iFISH chromosome spotting (IDR idr0123)

Seven-channel DNA FISH microscopy of human cell nuclei, from the Image Data Resource study idr0123 (Mota et al., Scientific Data 2022). Each nucleus carries six spectrally distinct probes marking loci along chromosome 1, plus a DAPI counterstain. This is the kind of data general-purpose annotation tools cannot show usefully: every channel needs its own window and level, and the signal you care about is a handful of sub-micron spots per fluorophore.

Open any file to see all seven channels as independent layers: toggle fluorophores on and off, drag each channel's window and level, and inspect the per-channel histograms.

Contents

Fields	3 (fields 001 to 003 of Dataset 5, "iFISH chr1 spotting, replicate 1")
Channels per field	7: DAPI, AF488, AT542, AF594, AT647N, AF700, AF790
Image size	1024 x 1024 px, 16-bit, 0.13 um per pixel
Format	One classic TIFF per field, one page per channel, OME-XML channel names in the header
Dataset	fields
Sample	Human cells, combinatorial multi-color iFISH targeting chromosome 1 loci

Using it

Browse a field to explore the channels. To download everything (free account required):

• ZIP: use the Download button on this project.
• Python SDK: pip install datatorch, then:

datatorch login
datatorch pull datatorch/ifish-chromosome-spotting-idr0123

Conversion notes

IDR ships each field as seven single-channel Z-stacks of 61 slices (0.2 um steps). The files here are maximum-intensity projections of each stack, one projection per channel, written as uncompressed 16-bit pages so the full dynamic range survives. Channel names come from the study's OME companion metadata (a488 = AF488, tmr = AT542, a594 = AF594, Cy5 = AT647N, a700 = AF700, ir800 = AF790). The original stacks, and the study's spot-detection tables, are on IDR under the data DOI below.

License and citation

CC BY 4.0. If you use this data, please cite:

Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M. Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH. Scientific Data 9, 47 (2022). https://doi.org/10.1038/s41597-022-01139-2

Data: Image Data Resource, https://doi.org/10.17867/10000175