Data Downloading

Table of contents for types of data available below

Programmatic data access

Automating access to our cell images & other data using Quilt

Download feature data

Download our cell feature analysis data for your own study

Download image data

Download our 31,987 3D cell image data in sets for use in desktop software

Label-free data

Download the data used to train models used in label-free determination

Drug perturbation pilot

Download image data from the drug-induced phenotypic signature pilot study

Genomics

Download whole exome sequencing and population RNA-Seq data

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

Access data via Quilt

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

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

https://downloads.allencell.org/AICS-7-part01.tar.gz 20.72GB
https://downloads.allencell.org/AICS-7-part02.tar.gz 16.56GB

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

https://downloads.allencell.org/AICS-10-part01.tar.gz 20.82GB
https://downloads.allencell.org/AICS-10-part02.tar.gz 20.65GB
https://downloads.allencell.org/AICS-10-part03.tar.gz 20.86GB
https://downloads.allencell.org/AICS-10-part04.tar.gz 20.92GB
https://downloads.allencell.org/AICS-10-part05.tar.gz 20.85GB
https://downloads.allencell.org/AICS-10-part06.tar.gz 20.91GB
https://downloads.allencell.org/AICS-10-part07.tar.gz 13.27GB

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

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

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

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

https://downloads.allencell.org/AICS-14-part01.tar.gz 20.91GB
https://downloads.allencell.org/AICS-14-part02.tar.gz 20.82GB
https://downloads.allencell.org/AICS-14-part03.tar.gz 19.18GB

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

https://downloads.allencell.org/AICS-16-part01.tar.gz 20.75GB
https://downloads.allencell.org/AICS-16-part02.tar.gz 20.70GB
https://downloads.allencell.org/AICS-16-part03.tar.gz 20.90GB
https://downloads.allencell.org/AICS-16-part04.tar.gz 20.85GB
https://downloads.allencell.org/AICS-16-part05.tar.gz 11.14GB

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

https://downloads.allencell.org/AICS-17-part01.tar.gz 20.70GB
https://downloads.allencell.org/AICS-17-part02.tar.gz 20.91GB
https://downloads.allencell.org/AICS-17-part03.tar.gz 20.83GB
https://downloads.allencell.org/AICS-17-part04.tar.gz 20.86GB
https://downloads.allencell.org/AICS-17-part05.tar.gz 20.88GB
https://downloads.allencell.org/AICS-17-part06.tar.gz 20.77GB
https://downloads.allencell.org/AICS-17-part07.tar.gz 20.75GB
https://downloads.allencell.org/AICS-17-part08.tar.gz 13.79GB

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

https://downloads.allencell.org/AICS-23-part01.tar.gz 20.74GB
https://downloads.allencell.org/AICS-23-part02.tar.gz 20.77GB
https://downloads.allencell.org/AICS-23-part03.tar.gz 20.90GB
https://downloads.allencell.org/AICS-23-part04.tar.gz 17.75GB

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

https://downloads.allencell.org/AICS-24-part01.tar.gz 20.88GB
https://downloads.allencell.org/AICS-24-part02.tar.gz 20.79GB
https://downloads.allencell.org/AICS-24-part03.tar.gz 20.74GB
https://downloads.allencell.org/AICS-24-part04.tar.gz 20.82GB
https://downloads.allencell.org/AICS-24-part05.tar.gz 20.80GB
https://downloads.allencell.org/AICS-24-part06.tar.gz 0.18GB

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

https://downloads.allencell.org/AICS-25-part01.tar.gz 20.81GB
https://downloads.allencell.org/AICS-25-part02.tar.gz 20.78GB
https://downloads.allencell.org/AICS-25-part03.tar.gz 20.77GB
https://downloads.allencell.org/AICS-25-part04.tar.gz 20.79GB
https://downloads.allencell.org/AICS-25-part05.tar.gz 3.29GB

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.

Label-free determination page

Actin Filament (beta actin)
25.2Gb

Actomyosin Bundle (myosin IIB)
22Gb

Desmosome (desmoplakin)
22.3Gb

Microtubule (alpha tubulin)
21.8Gb

Tight Junction (ZO1)
22.2Gb

ER (Sec61 beta)
24.3Gb

Golgi (ST6GAL1)
22.2Gb

Mitochondria (TOM20)
22.1Gb

Membrane (CAAX)
52.2Gb

Nucleoli (fibrillarin)
22.8Gb

Nuclear Envelope (lamin B1)
20.7Gb

Nuclear Envelope - DIC
10.2Gb

Wildtype TIME SERIES
1.3Gb

GitHub code for Label-free determination

Quilt package for Label-free Imaging Collection

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 pilot study page

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

Download File

Genomics Data

Whole exome sequencing and population 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.

Explore & download genomics & transcriptomics data