From 8395f344e369dcd4be76070d3e12d989075bedf8 Mon Sep 17 00:00:00 2001 From: aemmav <167151011+aemmav@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:21:53 -0400 Subject: [PATCH 1/3] Update README.md with more cellpose models --- src/cellmap_models/pytorch/cellpose/README.md | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/src/cellmap_models/pytorch/cellpose/README.md b/src/cellmap_models/pytorch/cellpose/README.md index 9426de6..4b2db52 100644 --- a/src/cellmap_models/pytorch/cellpose/README.md +++ b/src/cellmap_models/pytorch/cellpose/README.md @@ -10,22 +10,51 @@ This directory contains scripts for downloading finetuned Cellpose models, parti **jrc_mus-epididymis-2_nuc_cp:** +**jrc_mus-granule-neurons-1_nuc_cp:** Cellpose was trained on nuclei from 12 2D slices from jrc_mus-granule-neurons-1. + +**jrc_mus-granule-neurons-2_nuc_cp:** Cellpose was trained on nuclei from 10 2D slices from jrc_mus-granule-neurons-2. + +**jrc_mus-granule-neurons-3_nuc_cp:** Cellpose was trained on nuclei from 21 2D slices from jrc_mus-granule-neurons-3. + +**jrc_mus-guard-hair-follicle_nuc_cp:** Cellpose was trained on nuclei from 22 2D slices from jrc_mus-guard-hair-follicle. + **jrc_mus-heart-1_ecs_cp:** **jrc_mus-heart-1_nuc_cp:** **jrc_mus-hippocampus-1_nuc_cp:** +**jrc_mus-kidney_nuc_cp:** Cellpose was trained on nuclei from 28 2D slices from jrc_mus-kidney. + +**jrc_mus-kidney-2_nuc_cp:** Cellpose was trained on nuclei from 38 2D slices from jrc_mus-kidney-2. + **jrc_mus-kidney-3_nuc_cp:** +**jrc_mus-liver-2_nuc_cp:** Cellpose was trained on nuclei from 29 2D slices from jrc_mus-liver-2. + **jrc_mus-liver-3_nuc_cp:** +**jrc_mus-meisnner-corpuscle-1_nuc_cp:** Cellpose was trained on nuclei from 21 2D slices from jrc_mus-meisnner-corpuscle-1. + +**jrc_mus-meisnner-corpuscle-2_nuc_cp:** Cellpose was trained on nuclei from 27 2D slices from jrc_mus-meisnner-corpuscle-2. + +**jrc_mus-pacinian-corpuscle_nuc_cp:** Cellpose was trained on nuclei from 31 2D slices from jrc_mus-pacinian-corpuscle. + +**jrc_mus-pancreas-1_nuc_cp:** Cellpose was trained on nuclei from 34 2D slices from jrc_mus-pancreas-1. + +**jrc_mus-pancreas-2_nuc_cp:** Cellpose was trained on nuclei from 30 2D slices from jrc_mus-pancreas-2. + +**jrc_mus-pancreas-3_nuc_cp:** Cellpose was trained on nuclei from 4 2D slices from jrc_mus-pancreas-3. + **jrc_mus-pancreas-4_nuc_cp:** Cellpose was trained on nuclei from 17 2D slices from jrc_mus-pancreas-4. **jrc_mus-skin-1_nuc_cp:** **jrc_mus-thymus-1_nuc_cp:** +### Trained on fly tissues +**jrc_fly-mb-z0419-20:** Cellpose was trained on nuclei from 32 2D slices from jrc_fly-mb-z0419-20. + ## Usage Once you have chosen a model based on the descriptions above, you can download its weights from the `cellmap-models` repository and use them as described below: From 091ba7ad305f45561dc1f92e2be1092c3d063c3e Mon Sep 17 00:00:00 2001 From: aemmav <167151011+aemmav@users.noreply.github.com> Date: Mon, 5 Aug 2024 09:50:00 -0400 Subject: [PATCH 2/3] Update __init__.py added cellpose datasets to models_dict --- src/cellmap_models/pytorch/cellpose/__init__.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/cellmap_models/pytorch/cellpose/__init__.py b/src/cellmap_models/pytorch/cellpose/__init__.py index 97a9ec5..5e42a41 100644 --- a/src/cellmap_models/pytorch/cellpose/__init__.py +++ b/src/cellmap_models/pytorch/cellpose/__init__.py @@ -4,13 +4,27 @@ from .download_checkpoint import download_checkpoint models_dict = { + "jrc_fly-mb-z0419-20_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_fly-mb-z0419-20_nuc_cp", "jrc_mus-epididymis-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-1_nuc_cp", "jrc_mus-epididymis-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-2_nuc_cp", + "jrc_mus-granule-neurons-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-1_nuc_cp", + "jrc_mus-granule-neurons-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-2_nuc_cp", + "jrc_mus-granule-neurons-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-3_nuc_cp", + "jrc_mus-guard-hair-follicle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-guard-hair-follicle_nuc_cp", "jrc_mus-heart-1_ecs_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_ecs_cp", "jrc_mus-heart-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_nuc_cp", "jrc_mus-hippocampus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-hippocampus-1_nuc_cp", + "jrc_mus-kidney_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney_nuc_cp", + "jrc_mus-kidney-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-2_nuc_cp", "jrc_mus-kidney-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-3_nuc_cp", + "jrc_mus-liver-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-liver-2_nuc_cp", "jrc_mus-liver-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-liver-3_nuc_cp", + "jrc_mus-meissner-corpuscle-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-meissner-corpuscle-1_nuc_cp", + "jrc_mus-meissner-corpuscle-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-meissner-corpuscle-2_nuc_cp", + "jrc_mus-pacinian-corpuscle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pacinian-corpuscle_nuc_cp", + "jrc_mus-pancreas_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas_nuc_cp", + "jrc_mus-pancreas-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-2_nuc_cp", + "jrc_mus-pancreas-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-3_nuc_cp", "jrc_mus-pancreas-4_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-4_nuc_cp", "jrc_mus-skin-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-skin-1_nuc_cp", "jrc_mus-thymus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-thymus-1_nuc_cp", From 8f047c6d7549888277ab16bf76bb692fd20524de Mon Sep 17 00:00:00 2001 From: Emma Avetissian <167151011+aemmav@users.noreply.github.com> Date: Tue, 6 Aug 2024 10:57:55 -0400 Subject: [PATCH 3/3] Update __init__.py edited links to be accurate --- .../pytorch/cellpose/__init__.py | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/cellmap_models/pytorch/cellpose/__init__.py b/src/cellmap_models/pytorch/cellpose/__init__.py index 5e42a41..153f67f 100644 --- a/src/cellmap_models/pytorch/cellpose/__init__.py +++ b/src/cellmap_models/pytorch/cellpose/__init__.py @@ -4,27 +4,27 @@ from .download_checkpoint import download_checkpoint models_dict = { - "jrc_fly-mb-z0419-20_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_fly-mb-z0419-20_nuc_cp", + "jrc_fly-mb-z0419-20_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_fly-mb-z0419-20_nuc_cp", "jrc_mus-epididymis-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-1_nuc_cp", "jrc_mus-epididymis-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-epididymis-2_nuc_cp", - "jrc_mus-granule-neurons-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-1_nuc_cp", - "jrc_mus-granule-neurons-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-2_nuc_cp", - "jrc_mus-granule-neurons-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-granule-neurons-3_nuc_cp", - "jrc_mus-guard-hair-follicle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-guard-hair-follicle_nuc_cp", + "jrc_mus-granule-neurons-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-1_nuc_cp", + "jrc_mus-granule-neurons-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-2_nuc_cp", + "jrc_mus-granule-neurons-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-granule-neurons-3_nuc_cp", + "jrc_mus-guard-hair-follicle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-guard-hair-follicle_nuc_cp", "jrc_mus-heart-1_ecs_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_ecs_cp", "jrc_mus-heart-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-heart-1_nuc_cp", "jrc_mus-hippocampus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-hippocampus-1_nuc_cp", - "jrc_mus-kidney_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney_nuc_cp", - "jrc_mus-kidney-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-2_nuc_cp", + "jrc_mus-kidney_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-kidney_nuc_cp", + "jrc_mus-kidney-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-kidney-2_nuc_cp", "jrc_mus-kidney-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-kidney-3_nuc_cp", - "jrc_mus-liver-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-liver-2_nuc_cp", + "jrc_mus-liver-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-liver-2_nuc_cp", "jrc_mus-liver-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-liver-3_nuc_cp", - "jrc_mus-meissner-corpuscle-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-meissner-corpuscle-1_nuc_cp", - "jrc_mus-meissner-corpuscle-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-meissner-corpuscle-2_nuc_cp", - "jrc_mus-pacinian-corpuscle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pacinian-corpuscle_nuc_cp", - "jrc_mus-pancreas_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas_nuc_cp", - "jrc_mus-pancreas-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-2_nuc_cp", - "jrc_mus-pancreas-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-3_nuc_cp", + "jrc_mus-meissner-corpuscle-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-meissner-corpuscle-1_nuc_cp", + "jrc_mus-meissner-corpuscle-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-meissner-corpuscle-2_nuc_cp", + "jrc_mus-pacinian-corpuscle_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06jrc_mus-pacinian-corpuscle_nuc_cp", + "jrc_mus-pancreas-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-1_nuc_cp", + "jrc_mus-pancreas-2_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-2_nuc_cp", + "jrc_mus-pancreas-3_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.08.06/jrc_mus-pancreas-3_nuc_cp", "jrc_mus-pancreas-4_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-pancreas-4_nuc_cp", "jrc_mus-skin-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-skin-1_nuc_cp", "jrc_mus-thymus-1_nuc_cp": "https://github.com/janelia-cellmap/cellmap-models/releases/download/2024.03.08/jrc_mus-thymus-1_nuc_cp",