Release v1.4.0

pyproject.toml

@@ -23,7 +23,7 @@ warn_unused_configs = true
 no_implicit_reexport = true
 
 [tool.bumpver]
-current_version = "1.3.0"
+current_version = "1.4.0"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false       # We do version bumping in CI, not as a commit
 tag = false          # Git tag already exists — we don't auto-tag

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = slide2vec
-version = 1.3.0
+version = 1.4.0
 description = Embedding of whole slide images with Foundation Models
 author = Clément Grisi
 platforms = unix, linux, osx, cygwin, win32

slide2vec/__init__.py

@@ -1 +1 @@
-__version__ = "1.3.0"
+__version__ = "1.4.0"

slide2vec/configs/conch.yaml

@@ -1,4 +1,4 @@
-csv: # path to csv containing slide paths
+csv: "/data/temporary/clement/notebooks/discern/prostate-bladder-breast-debug.csv" # path to csv containing slide paths
 
 output_dir: "output" # output directory
 
@@ -15,4 +15,11 @@ model:
   batch_size: 1
 
 speed:
-  fp16: true # use mixed precision during model inference
+  fp16: true # use mixed precision during model inference
+
+wandb:
+  enable: true
+  project: "discern"
+  username: "clemsg"
+  exp_name: "features"
+  tags: ["features", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]

slide2vec/configs/default.yaml

@@ -41,7 +41,7 @@ model:
   mode: "cls" # embedding mode ["cls", "full"]
   arch: # architecture of custom model
   pretrained_weights: # path to the pretrained weights when using a custom model
-  batch_size: 1
+  batch_size: 256
   tile_size: ${tiling.params.tile_size}
   patch_size: 256 # if level is "region", size used to unroll the region into patches
   save_tile_embeddings: false # whether to save tile embeddings alongside the pooled slide embedding when level is "slide"

slide2vec/configs/virchow2.yaml

@@ -1,24 +1,21 @@
 # csv: "/data/temporary/clement/dataset/tcga-prad/mutations/tcga-prad-tp53-slide2vec.csv"
 # csv: "/data/temporary/clement/dataset/tcga-blca/mutations/tcga-blca-tp53-slide2vec.csv"
 # csv: "/data/temporary/clement/dataset/tcga-brca/mutations/tcga-brca-tp53-slide2vec.csv"
-csv: "/data/temporary/clement/leopard/csvs/dev-slide2vec.csv"
+csv: "/data/temporary/clement/leopard/csvs/brazil-slide2vec-august-2025-revision.csv"
 
-output_dir: "output"
+output_dir: "/data/temporary/clement/code/slide2vec/output"
 
 visualize: true
 
 tiling:
   # read_coordinates_from: "/data/temporary/clement/code/slide2vec/output/vjh3hrr6/coordinates"
   params:
     spacing: 0.5 # spacing at which to tile the slide, in microns per pixel
-    # tolerance: 0.07 # tolerance for matching the spacing (float between 0 and 1, deciding how much the spacing can deviate from the one specified in the slide metadata)
     tolerance: 0.05 # tolerance for matching the spacing (float between 0 and 1, deciding how much the spacing can deviate from the one specified in the slide metadata)
     tile_size: 2048 # size of the tiles to extract, in pixels
-    # min_tissue_percentage: 0.1 # threshold used to filter out tiles that have less tissue than this value (percentage)
-    min_tissue_percentage: 0.01 # threshold used to filter out tiles that have less tissue than this value (percentage)
+    min_tissue_percentage: 0.1 # threshold used to filter out tiles that have less tissue than this value (percentage)
   filter_params:
-    # ref_tile_size: 224
-    ref_tile_size: 16
+    ref_tile_size: 256
 
 model:
   level: "region"
@@ -29,10 +26,10 @@ speed:
   fp16: true
 
 wandb:
-  enable: false
-  project: "mut-pred"
+  enable: true
+  project: "leopard"
   username: "clemsg"
   exp_name: "features"
-  tags: ["features", "tcga-prad", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]
+  tags: ["features", "brazil", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]
   # tags: ["features", "tcga-blca", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]
-  # tags: ["features", "tcga-brca", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]
+  # tags: ["features", "tcga-brca", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]