From a08873aa31a0489d6dfcdc34f323e8b05671c68d Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Fri, 19 Jun 2026 19:01:51 +0200 Subject: [PATCH 1/3] adjust mem --- src/datasets/loaders/bruker_cosmx/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/loaders/bruker_cosmx/config.vsh.yaml b/src/datasets/loaders/bruker_cosmx/config.vsh.yaml index 5fd748df..2fee3340 100644 --- a/src/datasets/loaders/bruker_cosmx/config.vsh.yaml +++ b/src/datasets/loaders/bruker_cosmx/config.vsh.yaml @@ -76,4 +76,4 @@ runners: - type: executable - type: nextflow directives: - label: [midmem, midcpu, hightime] + label: [highmem, midcpu, hightime] From 5a3814041356153bf56b1c8faed0f87979422c75 Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Sat, 20 Jun 2026 09:03:04 +0200 Subject: [PATCH 2/3] fix FOVs --- src/datasets/loaders/allen_brain_cell_atlas_merfish/script.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/datasets/loaders/allen_brain_cell_atlas_merfish/script.py b/src/datasets/loaders/allen_brain_cell_atlas_merfish/script.py index 1469e2c4..01afc383 100644 --- a/src/datasets/loaders/allen_brain_cell_atlas_merfish/script.py +++ b/src/datasets/loaders/allen_brain_cell_atlas_merfish/script.py @@ -344,7 +344,9 @@ def um_to_px_y(y): fov_img = fov_img[:, OVERLAP_SIZE:, :] xp += OVERLAP_SIZE - complete_img[:, xp:xp + fov_img.shape[1], yp:yp + fov_img.shape[2]] = fov_img + h = min(fov_img.shape[1], complete_img.shape[1] - xp) + w = min(fov_img.shape[2], complete_img.shape[2] - yp) + complete_img[:, xp:xp + h, yp:yp + w] = fov_img[:, :h, :w] if fov % 10 == 0: delete_dax_files() From 737e51f1fa9a997592aff5c33e4f794521a518e6 Mon Sep 17 00:00:00 2001 From: dariarom94 Date: Sat, 20 Jun 2026 09:04:47 +0200 Subject: [PATCH 3/3] fix mem config --- .../loaders/allen_brain_cell_atlas_merfish/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/loaders/allen_brain_cell_atlas_merfish/config.vsh.yaml b/src/datasets/loaders/allen_brain_cell_atlas_merfish/config.vsh.yaml index 8c7a249a..70061623 100644 --- a/src/datasets/loaders/allen_brain_cell_atlas_merfish/config.vsh.yaml +++ b/src/datasets/loaders/allen_brain_cell_atlas_merfish/config.vsh.yaml @@ -91,4 +91,4 @@ runners: - type: executable - type: nextflow directives: - label: [midmem, midcpu, hightime] + label: [highmem, midcpu, hightime]