Reagent or Resource	Source	Identifier
Antibodies
Mouse Anti-Cdx2	BioGenex	MU392A-UC; RRID: AB_2335627
Anti-Sox2	R&D Systems,	AF2018; RRID: AB_355110
Chemicals, Peptides, and Recombinant Proteins
Pregnant Mare’s Serum Gonadotropin	Intervet	Intergonan
Human Chorionic Gonadotropin	Intervet	Ovogest 1500
KSOMaa	Zenith biotech	ZEKS-050
KSOMaa with HEPES	Zenith biotech	ZEHP-050
KSOMaa without Ca2+ and Mg2+ Custom-Made N/A	Custom-made	N/A
Mineral Oil	Sigma	M8410
Hyaluronidase	Sigma	H4272
Pluronic® F-127	Sigma	P2443-250G
Fibronectin	Sigma	F4759
Trimethylchlorosilane	Sigma	386529–25ML
Sylgard 184 1,1 kg Kit	Dow Corning	N/A
SU-8 2025	MicroChem	Y111069
SU-8 2015	MicroChem	Y111064
PVP-40	Sigma	P0930
Critical Commercial Assays
mMessage m Machine Transcription Kit	Ambion	AM1348
Experimental Models: Cells
R1/E ES Cells	Transgenic Core Facility at Max Planck Insititute of Molecular ell Biology and Genetics	N/A
Experimental Models: Organisms/Strains
Mouse: (C57BL/6xC3H) F1	Laboratory Animal Resources at the European Molecular Biology Laboratory	N/A
Mouse: R26-H2B-MCherry	Laboratories of Animal Resource development and Genetic Engineering, RIKEN Center for Life Science Technologies; Abe et al., 2011	CDB0239K
Mouse: mTmG	The Jackson Laboratory; Muzumdar et al., 2007	007676
Mouse: mG	The Jackson Laboratory; Muzumdar et al., 2007	007676
H2B-EGFP	Hadjantonakis and Papaioannou, 2004	006069
Mouse: Pard6b-GFP BAC Transgenic	This study	N/A
Recombinant DNA
pRN3-Ezrin-GFP	S. Louvet-Vallée	N/A
BAC#HS.E052.F15 (for Pard6b-GFP)	BACPAC Resource Center (BPRC)	N/A
LAP Tagging Cassette	Poser et al., 2008	N/A
Oligonucleotides
See Table S1 for Genotyping Primer List	N/A	N/A
Software and Algorithms
MATLAB	MathWorks	https://www.mathworks.com/products/matlab.html
R	N/A	https://www.r-project.org
Fiji	Schindelin et al., 2012	https://fiji.sc
Imaris	BITPLANE	https://imaris.oxinst.com
Ilastik	Sommer et al., 2011	http://ilastik.org
StarryNite	Bao et al., 2006, Santella et al., 2010	http://starrynite.sourceforge.net
AceTree	Boyle et al., 2006	http://starrynite.sourceforge.net
Python	N/A	https://www.python.org/
AutofocusScreen	Rabut and Ellenberg, 2004	https://www-ellenberg.embl.de/resources/microscopyautomation
C++	N/A	N/A
Point Cloud Library	PointCloudLibrary	http://www.pointclouds.org
Sparse Field Methods for Active Contours	Shawn Lankton	https://www.mathworks.com/matlabcentral/fileexchange/23847-sparse-field-methods-for-active-contours