From 3fcc96934cdcde67dec4ef3ed31c58829d8c1f21 Mon Sep 17 00:00:00 2001 From: Qin Yu Date: Tue, 6 Feb 2024 20:24:20 +0100 Subject: [PATCH] Rename generic plant nuclear model, fix #192 Also remove `confocal_3D_unet_ovules_nuclei_ds1x` as requested by Athul. --- plantseg/resources/models_zoo.yaml | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/plantseg/resources/models_zoo.yaml b/plantseg/resources/models_zoo.yaml index 7beb2deb..981af22a 100644 --- a/plantseg/resources/models_zoo.yaml +++ b/plantseg/resources/models_zoo.yaml @@ -57,15 +57,6 @@ confocal_2D_unet_ovules_ds2x: recommended_patch_size: [1, 256, 256] output_type: "boundaries" -confocal_3D_unet_ovules_nuclei_ds1x: - model_url: https://zenodo.org/record/7774321/files/confocal_3D_unet_ovules_nuclei_ds1x.pytorch - resolution: [0.35, 0.1, 0.1] - description: "Unet trained on confocal images of Arabidopsis Ovules nuclei stain on original resolution with BCEDiceLoss. The network predicts 1 channel: nuclei probability maps" - dimensionality: "3D" - modality: "confocal" - recommended_patch_size: [80, 160, 160] - output_type: "nuclei" - ## Root lightsheet_3D_unet_root_ds1x: model_url: https://zenodo.org/record/7765026/files/unet3d-lateral-root-lightsheet-ds1x.pytorch @@ -159,11 +150,11 @@ confocal_3D_unet_mouse_embryo_nuclei: recommended_patch_size: [40, 220, 220] output_type: "nuclei" -generic_plant_nuclei_3D: +PlantSeg_3Dnuc_platinum: model_url: https://zenodo.org/records/10070349/files/FOR2581_PlantSeg_Plant_Nuclei_3D.pytorch resolution: [0.2837 0.1268 0.1268] description: "A generic 3D U-Net trained to predict the nuclei and their boundaries in plant. Voxel size: (0.1268×0.1268×0.2837 µm^3) (XYZ)" dimensionality: "3D" modality: "confocal" - recommended_patch_size: [80, 160, 160] + recommended_patch_size: [128, 256, 256] output_type: "nuclei"