, Run is the next step.
 
 ## Size
 
-`spacr-example-invasion.tar`: 106,915,840 bytes (107 MB), an uncompressed tar.
-SHA-256 `881e512447079719d0465d31950bb33ed68ccc099ea7a3024e17f787fbb682d2`.
+`spacr-example-invasion.tar`: 106,885,120 bytes (107 MB), an uncompressed tar.
+SHA-256 `135ebf64cf3b5d7c3e77e3b64f73da9cc063bb237e0a41e13c65825ef834714b`.
 
 ## How it was generated
 
@@ -31,12 +31,12 @@ SHA-256 `881e512447079719d0465d31950bb33ed68ccc099ea7a3024e17f787fbb682d2`.
 fields with the lattice, object shapes and noise model of `spacr.qt.synthetic`
 (seeded from well and field, so reproducible byte for byte) and writes each
 field as the merged stack spaCR's Mask module produces: four image planes,
-then cell, nucleus and pathogen label planes. **The label planes are the
-objects the generator drew, not a Cellpose segmentation**: Mask with
-Cellpose-SAM did not finish one plate row in 40 minutes on CPU, and the GPU
-was not available. **spaCR's own Measure module** then measured every field,
-so `measurements.db` holds measured intensities, not the generator's
-numbers. `--segment` on the builder runs Mask instead, for a rebuild on a GPU.
+then cell, nucleus and pathogen label planes. **The label planes are spaCR's own Mask output**
+(Cellpose-SAM on the nucleus, cell and total-parasite channels, run on a GPU
+with `--segment`), so they carry a real segmentation's misses and merges;
+`ground_truth.csv` is still the generator's list of what was drawn. **spaCR's own Measure
+module** then measured every field, so `measurements.db` holds measured
+intensities, not the generator's numbers.
 
 The design is the one the Invasion tutorial's synthetic data used: a
 staining-control column and two conditions with a known mixture of invaded
@@ -67,7 +67,7 @@ has something to get wrong.
 - `measurements/measurements.db` -- Measure's tables (cell, nucleus,
   pathogen, cytoplasm).
 - `merged/` -- the 24 merged stacks: four image planes, then the cell,
-  nucleus and pathogen masks (drawn, see above).
+  nucleus and pathogen masks (segmented by Mask).
 - `ground_truth.csv` -- every parasite the generator drew, with its position,
   host cell and state. Compare the module's calls against it:
 

spacr-example-invasion.tar

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:881e512447079719d0465d31950bb33ed68ccc099ea7a3024e17f787fbb682d2
-size 106915840
+oid sha256:135ebf64cf3b5d7c3e77e3b64f73da9cc063bb237e0a41e13c65825ef834714b
+size 106885120