From f92971841c0f8315b9f6dcd15920af5d1e0331db Mon Sep 17 00:00:00 2001 From: clemsgrs Date: Thu, 8 Jan 2026 12:29:42 +0000 Subject: [PATCH] Bump version to 2.0.1 --- pyproject.toml | 2 +- setup.cfg | 2 +- slide2vec/__init__.py | 2 +- slide2vec/configs/conch.yaml | 29 ++++++++++++++++++++++++----- 4 files changed, 27 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 56d04d7..57f56a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ warn_unused_configs = true no_implicit_reexport = true [tool.bumpver] -current_version = "2.0.0" +current_version = "2.0.1" 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 diff --git a/setup.cfg b/setup.cfg index 7b17bd6..7f7b10e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = slide2vec -version = 2.0.0 +version = 2.0.1 description = Embedding of whole slide images with Foundation Models author = Clément Grisi platforms = unix, linux, osx, cygwin, win32 diff --git a/slide2vec/__init__.py b/slide2vec/__init__.py index 1e97492..010388e 100644 --- a/slide2vec/__init__.py +++ b/slide2vec/__init__.py @@ -1,4 +1,4 @@ -__version__ = "2.0.0" +__version__ = "2.0.1" import sys import os diff --git a/slide2vec/configs/conch.yaml b/slide2vec/configs/conch.yaml index ce4ae76..e97d1ef 100644 --- a/slide2vec/configs/conch.yaml +++ b/slide2vec/configs/conch.yaml @@ -1,6 +1,7 @@ -csv: "/data/temporary/clement/discern/multi-organ-1k.csv" # path to csv containing slide paths +# csv: "/data/temporary/clement/discern/multi-organ-1k.csv" +csv: "/data/pathology/projects/clement/discern/multi-center-prostate-no-mask.csv" -output_dir: "/data/temporary/clement/discern/slide2vec" # output directory +output_dir: "/data/pathology/projects/clement/discern/hs2p" # output directory visualize: true @@ -8,18 +9,36 @@ tiling: params: spacing: 0.5 # spacing at which to tile the slide, in microns per pixel tile_size: 448 # 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) + seg_params: + downsample: 16 # find the closest downsample in the slide for tissue segmentation + filter_params: + ref_tile_size: 448 # reference tile size at spacing tiling.spacing + a_t: 16 # area filter threshold for tissue ; positive integer, the minimum size of detected foreground contours to consider, relative to the reference tile size ref_tile_size + # e.g. a value 10 means only detected foreground contours of size greater than 10 [ref_tile_size, ref_tile_size] tiles at spacing tiling.spacing will be kept + a_h: 4 # area filter threshold for holes ; positive integer, the minimum size of detected holes/cavities in foreground contours to avoid, once again relative to the reference tile size ref_tile_size + max_n_holes: 8 # maximum of holes to consider per detected foreground contours (positive integer, higher values lead to more accurate patching but increase computational cost ; keeps the biggest holes) + filter_white: true # whether to filter out mostly white tiles + filter_black: true # whether to filter out mostly black tiles + white_threshold: 220 # threshold for white pixels (0-255) + black_threshold: 25 # threshold for black pixels (0-255) + fraction_threshold: 0.9 # fraction of pixels that must be white/black to filter out the tile model: level: "tile" # level at which to extract the features ("tile", "region" or "slide") name: "conch" - batch_size: 32 + batch_size: 64 speed: fp16: true # use mixed precision during model inference + num_workers: 16 # number of workers for tiling slides + num_workers_embedding: 16 # number of workers for data loading when embedding slides wandb: enable: true project: "discern" username: "clemsg" - exp_name: "features" - tags: ["features", "${model.name}", "${model.level}", "${tiling.params.tile_size}"] + exp_name: "tiling" + # exp_name: "features" + tags: ["tiling", "${tiling.params.tile_size}"] + # tags: ["features", "${model.name}", "${model.level}", "${tiling.params.tile_size}"]