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2021-Chen and Murphy-preprint

PostPosted: Mon Sep 20, 2021 3:22 pm
by mleipold
"Evaluation of cell segmentation methods without reference segmentations"
Haoran Chen, Robert F. Murphy
bioRxiv, posted September 19, 2021

- will update when/if this is peer-reviewed and published

No references or accessions for these datasets, so unclear if new or previously-published
- "We obtained ten 29-channel MIBI datasets."
- "Three 2D 39-channel IMC datasets of spleen, thymus, and lymph node, respectively, are provided by the U of Florida TMC"
- "A Reproducible Research Archive containing all data and code will be made available upon publicationat

Re: 2021-Chen and Murphy-preprint

PostPosted: Thu Dec 15, 2022 5:22 pm
by mleipold
Now published:

Mol Biol Cell 2022

- "We obtained image data from the HuBMAP project, for 4 multiplexed modalities. For each modality, the nuclear, cytoplasmic, and cell membrane channels chosen for segmentation (Supplementary Table 1) were either those recommended by the Tissue Mapping Center (TMC) that produced the datasets, or selected based on peer-reviewed literature and subcellular localization of antibody targeted protein annotated by UniProt or Gene Ontology. Details about input markers are summarized in Supplementary Table 2."

- 13 IMC datasets appear to be here: ... data_types[0]=Imaging%20Mass%20Cytometry%20%282D%29&entity_type[0]=Dataset
- listed as "Published", but not at all clear whether that just means publicly available, or whether they're from an article: I couldn't find a reference.

- "We obtained 10 29-channel MIBI datasets.
- no idea where these are from: I can't find any MIBI datasets. "MIBI", "Multiplexed Ion Beam Imaging", "SIMS" etc searches returned nothing, as did "HH3" marker as a search term. No listed assay types including "MS" appeared to be correct.
- no literature citation either