Table of contents for types of data available below

Automating access to our cell images & other data using Quilt
Download scRNA-seq dataset from our publication
Download imaging dataset from our publication
Download imaging dataset from our publication
Download whole exome sequencing, population RNA-seq data, and single cell RNA-seq data
Download our cell feature analysis data for your own study
Download the data used to train models used in label-free determination
Download image data from the drug-induced phenotypic signature pilot study
Download our 31,987 3D cell image data in sets for use in desktop software

Programmatic access to our cell images & metadata


    












Instructions and an overview of a methods to access our data programmatically:
  • allows easy downloads
  • allows versioning of datasets
  • ​works well within the standard Python data science Jupyter stack




  











    








			

		

      


	





	

		

          

			

				
Gene expression in cardiomyocytes data



Download the scRNA-seq dataset from our following publication​:
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes




  










			

		

      


	





	

		

          

			

				
Cell state in cardiomyocytes data



Download the imaging dataset from our following publication​:
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes





			

		

      


	





	

		

          

			

				
Variation in integrated hiPS cells



Download the imaging dataset from our following publication​:
Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable​





			

		

      


	





	

		

          

			

				
Download cell feature data






Downloading cell feature analysis data as .csv files
The .cvs file includes the data accessed by our Cell Feature Explorer plotting tools for use in your favorite analysis software. For all 39,200 cells in our current example population, the file references the tagged structure of interest, as well as the cell ID and includes 6 calculated features for each cell:
  • Cell volume
  • Nuclear volume
  • Cell surface area
  • Nuclear surface area
  • Apical proximity (as described below)
  • Radial proximity  (as described below)
 The feature calculation will be versioned and continually available for download as we expand our methods, and continuously improve our segmentation and feature extraction approaches.




  












 aics_cfe_cell-features_v1.8.csv.zip
File Size:  1580 kb
File Type:   zip
Download File






			

		

      


	





	

		

          

			

				
Genomics Data



Whole exome sequencing, population RNA-seq data, and single cell RNA-seq data that we use to evaluate any changes in the transcriptional profiles and exomes of our fluorescently tagged hiPSC lines relative to the parental WTC line are available on the Genomics page.






  








			

		

      


	





	

		

          

			

				
Label-free Prediction Training Data Download




	

		
			

				
					
						


As part of the Allen Integrated Cell, we have developed and implemented a label-free prediction method for determining the location of 3D structures inside the cell, directly from transmitted light images. The data used to train models described on the Label-free Determination page are provided here.



					
										
					
						




					
							

		
	






	

		
			

				
					
						







					
										
					
						












					
										
					
						







					
									

		
	













  










			

		

      


	





	

		

          

			

				
​Download drug-induced phenotypic signature cell image data as 3D ome-tif files




	

		
			

				
					
						


The goal of our drug perturbation pilot study is to identify signature profiles of cellular organization for a range of well-characterized agonists and antagonists commonly used to perturb specific cellular processes or pathways. ​The analysis not only shows the effects of these drugs on structures they are known to perturb but also on other structures providing a rich signature of pathway alterations.



					
										
					
						




					
							

		
	







 drug_perturbation_dataset_2.csv
File Size:  392 kb
File Type:   csv
Download File








https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug_nodye-part01.tar.gz        3.74GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug-part01.tar.gz       10.09GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug-part02.tar.gz        8.17GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug-part03.tar.gz        5.51GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug-part04.tar.gz       10.54GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_drug-part05.tar.gz       10.45GB

https://downloads.allencell.org/2018_04_18_drug/brefeldin_vehicle-part01.tar.gz        7.18GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug_nodye-part01.tar.gz        9.61GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug-part01.tar.gz       11.09GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug-part02.tar.gz       10.84GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug-part03.tar.gz       10.84GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug-part04.tar.gz       11.22GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_drug-part05.tar.gz        0.91GB

https://downloads.allencell.org/2018_04_18_drug/paclitaxol_vehicle-part01.tar.gz        9.26GB

https://downloads.allencell.org/2018_04_18_drug/rapamycin_drug_nodye-part01.tar.gz        3.07GB

https://downloads.allencell.org/2018_04_18_drug/rapamycin_drug-part01.tar.gz       11.33GB

https://downloads.allencell.org/2018_04_18_drug/rapamycin_drug-part02.tar.gz        7.18GB

https://downloads.allencell.org/2018_04_18_drug/rapamycin_vehicle-part01.tar.gz        4.31GB

https://downloads.allencell.org/2018_04_18_drug/s-nitro-blebbistatin_drug_nodye-part01.tar.gz        3.91GB

https://downloads.allencell.org/2018_04_18_drug/s-nitro-blebbistatin_drug-part01.tar.gz       10.66GB

https://downloads.allencell.org/2018_04_18_drug/s-nitro-blebbistatin_drug-part02.tar.gz       10.91GB

https://downloads.allencell.org/2018_04_18_drug/s-nitro-blebbistatin_drug-part03.tar.gz        9.52GB

https://downloads.allencell.org/2018_04_18_drug/s-nitro-blebbistatin_vehicle-part01.tar.gz        6.29GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_drug_nodye-part01.tar.gz        6.53GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_drug-part01.tar.gz       10.53GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_drug-part02.tar.gz       10.64GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_drug-part03.tar.gz       11.00GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_drug-part04.tar.gz        6.29GB

https://downloads.allencell.org/2018_04_18_drug/staurosporine_vehicle-part01.tar.gz        9.83GB








			

		

      


	





	

		

          

			

				
Download cell image data as ome-tif files






​​Instructions for downloading data for individual cells using the 3D Cell Viewer:​
  • Visit the 3D Cell Viewer page
  • Select the cell you want to download from the Images panel in order to load the volumetric data file into the Viewer and Tools panels
  • In the bottom right of the Viewer window (beneath the spinning cell you selected) click the [Download (ome.tif)] button
  • The data for this cell will download to your web browser's default downloads folder on your hard drive as an .ome.tif file













Download full-field data with multiple, single-cell segmentation channels per field in .ome-tif format here:

Tagged protein name: α-actinin    
  Primary structure labeled: actin
  Allen Institute Cell Line ID: AICS-7






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Tagged protein name: Sec61-ß    
  Primary structure labeled: Endoplasmic Reticulum
  Allen Institute Cell Line ID: AICS-10






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​Tagged protein name: Tom20    
  Primary structure labeled: Mitochondria
  Allen Institute Cell Line ID: AICS-11












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Tagged protein name: α-tubulin    
  Primary structure labeled: Microtubules
  Allen Institute Cell Line ID: AICS-12






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Tagged protein name: Lamin B1    
  Primary structure labeled: Nuclear envelope
  Allen Institute Cell Line ID: AICS-13






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Tagged protein name: Fibrillarin    
  Primary structure labeled: Nucleolus
  Allen Institute Cell Line ID: AICS-14







Tagged protein name: ß-actin    
  Primary structure labeled: Actin
  Allen Institute Cell Line ID: AICS-16







Tagged protein name: Desmoplakin    
  Primary structure labeled: Cell-cell junction
  Allen Institute Cell Line ID: AICS-17







Tagged protein name: Tight junction protein, ZO1    
  Primary structure labeled: Tight junctions
  Allen Institute Cell Line ID: AICS-23







Tagged protein name: Non-muscle myosin heavy chain IIB    
  Primary structure labeled: Myosin
  Allen Institute Cell Line ID: AICS-24







Tagged protein name: Sialyltransferase 1 
  Primary structure labeled: Golgi apparatus
  Allen Institute Cell Line ID: AICS-25



			

		

      


	







    

    
    

      

        











	












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