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Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples #70

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Merged
akhanf merged 2 commits into from
Feb 19, 2026
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Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples #70

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Debug: imaris_to_ome_zarr tweaks + add KI3 batch2 samples
Feb 19, 2026
cdfa8bc
Delete config/samples_ki3_batch2.tsv
akhanf Feb 19, 2026
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12 changes: 12 additions & 0 deletions config/samples_ki3_batch2.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
subject acq stain_0 stain_1 stain_2 sample_path
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Copilot AI Feb 19, 2026

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The header is missing the 'sample' column that is present in config/samples.tsv and is used throughout the workflow (e.g., workflow/rules/common.smk lines 99, 117, 134 and workflow/scripts/generate_aggregate_qc.py lines 18-19). This will cause KeyError exceptions when the workflow tries to access samples.loc[i, "sample"]. The header should be: subject, sample, acq, stain_0, stain_1, stain_2, sample_path

Suggested change
subject acq stain_0 stain_1 stain_2 sample_path
subject sample acq stain_0 stain_1 stain_2 sample_path

Copilot uses AI. Check for mistakes.
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
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Copilot AI Feb 19, 2026

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All data rows are missing the 'sample' column value. Based on config/samples.tsv, this should be inserted between the 'subject' and 'acq' columns. The existing file uses "brain" as the sample value for similar mouse brain samples. Each row should have a sample value (e.g., "brain") added as the second column.

Suggested change
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
subject sample acq stain_0 stain_1 stain_2 sample_path
AS9F7 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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 brain 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

Copilot uses AI. Check for mistakes.
5 changes: 3 additions & 2 deletions workflow/scripts/imaris_to_ome_zarr.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 = {
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