Downloading LabelFree Image From Quilt

Software & Code Download
,
1

Hi,
I would like to download the images from this page: https://open.quiltdata.com/b/allencell/packages/aics/label-free-imaging-collection

I was able to browse the data manifest.
If I would like to download part of the “Field Collection” or “Cell Image Collection”, which images should I download?

This is the top layer structure:
└─README.md
└─cells_2d/
└─fov-0_CellIndex-11.tiff
└─fov-0_CellIndex-12.tiff
└─fov-0_CellIndex-5.tiff
└─fov-0_CellIndex-6.tiff
└─fov-0_CellIndex-7.tiff
└─fov-0_CellIndex-9.tiff
└─fov-1000_CellIndex-1.tiff
└─fov-1000_CellIndex-5.tiff
└─fov-1001_CellIndex-2.tiff
└─fov-1001_CellIndex-5.tiff
└─fov-1001_CellIndex-8.tiff
└─fov-1001_CellIndex-9.tiff
└─fov-1002_CellIndex-2.tiff
└─fov-1003_CellIndex-1.tiff
└─cells_3d/
└─data_feats.csv
└─fovs/
└─reference_images/
…

I then looked into the cells_3d:
└─fov-0_CellIndex-11.tiff
└─fov-0_CellIndex-12.tiff
└─fov-0_CellIndex-5.tiff
└─fov-0_CellIndex-6.tiff
└─fov-0_CellIndex-7.tiff
└─fov-0_CellIndex-9.tiff
└─fov-1000_CellIndex-1.tiff
└─fov-1000_CellIndex-5.tiff
└─fov-1001_CellIndex-2.tiff
└─fov-1001_CellIndex-5.tiff
└─fov-1001_CellIndex-8.tiff
└─fov-1001_CellIndex-9.tiff
└─fov-1002_CellIndex-2.tiff
└─fov-1003_CellIndex-1.tiff
└─fov-1003_CellIndex-12.tiff
└─fov-1003_CellIndex-13.tiff

└─fov-1003_CellIndex-15.tiff

└─fov-1003_CellIndex-2.tiff
└─fov-1003_CellIndex-5.tiff
└─fov-1003_CellIndex-7.tiff

…

Thanks for all the help!
Hanxi

2

Hey @Hanxix

The “Field Collection” can be downloaded by specifying the fovs directory of the package:

from quilt3 import Package

label_free_dataset = Package.browse("aics/label-free-imaging-collection", "s3://allencell")
label_free_dataset["fovs"].fetch("path/to/save/directory")

The “Cell Image Collection” is broken up into two parts, 3D TIFFs or 2D PNGs of single cells. Instead of the fovs directory on the package you can simply use the cells_3d and cells_2d directories respectively. (label_free_dataset["cells_3d"].fetch("path/to/save/dir"), label_free_dataset["cells_2d"].fetch("path/to/save/dir"))

Once downloaded you can use them like any normal file on your file system! Hope this helps.

3

Thank you so much for your help!

4

Hi, i’m sorry i’m very new at this.
If I would like to download only mitochondria 3D images in the cells_3d, what should I specify?
Maybe I missed it, but I couldn’t find anything on the README
when I look into the cells_3d subdirectory, I see fov-1003-CellIndex-1.tiff for example, I don’t know how to tell witch images belongs to which sub-cellular structures. Thank you so much!

5

Ah, sorry, I understand the figures now. Sorry, I misread the README.md file. Thank you!