KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Cux1 (Clone M-222)	Santa Cruz Biotechnology	Cat#: sc-13024; RRID: AB_2261231
Rat anti-Ctip2 (Clone 25B6)	Abcam	Cat#: ab18465; RRID: AB_2064130
Rabbit anti-SATB2	Abcam	Cat#: ab51502; RRID: AB_2184455
Rabbit anti-Olig2	Millipore	Cat#: AB9610; RRID: AB_570666
Goat anti-GFAP	Abcam	Cat#: ab53554; RRID: 880202
Chemicals, peptides, and recombinant proteins
5-ethynyl-2′-deoxyuridine (EdU)	Cayman Chem	Cat#: 20518; CAS: 61135-33-9
TO-PRO-3 Iodide	Thermo Fisher	Cat#: T3065; CAS: 157199-63-8
Deposited data
Raw and analyzed imaging data	This study	https://braini.renci.org/
Experimental models: Organisms/strains
Mouse: Top1fl/fl	Mabb et al., 2016	N/A
Mouse: Nf1fl/fl	Jackson Laboratory	JAX: 017640
Mouse: Neurod6-Cre	Gift from Dr. Klaus-Armin Nave; Goebbels et al., 2006	RRID:IMSR_CARD:2562
Mouse: Emx1-Cre	Jackson Laboratory	JAX: 005628
Software and algorithms
NuMorph	This study; https://zenodo.org/record/5346838	https://bitbucket.org/steinlabunc/numorph/
MATLAB vR2020a	Mathworks	RRID:SCR_001622
Python v3.6	Python Software Foundation	RRID:SCR_008394
Elastix v4.9	Klein et al., 2010	RRID:SCR_009619
3DUnetCNN	(Ellis and Aizenberg, 2021)	https://github.com/ellisdg/3DUnetCNN
VLFeat	A. Vedaldi and B. Fulkerson	https://www.vlfeat.org/
SHARP-Track	Shamash et al., 2018	https://github.com/cortex-lab/allenCCF
Allen SDK	Allen Institute	RRID:SCR_018183
ClearMap	Renier et al., 2016	https://github.com/ChristophKirst/ClearMap
CUBIC-Informatics	Matsumoto et al., 2019	https://github.com/lsb-riken/CUBIC-informatics
Bitplane Imaris v9.4	Oxford Instruments	RRID:SCR_007370
FIJI	NIH	RRID:SCR_002285
Prism 9	GraphPad	RRID:SCR_002798
Gene Category Enrichment Analysis	Fulcher et al., 2021	https://github.com/benfulcher/GeneCategoryEnrichmentAnalysis