isoview 0.1.6

Multi-view light sheet microscopy image processing pipeline

IsoView Light Sheet Microscopy Pipeline

Input is a flat directory of raw SPC##_TM#####_ANG###_CM#_CHN##_PH#.stack files (little-endian uint16) with a push_config XML per channel describing the acquisition (dimensions, pixel/axial spacing, wavelength, exposure, stage, etc.).

Quickstart

1. Point input_dir in pipeline/correct_stack.py at your raw data directory.
2. Run pipeline/correct_stack.py (correction) then pipeline/multi_fuse.py (fusion).
3. Each step appends its config + isoview_version to isoview_config.json next to the data, so every run is reproducible.

Usage

Entrypoints: pipeline/correct_stack.py (correction) and pipeline/multi_fuse.py (fusion).

from pathlib import Path
from isoview import ProcessingConfig, correct_stack, multi_fuse

config = ProcessingConfig(
    input_dir=Path(r"E:\isoview\dataset"),
    # specimens=None,                       # auto-detect from SPC## in filenames
    # timepoints=None,                      # auto-detect from TM## in filenames
    output_suffix="",                       # appended as ".corrected_<suffix>" / ".fused_<suffix>" if set
    specimen=0,                             # default specimen index
    camera_pairs=[(0, 1), (2, 3)],          # ortho camera pairs to fuse

    # output
    output_format="tif",                    # tif, zarr, or klb
    compression="zstd",                     # zstd, lzw, deflate, or None
    compression_level=3,                    # 1-22 for zstd, 1-9 for others

    # transforms (applied to second camera in each pair)
    rotation=0,                             # 0=none, 1=90cw, -1=90ccw
    flip_horizontal=False,
    flip_vertical=False,

    # correction
    median_kernel=(3, 3),                   # dead pixel filter, None to disable
    background_percentile=5.0,
    mask_percentile=1.0,
    segment_mode=1,                         # 0=none, 1=segment+mask, 2=masks, 3=global

    # fusion
    blending_method="adaptive",             # adaptive, geometric, average, wavelet
    blending_range=20,                      # transition zone width (z-planes)

    # per-specimen overrides (tiled mode)
    # tile_crops={"SPM00": {"crop_depth": {0: 450}}}
    # view_orientation={"SPM00": {"flip_axis": 1}, "SPM01": {"flip_axis": 0}}
)

correct_stack(config)
multi_fuse(config)

Acquisition Modes

Raw input is always flat — SPC##_TM#####_ANG###_CM#_CHN##_PH#.stack files in a single directory. Mode is auto-detected from SPC/TM counts:

Condition	Mode	Description
Multiple TM values	timelapse	time series, any number of specimens
Single TM + multiple SPC	tiled	spatial tiles, one timepoint
Single TM + single SPC	single	treated as timelapse with 1 timepoint

XML Metadata

read_xml_metadata(xml_path) parses one push_config XML; read_all_xml_metadata(input_dir, specimen) returns (common, per_camera) — fields equal across cameras vs camera-specific.

Field	Type	Source	Notes
data_header	str	@data_header	acquisition session label
specimen_name	str	@specimen_name
timestamp	str	@timestamp	acquisition datetime
time_point	int	@time_point
specimen_XYZT	str	@specimen_XYZT	also parsed → stage_x/y/z (float, µm)
angle	float	@angle
camera_index	str	@camera_index	comma-separated per camera
camera_type	str	@camera_type
camera_roi	str	@camera_roi
wavelength	str	@wavelength	emission, per camera
illumination_arms	str	@illumination_arms	per camera
illumination_filter	str	@illumination_filter
exposure_time	float	@exposure_time	ms
detection_filter	str	@detection_filter
detection_objective	str	@detection_objective	also parsed → objective_mag (float)
dimensions	ndarray	@dimensions	(n_cameras, 3) from "WxHxD,WxHxD,…"
z_step	float	@z_step	µm; VW00 (Z-scan)
y_step	float	@y_step	µm; VW90 (Y-scan)
stack_direction	str	@stack_direction	drives camera_view_map
planes	str	@planes
laser_power	str	@laser_power
experiment_notes	str	@experiment_notes
zplanes	int	derived	dimensions[0][-1]
fps	float	derived	1000.0 / exposure_time
vps	float	derived	fps / zplanes
camera_pixel_size_um	float	constant	6.5 (Hamamatsu C11440-22C)
pixel_resolution_um	float	derived	camera_pixel_size_um / objective_mag
axial_step	float	merged	unifies z_step / y_step across XMLs
camera_view_map	dict	synthesized	from stack_direction: Z-scan → {0:0,1:0}, Y-scan → {2:90,3:90}

XML discovery order (in read_all_xml_metadata): ch*_spec{NN}.xml → ch*.xml → *_CHN*.xml. Channel inferred from filename via ch(\d+) → CHN(\d+) → VW(\d+).

Filename Tags

Tag	Meaning	Raw	Corrected	Fused
SPC## / SPM##	specimen / tile	SPC00	SPM00	SPM00
TM######	timepoint	TM00000	TM000000	TM000000
CM##	camera	CM0	CM00	CM00_CM01 (pair)
CHN##	acquisition channel	CHN00, CHN01	CHN00, CHN01	CHN00, CHN01
VW##	fused view (scan axis)	—	—	VW00 (z-scan), VW90 (y-scan)
ANG###	illumination angle	ANG000	—	—
PH#	phase	PH0	—	—

Correction iterates over all (camera, channel) pairs present in the raw data, so dual-channel acquisitions (same camera capturing multiple wavelengths) produce one corrected volume per (CM, CHN). Fusion fuses each camera pair separately for every channel both cameras share.

Output Layout

Correction writes to {input_dir.name}.corrected[_<output_suffix>] (default .corrected) and fusion writes to a sibling {input_dir.name}.fused[_<output_suffix>] (default .fused), both as siblings of the raw input directory. output_suffix is one shared field — a non-empty value is appended as _<value> to every per-step prefix (.corrected, .fused, .stitcher).

Correction (correct_stack.py)

Mode	Path	Filename
Timelapse	root.corrected/SPM00/TM000000/	SPM00_TM000000_CM00_CHN00.ome.tif
Tiled	root.corrected/SPM00/	SPM00_CM00_CHN00.ome.tif

Each tile gets a SPM0N folder, where N is the tile index. Each SPM## dir also contains a projections/ subfolder with per-view XY MIPs and a raw.xyProjection counterpart for QC. Masks share the same prefix with suffixes .segmentationMask, .xyMask, .xzMask. minIntensity.npz carries the percentile values used downstream.

Fusion (multi_fuse)

Mode	Path	Filename
Timelapse	root.fused/adaptive/SPM00/TM000000/	SPM00_TM000000_CM00_CM01_VW00_CHN00.ome.tif
Tiled	root.fused/adaptive/SPM00/	SPM00_CM00_CM01_VW00_CHN00.ome.tif

Default pairs: [(0, 1), (2, 3)] — cameras 0,1 fuse to VW00 (z-scan); cameras 2,3 fuse to VW90 (y-scan). The CHN value reflects the acquisition channel of the pair (in the standard Keller IsoView wiring, CHN00 for CM0/1 and CHN01 for CM2/3). For dual-channel acquisitions, each pair fuses once per shared channel, producing multiple outputs with the same VW## but different CHN##.

Only the second camera in each pair gets rotation/flip transforms.

Supported Output Formats

Format	Extension	Notes
OME-TIFF	.ome.tif	with metadata, optional resolution pyramids
Zarr v3	ome.zarr	OME-NGFF metadata
KLB	.klb	Keller Lab Block (bzip2)

.stack Reading

Raw .stack is little-endian uint16, shape (D, H, W), memmappable. (W, H) from XML @dimensions[0]; D derived from file size (stat().st_size // 2 // (H*W)) — XML's D may be stale on aborted acquisitions.