Merge pull request #147 from fmi-basel/register

Update registration and linking tasks

Author: nrepina

setup.cfg

@@ -58,7 +58,7 @@ where = src
 fractal-tasks =
     anndata
     fractal-tasks-core==1.3.4
-    ngio==0.2.10
+    ngio==0.2.12
 spherical-harmonics =
     pyshtools
 plotting =
@@ -76,6 +76,8 @@ test =
     devtools
 prefect =
     prefect==1.4
+warpfield =
+    warpfield==0.2.0
 
 [options.package_data]
 scmultiplex = __FRACTAL_MANIFEST__.json

src/scmultiplex/__FRACTAL_MANIFEST__.json

@@ -0,0 +1,11 @@
+### Purpose
+- Apply warp map (output of calculate_warpfield_registration) to all channels of moving image.
+
+### Outputs
+- New registered 3D OME-Zarr image that is aligned to reference round
+- This image has same dimensions and placement of linked object regions as reference round
+- Label images and ROI tables are optionally copied to this new image
+
+### Limitations
+- Uses masking ROI tables to load object pairs between reference/moving round
+- Assumes objects have been linked across rounds to have same label id and shape (no padding supported)

src/scmultiplex/dev/task_info/apply_warpfield_registration.md

@@ -0,0 +1,11 @@
+### Purpose
+- Calculate warpfield warp map between reference/moving object pairs in multiplexing rounds
+- GPU-based 3D non-rigid volumetric registration
+- See https://github.com/danionella/warpfield/tree/main
+
+### Outputs
+- Warmap for each moving object, saved in 'registration' folder as .npz file
+
+### Limitations
+- Uses masking ROI tables to load object pairs between reference/moving round
+- Assumes objects have been linked across rounds to have same label id and shape (no padding supported)

src/scmultiplex/dev/task_info/calculate_warpfield_registration.md

@@ -0,0 +1,18 @@
+### Purpose
+- Series of cleanups after running Warpfield registration.
+- Since only moving rounds are registered to a reference, the reference itself needs to be registered (Cleanup 1)
+- Then tables, labels (Cleanup 2) and misc folders (Cleanup 3) can be moved from unregistered rounds to the registered one.
+
+### Outputs
+- Cleanup 1: must be run separately from Cleanup 2 & 3. Submit only unregistered reference zarr on Fractal server.
+        Image data (all channels) from selected ROIs are copied from this reference, e.g. "0_fused" to a new reference
+        image e.g. "0_fused_registered". Inputs should mirror Apply Warpfield Registration task inputs.
+- Cleanup 2: tables and labels from the e.g. "0_fused" unregistered reference round can be copied to the
+        subsequent registered moving rounds e.g. "0_fused_registered", "1_fused_registered", etc.
+        Submit all registered rounds to Fractal server.
+- Cleanup 3: misc folders e.g. ["plots", "registration"] can be copied from the unregistered rounds
+        e.g. "0_fused", "1_fused", etc, to the corresponding registered round e.g.
+        "0_fused_registered", "1_fused_registered", etc. Submit all registered rounds to Fractal server.
+
+### Limitations
+- Assumes 3D image, not tested for 2D

src/scmultiplex/dev/task_info/post_registration_cleanup.md

@@ -0,0 +1,13 @@
+### Purpose
+- Copy and shift 2D or 3D label image from reference round to moving round(s)
+- Shift using pre-calculated x,y,z translations, e.g. from Calculate Linking Consensus task
+- Allows user to propogate segmentation run only on reference round to subsequent rounds, using rough registration
+- Useful for copying over organoid-level segmentation prior to more high-res registration on single-cell level
+
+### Outputs
+- A new **label image** saved as a label in moving rounds with '_shifted' suffix
+- A new corresponding **masking ROI table** saved as `{new_label_name}_ROI_table` in the moving rounds
+
+### Limitations
+- Applies x,y,z translation only
+- Translation must have been saved in a ROI table with columns "translation_z", "translation_y", "translation_x"

src/scmultiplex/dev/task_info/shift_by_shift.md

@@ -19,7 +19,7 @@
 TASK_LIST = [
     CompoundTask(
         name="scMultiplex Calculate Object Linking",
-        executable_init="fractal/_image_based_registration_hcs_init.py",
+        executable_init="fractal/init_select_multiplexing_pairs.py",
         executable="fractal/calculate_object_linking.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -30,7 +30,7 @@
     ),
     CompoundTask(
         name="scMultiplex Calculate Linking Consensus",
-        executable_init="fractal/_init_group_by_well_for_multiplexing.py",
+        executable_init="fractal/init_select_reference_knowing_all.py",
         executable="fractal/calculate_linking_consensus.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -41,7 +41,7 @@
     ),
     CompoundTask(
         name="scMultiplex Relabel by Linking Consensus",
-        executable_init="fractal/_image_based_registration_hcs_allrounds_init.py",
+        executable_init="fractal/init_select_all_knowing_reference.py",
         executable="fractal/relabel_by_linking_consensus.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 64000},
@@ -52,7 +52,7 @@
     ),
     CompoundTask(
         name="scMultiplex Calculate Platymatch Registration",
-        executable_init="fractal/_image_based_registration_hcs_init.py",
+        executable_init="fractal/init_select_multiplexing_pairs.py",
         executable="fractal/calculate_platymatch_registration.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -63,7 +63,7 @@
     ),
     CompoundTask(
         name="scMultiplex Surface Mesh Multiscale",
-        executable_init="fractal/_init_group_by_well_for_multiplexing.py",
+        executable_init="fractal/init_select_reference_knowing_all.py",
         executable="fractal/surface_mesh_multiscale.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -85,7 +85,7 @@
     ),
     CompoundTask(
         name="scMultiplex Spherical Harmonics from Label Image",
-        executable_init="fractal/_init_group_by_well_for_multiplexing.py",
+        executable_init="fractal/init_select_reference_knowing_all.py",
         executable="fractal/spherical_harmonics_from_labelimage.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -96,7 +96,7 @@
     ),
     CompoundTask(
         name="scMultiplex Mesh Measurements",
-        executable_init="fractal/_init_group_by_well_for_multiplexing.py",
+        executable_init="fractal/init_select_reference_knowing_all.py",
         executable="fractal/scmultiplex_mesh_measurements.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -123,7 +123,7 @@
     ),
     CompoundTask(
         name="scMultiplex Calculate Z-Illumination Correction",
-        executable_init="fractal/init_select_multiplexing_round.py",
+        executable_init="fractal/init_select_single_round.py",
         executable="fractal/calculate_z_illumination_correction.py",
         meta_init={"cpus_per_task": 1, "mem": 1000},
         meta={"cpus_per_task": 4, "mem": 16000},
@@ -190,4 +190,53 @@
         tags=["3D"],
         docs_info="file:task_info/cleanup_3d_child_labels.md",
     ),
+    CompoundTask(
+        name="scMultiplex Shift by Shift",
+        executable_init="fractal/init_select_multiplexing_pairs.py",
+        executable="fractal/shift_by_shift.py",
+        meta_init={"cpus_per_task": 1, "mem": 1000},
+        meta={"cpus_per_task": 4, "mem": 16000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "2D", "3D"],
+        docs_info="file:task_info/shift_by_shift.md",
+    ),
+    CompoundTask(
+        name="scMultiplex Calculate Warpfield Registration",
+        executable_init="fractal/init_select_multiplexing_pairs.py",
+        executable="fractal/calculate_warpfield_registration.py",
+        meta_init={"cpus_per_task": 1, "mem": 1000},
+        meta={"cpus_per_task": 4, "mem": 16000, "needs_gpu": True},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "3D"],
+        docs_info="file:task_info/calculate_warpfield_registration.md",
+        input_types=dict(is_3D=True),
+    ),
+    CompoundTask(
+        name="scMultiplex Apply Warpfield Registration",
+        executable_init="fractal/init_select_multiplexing_pairs.py",
+        executable="fractal/apply_warpfield_registration.py",
+        meta_init={"cpus_per_task": 1, "mem": 1000},
+        meta={"cpus_per_task": 4, "mem": 16000, "needs_gpu": True},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "3D"],
+        docs_info="file:task_info/apply_warpfield_registration.md",
+        input_types=dict(registered=False, is_3D=True),
+        output_types=dict(registered=True, is_3D=True),
+    ),
+    CompoundTask(
+        name="scMultiplex Post Registration Cleanup",
+        executable_init="fractal/init_select_all_knowing_reference.py",
+        executable="fractal/post_registration_cleanup.py",
+        meta_init={"cpus_per_task": 1, "mem": 1000},
+        meta={"cpus_per_task": 4, "mem": 16000},
+        category="Registration",
+        modality="HCS",
+        tags=["multiplexing", "3D"],
+        docs_info="file:task_info/post_registration_cleanup.md",
+        input_types=dict(is_3D=True),
+        output_types=dict(registered=True, is_3D=True),
+    ),
 ]