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Merge pull request #68 from computational-cell-analytics/update_measure_synapses
The script `measure_synapses.py` has been updated and is functional. Other minor fixes have been performed which can be ordered in a later commit.
2 parents 13fe35a + 17a6778 commit 5430b6e

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13 files changed

+426
-13
lines changed

13 files changed

+426
-13
lines changed

‎flamingo_tools/segmentation/synapse_detection.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -175,14 +175,18 @@ def marker_detection(
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if os.path.exists(output_path) and prediction_key in zarr.open(output_path, "r"):
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skip_prediction = True
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# skip prediction if post-processed output exists
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detection_path = os.path.join(output_folder, "synapse_detection.tsv")
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if os.path.exists(detection_path):
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skip_prediction = True
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if not skip_prediction:
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prediction_impl(
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input_path, input_key, output_folder, model_path,
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scale=None, block_shape=block_shape, halo=halo,
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apply_postprocessing=False, output_channels=1,
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)
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detection_path = os.path.join(output_folder, "synapse_detection.tsv")
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if not os.path.exists(detection_path):
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input_ = zarr.open(output_path, "r")[prediction_key]
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detections = find_local_maxima(

‎reproducibility/block_extraction/GEK233L_IHC.json‎

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[
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{
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"cochlea": "G_EK_000233_L",
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"image_channel": [
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"Vglut3",
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"IHC_v6"
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],
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"halo_size": [
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196,
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80
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],
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"crop_centers": [
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],
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],
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[
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],
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[
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],
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[
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1120,
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875,
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]
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]
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}
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]

‎reproducibility/block_extraction/GLR233R_SGN_DA.json‎

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[
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{
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"cochlea": "G_LR_000233_R",
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"image_channel": [
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],
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[
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]
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]
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}
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]

‎reproducibility/block_extraction/GLR233R_SGN_train.json‎

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[
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{
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"cochlea": "G_LR_000233_R",
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"image_channel": [
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"PV",
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"SGN_v2-DA"
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],
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"halo_size": [
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48
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],
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"crop_centers": [
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],
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],
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[
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],
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[
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1603,
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1240,
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]
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]
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}
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]

‎reproducibility/block_extraction/LaVision-M04_SGN.json‎

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[
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{
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"cochlea": "LaVision-M04",
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"image_channel": [
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"PV"
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],
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"resolution" : [
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1.887779,
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1.887779,
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3.0
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],
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"halo_size": [
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64
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],
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"crop_centers": [
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[
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]
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]
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}
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]

‎reproducibility/block_extraction/LaVision_IHC_M04.json‎

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[
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{
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"cochlea": "LaVision-M04",
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"image_channel": [
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"MYO",
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"IHC_LOWRES-v1"
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],
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"resolution" : [
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"halo_size": [
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"crop_centers": [
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[
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]
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]
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}
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]

‎reproducibility/block_extraction/LaVision_OTOF_IHC.json‎

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[
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{
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"cochlea": "LaVision-OTOF23R",
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"image_channel": [
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"IHC_LOWRES-v2"
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],
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"resolution" : [
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"halo_size": [
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],
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[
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]
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]
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},
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{
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"cochlea": "LaVision-OTOF25R",
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"image_channel": [
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"CR",
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"IHC_LOWRES-v2"
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],
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"resolution" : [
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],
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"halo_size": [
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"crop_centers": [
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[
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]
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]
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},
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{
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"cochlea": "LaVision-OTOF36R",
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"image_channel": [
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"CR",
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"IHC_LOWRES-v2"
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],
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"resolution" : [
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],
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"halo_size": [
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],
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"crop_centers": [
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[
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]
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]
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}
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]

‎reproducibility/block_extraction/LaVision_SGN_empty.json‎

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[
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{
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"cochlea": "LaVision-M04",
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"image_channel": [
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"PV"
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],
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"resolution" : [
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"halo_size": [
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"crop_centers": [
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},
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{
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"cochlea": "LaVision-Mar05",
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"image_channel": [
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],
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]
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]
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}
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]

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