REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Low MP agarose	Fisher	BP165-25
Gelatin	Sigma	G1890
Rat serum, special collection	Valley Biomedical	AS3061-SC, must be individually requested by purchaser; specify to “dispense in 125 mL aliquots”
Fetal bovine serum	Thermo Fisher Scientific	10082139
DMEM/F-12	Thermo Fisher Scientific	11039021
GlutaMAX	Thermo Fisher Scientific	35050061
ITS-X	Thermo Fisher Scientific	51500056
Penicillin/Streptomycin	Thermo Fisher Scientific	15070063
b-estradiol	Sigma	E8875
Progesterone	Sigma	P3972
N-acetyl cysteine “NAC”	Sigma	A7250
CB-DMB	Sigma	C5374
Phosphate-buffered saline (PBS)	Thermo Fisher Scientific	10010023
Glass capillaries and piston, large (at least 4–5 per experiment)	Sigma	Z328502 and BR701938 (green)
Glass capillaries and piston, small (at least 4–5 per experiment)	Sigma	Z328480 and BR701932 (black)
Wide orifice low-retention tips	Rainin	30389197
Cell culture grade sterile water	MilliporeSigma	W3500
Parafilm M	Any	N/A
Chemstrip 10 MD urine test strips (or similar)	Roche	03260763160
pH test paper, narrow range 6.0 to 8.0 (or similar)	Fisherbrand	13-640-502
Deposited data
Example raw .czi images for mouse embryo dataset at E7.5/ EHF, captured in two frontal-lateral oblique views (100° offset). Channel 1 acquired with 488 nm laser and GFP emission filter, representing Smarcd3-F6-nGFP. Channel 2 acquired with 561 nm laser and RFP emission filter, representing Mesp1-Cre lineage through RCL-H2B-mCherry reporter	This paper	https://datadryad.org/stash/dataset/doi:10.5061/dryad.nk98sf823
Fused .klb files for mouse example dataset above	This paper	https://datadryad.org/stash/dataset/doi:10.5061/dryad.nk98sf823
Intermediate (source and result) data files for above .klb dataset, processed as described herein	This paper	https://github.com/mhdominguez/Dominguez-Protocols-2024-TrackingFiles/tree/main/intermediate-data
Experimental models: Organisms/strains
Mouse: Mesp1-Cre, heterozygous embryos (E6 to E8) of either gender, bred with below strains	Saga et al.4	N/A
Mouse: RCL-H2B-mCherry, heterozygous embryos (E6 to E8) of either gender, bred with above and below strains	Jackson Laboratory	cat: 023139
Mouse: Smarcd3-F6-nGFP, heterozygous embryos (E6 to E8) of either gender, bred with above strains	Devine et al.5	N/A
Software and algorithms
Fiji (base ImageJ v.1.53f)	Schindelin et al.6	https://github.com/fiji/fiji
ZLAPS (ZEN lightsheet adaptive positioning system)	N/A	https://github.com/mhdominguez/ZLAPS
F-TGMM v.2.5	McDole et al.2 and Dominguez et al.1	https://github.com/mhdominguez/F-TGMM
“SVF” (TGMM2SVF and SVF2MaMuT)	McDole et al.2 and Dominguez et al.1	https://github.com/mhdominguez/SVF
LSFM Processing Scripts	Dominguez et al.1	https://github.com/mhdominguez/LSFMProcessing
PSF Generator	Biomedical Imaging Group at EPFL	http://bigwww.epfl.ch/algorithms/psfgenerator/
Parallel Spectral Deconvolution	Piotr Wendykier	https://sites.google.com/site/piotrwendykier/software/deconvolution/parallelspectraldeconvolution
BigStitcher	Hörl et al.7 and Dominguez et al.1	https://github.com/PreibischLab/BigStitcher and https://github.com/mhdominguez/multiview-reconstruction
KLB file format (including system library and script wrappers)	McDole et al.2	https://github.com/JaneliaSciComp/keller-lab-block-filetype/
KLB Fiji integration	McDole et al.2 and Dominguez et al.1	https://github.com/mhdominguez/klb-bdv
MaMuT	Wolf et al.8,9	https://github.com/mhdominguez/MaMuT
MaMuT script library	Dominguez et al.1	https://github.com/mhdominguez/MaMuTLibrary
TrackingFiles for handling example data with LSFMProcessing, F-TGMM, SVF, and MaMuT	This paper	https://github.com/mhdominguez/Dominguez-Protocols-2024-TrackingFiles
“LSFMProcessing-Kubuntu” - stable, custom Linux environment, with all software above included	This paper	https://gitlab.com/mhdominguez1/LSFMProcessing-Kubuntu24.04
Kubuntu 24.04 LTS	Canonical and Kubuntu developers	https://kubuntu.org/getkubuntu/
nVidia driver (versions 450 to 550)	nVidia corporation	N/A
Other
Zeiss Z.1 “Lightsheet” Microscope with installed features: - laser lines and emission filters for desired fluorophores - dual pco.edge 4.2 cameras with liquid cooling - Zeiss incubation with CO2 setup	Zeiss	RRID:SCR_020919
Zeiss 20×/1.0 “W Plan-APOCHROMAT” multi-immersion objective	Zeiss	similar to 421452-9700-000
M32 × 0.075 to M27 × 0.75 10 mm-offset ring for 20×/1.0 W objective	Zeiss	N/A
Dual Zeiss “LSFM” 10×/0.2 illumination objectives	Zeiss	N/A
Zeiss Z.1 Lightsheet incubation sample chamber with temperature probe	N/A	N/A
Sample holder for capillaries	N/A	N/A
Sample chamber lid with small slit	N/A	N/A
Windows Workstation with ZEN	Zeiss/HP	RRID:SCR_018163
Syringe pump capable of 2–30 μL / min infusion flow	World Precision Instruments	AL-300
20 mL Luer Lock syringes	VWR	76290-384
60 mL Luer Lock syringes	VWR	76290-388
3-way (2 female) stopcocks	Medex supply	MX5311L
Tubing with Luer ends	Cole Parmer	UX-30526-18
Stereo dissection microscope - fluorescence is preferred but not absolutely necessary	Leica	MZ 12, MZ FLIII, or similar
P200 micropipette	N/A	N/A
200 μL wide-orifice low-retention micropipette tips	Rainin	30389188
Serological pipettes, 2–50 mL	N/A	N/A
Center well IVF dish	Thermo Fisher Scientific	12-565-024
6 cm Petri dishes	MilliporeSigma	P5481
10 cm Petri dishes	MilliporeSigma	P5731
Temperature-controllable warming plate (need two)	Fisher Scientific	NC0987506
Benchtop incubator	Benchmark Scientific	H2200-HC
Benchtop digital dry bath with removable blocks (need two)	Benchmark Scientific	BSH1001
Microdissection forceps #5, Inox, Tip Size .05 × .01 mm (qty 2+)	VWR	100190-496
Mouse dissection toolkit (qty 1+ each)	Medline	MDS1012011, MDS1017012, MDS0859411, and MDS0811013
Microcentrifuge tubes	N/A	N/A
50 mL conical vials	N/A	N/A
50 mL conical vials w/ 0.22 μm vacuum-driven filter	Thermo Fisher Scientific	SCGP00525
Cell culture hood with vacuum aspiration setup	Any	N/A
Tissue culture incubator at 37°C and 5% CO2	Any	N/A
Spray bottle with 70% ethanol	Any	N/A
Laboratory refrigerator and freezer	Any	N/A
Microwave	Any	N/A
Oxygen and isoflurane vaporizer setup for mouse euthanasia	Any	N/A
8+ TB external hard drives	Seagate	STKP14000400
Workstation PC - 8+ core x86 CPU - 128 GB RAM - nVidia GPU with 8+ GB RAM - 2+ TB storage including ample swap partition / pagefile	Lenovo, Dell, HP, or similar	N/A
USB 3.1 thumb drive, 128+ GB	Any	N/A