From 073e45bce1f8031e80c59a9637289ef98233fd45 Mon Sep 17 00:00:00 2001 From: apooladi Date: Thu, 19 Feb 2026 01:35:56 -0500 Subject: [PATCH 1/2] Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples --- config/samples_ki3_batch2.tsv | 12 ++++++++++++ workflow/scripts/imaris_to_ome_zarr.py | 5 +++-- 2 files changed, 15 insertions(+), 2 deletions(-) create mode 100644 config/samples_ki3_batch2.tsv diff --git a/config/samples_ki3_batch2.tsv b/config/samples_ki3_batch2.tsv new file mode 100644 index 0000000..e0d3763 --- /dev/null +++ b/config/samples_ki3_batch2.tsv @@ -0,0 +1,12 @@ +subject acq stain_0 stain_1 stain_2 sample_path +AS9F7 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/A_AS9F7/16-51-02_a-AS9F7 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims +AS11F4 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/B_AS11F4/22-49-58_b-AS11F4 IK3 PBS IBA1 647 ab RedX CD31 488 4X1 stitched.ims +AS37F30 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/C_AS37F30/07-04-14_c-AS37F30 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims +AS8M1 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/D_AS8M1/15-34-54_d AS8M1 IK3 PBS IBA1 647 ab RedX CD31 488 1X1_Blaze_C00.ome.ims +AS8M4 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/E_AS8M4/21-43-06_e AS8M4 IK3 PBS IBA1 647 ab RedX CD31 488 1X1_Blaze_C02.ome.ims +AS7F2 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/F_AS7F2/16-54-24_f AS7F2 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims +AS11F1e imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/G_AS11F1e/23-36-04_g AS11F1e IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims +AS11F3 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/H_AS11F3/06-11-22_h AS11F3 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims +AS39Me0 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/J_AS39Me0/12-43-19_j as39me0 (54) ik3 lecanemab iba1 647 ab redx cd31 488 4x1stitched.ims +AS7F1 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/K_AS7F1/k AS 7 F1 IK3 neg ctrl BA1 647 ab RedX CD31 488 4X1 stitched.ims +AS39Me2 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/i_AS39Me2/i AS39Me2 IK3 lecanemab IBA1 647 ab RedX CD31 488 4X1 stitched.ims diff --git a/workflow/scripts/imaris_to_ome_zarr.py b/workflow/scripts/imaris_to_ome_zarr.py index 7440083..bc8e6a0 100644 --- a/workflow/scripts/imaris_to_ome_zarr.py +++ b/workflow/scripts/imaris_to_ome_zarr.py @@ -92,8 +92,9 @@ darr_list = [] for zarr_i, in_zarr in enumerate(snakemake.input.zarr): # open zarr to get group name - zi = zarr.open(in_zarr) - darr_list.append(da.from_zarr(in_zarr, component="Data").rechunk(rechunk_size)) + in_store = zarr.ZipStore(in_zarr, mode="r") + zi = zarr.open(in_store, mode="r") + darr_list.append(da.from_zarr(in_store, component="Data").rechunk(rechunk_size)) # append to omero metadata channel_metadata = { From cdfa8bc8e2a2cf86029d92d75340d25076fb5e3f Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Thu, 19 Feb 2026 13:50:39 -0500 Subject: [PATCH 2/2] Delete config/samples_ki3_batch2.tsv --- config/samples_ki3_batch2.tsv | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 config/samples_ki3_batch2.tsv diff --git a/config/samples_ki3_batch2.tsv b/config/samples_ki3_batch2.tsv deleted file mode 100644 index e0d3763..0000000 --- a/config/samples_ki3_batch2.tsv +++ /dev/null @@ -1,12 +0,0 @@ -subject acq stain_0 stain_1 stain_2 sample_path -AS9F7 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/A_AS9F7/16-51-02_a-AS9F7 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims -AS11F4 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/B_AS11F4/22-49-58_b-AS11F4 IK3 PBS IBA1 647 ab RedX CD31 488 4X1 stitched.ims -AS37F30 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/C_AS37F30/07-04-14_c-AS37F30 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims -AS8M1 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/D_AS8M1/15-34-54_d AS8M1 IK3 PBS IBA1 647 ab RedX CD31 488 1X1_Blaze_C00.ome.ims -AS8M4 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/E_AS8M4/21-43-06_e AS8M4 IK3 PBS IBA1 647 ab RedX CD31 488 1X1_Blaze_C02.ome.ims -AS7F2 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/F_AS7F2/16-54-24_f AS7F2 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims -AS11F1e imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/G_AS11F1e/23-36-04_g AS11F1e IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims -AS11F3 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/H_AS11F3/06-11-22_h AS11F3 IK3 PBS IBA1 647 ab RedX CD31 488 4X1_Blaze_C00.ome.ims -AS39Me0 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/J_AS39Me0/12-43-19_j as39me0 (54) ik3 lecanemab iba1 647 ab redx cd31 488 4x1stitched.ims -AS7F1 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/K_AS7F1/k AS 7 F1 IK3 neg ctrl BA1 647 ab RedX CD31 488 4X1 stitched.ims -AS39Me2 imaris4x IBA1 Abeta CD31 /nfs/trident3/lightsheet/prado/mouse_app_lecanemab_ki3_batch2/raw/ims_4x_stitched/i_AS39Me2/i AS39Me2 IK3 lecanemab IBA1 647 ab RedX CD31 488 4X1 stitched.ims