REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals
mTeSR™1 Medium	STEMCELL Technologies	Cat# 85850
mTeSR™1 Medium Without Phenol Red	STEMCELL Technologies	Cat# 05876
Penicillin-Streptomycin	Thermo Fisher Scientific	Cat# 15070063
Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix, Phenol Red-free, LDEV-free	Corning	Cat# 356231
DMEM/F12 (1:1) 1X	Thermo Fischer Scientific	Cat# 11039021
Gibco DPBS (1X)	Thermo Fischer Scientific	Cat# 14190
Gibco StemPro™ Accutase™ Cell Dissociation Reagent	Thermo Fischer Scientific	Cat# A1110501
Y-27632 ROCK inhibitor	STEMCELL Technologies	Cat# 72308
Importazole	Sigma-Aldrich	Cat# 401105
Aphidicolin	Sigma-Aldrich	Cat# 178273
Puromycin	ThermoFisher	Cat# A1113803
Rapamycin	Selleckchem	Cat# S1039
2-aminopurine	Sigma Aldrich	Cat# A3509
Click-iT™ EdU Pacific Blue™ Flow Cytometry Assay Kit	ThermoFisher Scientific	Cat# C10418
Paraformaldehyde	Electron Microscopy Sciences	Cat# 15710
DNA dye, Spy650	Spirochrome	Cat# SC501
Antibodies
Mouse-anti-PCNA	Cell Signaling	Cat# 2586S
Goat anti-mouse AlexaFluor 568	ThermoFisher Scientific	Cat# A-11031
Experimental models: Cell lines
Human induced pluripotent stem cell: AICS-0013 cl 210, lamin B1	Available through Coriell	RRID: CVCL_IR32
Human induced pluripotent stem cell: AICS-0088 cl 83, proliferating cell nuclear antigen	Available through Coriell	RRID: CVCL_A8RT
Deposited data
WTC-11 hiPSC FOV-nuclei timelapse dataset V1	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/
hiPSC FOV-nuclei timelapse data for pretraining Vision Transformer	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_for_pretraining_vision_transformer/
hiPSC FOV-nuclei timelapse data used for analysis	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis
Baseline colonies FOV timelapse dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/
DNA replication inhibitor FOV timelapse dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/dna_replication_inhibitor_fov_timelapse_dataset/
Nuclear import inhibitor FOV timelapse dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_anaysis/nuclear_import_inhibitor_fov_timelapse_dataset/
Feeding control FOV timelapse dataset:	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/feeding_control_fov_timelapse_dataset/
Fixed control FOV timelapse dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/fixed_control_fov_timelapse_dataset/
PCNA + DNA dye FOV timelapse dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/ysis/pcna_dna_dye_fov_timelapse_dataset/
hiPSC single-nuclei timelapse analysis datasets	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_single_nuclei_timelapse_analysis_datasets/
hiPSC nuclei image datasets for training deep-learning models	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_nuclei_image_datasets_for_training_deep_learning_models/
Segmentation decoder training FOV dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_nuclei_image_datasets_for_training_deep_learning_models/segmentation_decoder_training_fov_dataset/
Interphase detector single-nuclei image dataset	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/hipsc_nuclei_image_datasets_for_training_deep_learning_models/interphase_detector_single_nuclei_image_dataset/
Timelapse Feature Explorer datasets	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/timelapse_feature_explorer_datasets/
Software and algorithms
Zen 2.3, 2.6 software (blue edition)	ZEISS
Original/source data for figures in the paper	This paper	https://github.com/AllenCell/nuc-morph-analysis
The Vision Transformers are implemented using CytoDL, a Python package that we developed for configurable 2D and 3D image-to-image deep learning transformations and representation learning	N/A	https://github.com/AllenCellModeling/cyto-dl
Code to perform nuclear instance segmentation, formation and breakdown classification, and extraction of quantitative shape features	This paper	https://github.com/AllenCell/morflowgenesis
Configuration files to execute image processing workflows	This paper	https://open.quiltdata.com/b/allencell/tree/aics/nuc-morph-dataset/supplemental_files/
Code used to track single nuclei over timelapse movie	This paper	https://github.com/AllenCell/aics-timelapse-tracking
Code used to perform morphing, compute Shape Modes	Viana et al., 2023	https://github.com/AllenCell/cvapipe_analysis
Code for custom Paraview plugin used to support manual curation of nuclear trajectories	This paper	https://github.com/AllenCell/aics-track-curator
Code used to prepare data for the Timelapse Feature Explorer	This paper	https://github.com/allen-cell-animated/colorizer-data
Code used to create the Timelapse Feature Explorer	This paper	https://github.com/allen-cell-animated/nucmorph-colorizer.
Timelapse Feature Explorer	This paper	https://timelapse.allencell.org.
Paraview	Ayachit 2015	https://www.paraview.org/
AGAVE	Toloudis 2024	https://allencell.org/pathtrace-rendering.html.
Source code for volume viewer front end web application	N/A	https://github.com/allen-cell-animated/website-3d-cell-viewer
Volume viewer volume loading and rendering component	N/A	https://github.com/allen-cell-animated/volume-viewer
Volume viewer	N/A	https://volumeviewer.allencell.org
Other
Falcon 60 mm TC-treated Cell Culture Dish	Corning	Cat# 353002
Falcon 6-well Clear Flat Bottom TC-treated Multiwell Cell Culture Plate	Corning	Cat# 353046
96-well glass bottom plate with high performance #1.5 grade cover glass	Cellvis	Cat# P96-1.5H-N
24-well glass bottom plate with high performance #1.5 grade cover glass	Cellvis	Cat# P24-1.5H-N