REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K36me3	Abcam	ab194677
Critical commercial assays
RNeasy micro kit	QIAGEN columns	Cat. No. / ID: 74004
Click-iT EdU kit	Invitrogen	Catalog number: C10340
Deposited data
The Electron Microscopy data and EM based segmentation	This paper	http://www.ebi.ac.uk/pdbe/emdb/empiar Accession id 10365
Gene expression maps, prospr segmentations, and registration files	This paper	https://www.ebi.ac.uk/biostudies Accession id S-BIAD14
The tabular data derived from images and segmentations	This paper	https://github.com/mobie/platybrowser-datasets/tree/master/data/1.0.1/tables
Experimental models: Organisms/strains
6 dpf Platynereis dumerilii	EMBL Heidelberg	N/A
Software and algorithms
SBEMImage	Titze et al., 2018	https://github.com/SBEMimage/SBEMimage
Virtual cell generation	This paper	https://github.com/mobie/prospr-vc-generation
EM segmentation, morphological, and genetic analysis of segmented cells	This paper	https://github.com/mobie/platybrowser-datasets
Intensity Correction	This paper	https://github.com/mobie/platybrowser-datasets/tree/master/misc/intensity_correction
SoftWoRx 6.2	GE Healthcare	N/A
Chromagnon image registration software	Matsuda et al., 2018	https://github.com/macronucleus/Chromagnon
SIMcheck	Ball et al., 2015	https://github.com/MicronOxford/SIMcheck
Mutex Watershed	Wolf et al., 2018	https://github.com/hci-unihd/mutex-watershed
Multicut solver	Pape et al., 2019	https://github.com/constantinpape/cluster_tools
Paintera	Hanslovsky et al., 2020	https://github.com/saalfeldlab/paintera
KNOSSOS	N/A	https://github.com/knossos-project/knossos
PyKNOSSOS	Wanner et al., 2016b	https://github.com/adwanner/PyKNOSSOS
TrackEM	Cardona et al., 2012	https://imagej.net/plugins/trakem2
elastix	Klein et al., 2010; Shamonin et al., 2014	https://github.com/SuperElastix/elastix
ElastixWrapper	Tischer, 2019	https://github.com/embl-cba/elastixWrapper
ImageJ	Schindelin et al., 2012	https://imagej.nih.gov/ij/
Ilastik	Berg et al., 2019	https://www.ilastik.org/
Python Louvain	N/A	https://github.com/taynaud/python-louvain
UMAP	McInnes et al., 2018	https://umap-learn.readthedocs.io/en/latest/
scikit-image	van der Walt et al., 2014	https://scikit-image.org/
scikit-learn	Pedregosa et al., 2012	https://scikit-learn.org
vigra	N/A	http://ukoethe.github.io/vigra/
mahotas	Coelho, 2012	https://mahotas.readthedocs.io/en/latest/
networkx	Hagberg et al., 2008	https://networkx.org/
pandas	McKinney, 2010	https://pandas.pydata.org/
scipy	Virtanen et al., 2020	https://www.scipy.org/
numpy	van der Walt et al., 2011	https://numpy.org/
snakemake	Köster and Rahmann, 2012	https://snakemake.readthedocs.io/en/stable/
tidyverse	Wickham et al., 2017	https://www.tidyverse.org/
rgl	CRAN	https://cran.r-project.org/web/packages/rgl/index.html
vegan	CRAN	https://cran.r-project.org/web/packages/vegan/vegan.pdf
MoBIE	This paper	https://github.com/mobie/mobie#mobie