Genome Biol May 2023 PMID 37198601

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data.

Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał, Igor Filipiuk, Alicja Rączkowska, Paulina Szymczak, Hosein Toosi, Leszek Kaczmarek, Łukasz Koperski, Jens Lagergren, Dominika Nowis, Ewa Szczurek

Mentions

65
Peak: 42 in May 2023
across 3 sources since May 2022

Extended reach

701,381
potential audience

Total likes

129

Video views

15

Mentions per month

May 2022 – Jan 2025

Where it's discussed

  • X / Twitter62 posts
  • Blogs2 articles
  • YouTube1 videos

AI synopsis

What people are saying

The discussions reflect excitement around the innovative methods proposed in the study, with phrases like 'step forward' and 'awesome' illustrating a positive reception. Users frequently emphasize the practical applications of Celloscope, hinting at its transformative potential in biological research, which enriches the overall sentiment of achievement and relevance associated with the publication.

AgreementModerate agreement

While some posts focus on specific spelling errors or technicalities, many express a favorable view towards the model presented in the study.

InterestHigh interest

There is a high level of interest in the topic, as many users are discussing the innovative aspects of the Celloscope model and its relevance to spatial transcriptomics.

EngagementModerate engagement

Several posts delve into the significance of the improved methodology, but most are brief and do not explore the topic in-depth.

ImpactHigh impact

Many users recognize the publication's potential to influence the field of bioinformatics and spatial transcriptomics, indicating it may lead to significant advancements.

Abstract in brief

  • Spatial transcriptomics allows researchers to see where genes are expressed in tissues, but it complicates the process of identifying different cell types due to the mixing of cells at measurement spots.
  • The proposed model, Celloscope, uses prior knowledge of marker genes to accurately deconvolute the mixed signals from spatial transcriptomics data.
  • Celloscope shows superior performance compared to other methods on simulated data and can effectively identify brain structures and distinguish neuron types in mouse brain tissue, as well as analyze immune cell composition in prostate tissue.

Top posts

Most liked on X and Bluesky
antisense.
@razoralign · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/yp5zVZCssq https://t.co/sMBJ3bgNkQ

May 17, 2023 · 59 likes · 17 shares · 15,931 followers View post →
Ewa Szczurek
@ewa_szczurek · X

Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expression across tissues, but it does not specify which cell types are where. Celloscope uses marker genes to find them and to deconvolute mixtures of cells in spots!

May 17, 2023 · 17 likes · 5 shares · 759 followers View post →
Genome Biology
@GenomeBiology · X

Celloscope, presented by @ewa_szczurek @ShadiShafighi @animgoeth @jens_lagergren & co. @UniWarszawski is a step forward in developing new probabilistic methods used to analyze #spatialtranscriptomics data & answer diverse biological questions https://t.co/ju0EoXSGoP https://t.co/Gap4Ka9Nm1

May 18, 2023 · 13 likes · 4 shares · 90,004 followers View post →
Lukas Valihrach
@LukasValihrach · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

May 22, 2023 · 11 likes · 3 shares · 3,423 followers View post →
RNA-Seq Blog
@RNASeqBlog · X

Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowledge on marker #genes for cell type deconvolution from #spatialtranscriptomics data. https://t.co/p1Xuz3sPV0

May 26, 2023 · 7 likes · 10 shares · 8,594 followers View post →
public4safety
@public4safety · X

@2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Jan 17, 2025 · 5 likes · 2 shares · 61 followers View post →

All mentions

Ahmad Majed
@2c817a7338f14a3 · X

RT @public4safety: @2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model…

Jan 17, 2025 · 2 shares · 5,563 followers View post →
public4safety
@public4safety · X

RT @public4safety: @2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model…

Jan 17, 2025 · 2 shares · 61 followers View post →
public4safety
@public4safety · X

@2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

Jan 17, 2025 · 5 likes · 2 shares · 61 followers View post →
Charles Dussiau
@DussiauC · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Nov 4, 2024 · 17 shares · 215 followers View post →
Taco Jesse
@TJesse62 · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Oct 30, 2024 · 17 shares · 1,732 followers View post →
Karol Kaiser
@KarolKaiser1 · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Oct 30, 2024 · 17 shares · 150 followers View post →
antisense.
@razoralign · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Oct 30, 2024 · 17 shares · 15,931 followers View post →
Max von Hades
@Densifiy · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Jul 13, 2024 · 17 shares · 580 followers View post →
antisense.
@razoralign · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

Jul 13, 2024 · 17 shares · 15,931 followers View post →
Mar Muñiz Moreno
@marmmmoreno · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 27, 2023 · 10 shares · 563 followers View post →
Startup Or Scaleup
@StartupNScaleup · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 31,782 followers View post →
A Coffee with Technology
@CoffeTechnology · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 34,640 followers View post →
Techie Girl
@CandyTech1 · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 39,041 followers View post →
Ciso Online Club
@CisoOnlineClub · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 25,777 followers View post →
DATA DAVE
@Dare2Digitize · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 36,149 followers View post →
Digi Biz Insight
@digibizinsight · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 29,843 followers View post →
Karol Kaiser
@KarolKaiser1 · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 150 followers View post →
CIO Connection
@CIOConnection · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 37,813 followers View post →
Vince Beltran, Ph.D.
@levin_beltran · X

RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…

May 26, 2023 · 10 shares · 11,763 followers View post →
RNA-Seq Blog
@RNASeqBlog · X

Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowledge on marker #genes for cell type deconvolution from #spatialtranscriptomics data. https://t.co/p1Xuz3sPV0

May 26, 2023 · 7 likes · 10 shares · 8,594 followers View post →
wook
@wook20120711 · X

RT @BioDecoded: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data | Genome B…

May 26, 2023 · 1 share · 15 followers View post →
BioDecoded
@BioDecoded · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data | Genome Biology https://t.co/X9GHgHbPFc #Bioinformatics https://t.co/nSIOfWKzxb

May 25, 2023 · 3 likes · 1 share · 8,900 followers View post →
Alexis Lomakin, Ph.D. (אל) אַלעקסיס לאָמאַקין
@Alexis_Lomakin · X

RT @LukasValihrach: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

May 22, 2023 · 3 shares · 3,647 followers View post →
AiiHC International Ltd.
@AiihcLtd2022 · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 22, 2023 · 1 share · 818 followers View post →
antisense.
@razoralign · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/yp5zVZCssq https://t.co/kH5UAX0f4L

May 22, 2023 · 3 likes · 1 share · 15,931 followers View post →
choiLab
@jungminchoilab · X

RT @LukasValihrach: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

May 22, 2023 · 3 shares · 330 followers View post →
Phenomics
@Phenomics_J · X

RT @LukasValihrach: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

May 22, 2023 · 3 shares · 1,528 followers View post →
Lukas Valihrach
@LukasValihrach · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data

May 22, 2023 · 11 likes · 3 shares · 3,423 followers View post →
Sevenn
@renxwise · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 19, 2023 · 17 shares · 50 followers View post →
Hamim Zafar
@Quasarzafar · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 19, 2023 · 17 shares · 552 followers View post →
Transcriptomes
@transcriptomes · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial t... https://t.co/atA4sngv2Z

May 18, 2023 · 1,808 followers View post →
Ewa Szczurek
@ewa_szczurek · X

RT @GenomeBiology: Celloscope, presented by @ewa_szczurek @ShadiShafighi @animgoeth @jens_lagergren & co. @UniWarszawski is a step forward…

May 18, 2023 · 4 shares · 759 followers View post →
Genome Biology
@GenomeBiology · X

Celloscope, presented by @ewa_szczurek @ShadiShafighi @animgoeth @jens_lagergren & co. @UniWarszawski is a step forward in developing new probabilistic methods used to analyze #spatialtranscriptomics data & answer diverse biological questions https://t.co/ju0EoXSGoP https://t.co/Gap4Ka9Nm1

May 18, 2023 · 13 likes · 4 shares · 90,004 followers View post →
Paolo Devanna
@PaoloDevanna · X

RT @ewa_szczurek: Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expressi…

May 18, 2023 · 5 shares · 41 followers View post →
ashley
@notashleel · X

RT @ewa_szczurek: Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expressi…

May 18, 2023 · 5 shares · 182 followers View post →
Marcel Schulz - @marcelschulz@genomic.social
@TheMarcelSchulz · X

RT @ewa_szczurek: Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expressi…

May 18, 2023 · 5 shares · 940 followers View post →
Michael Love
@mikelove · X

RT @ewa_szczurek: Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expressi…

May 18, 2023 · 5 shares · 16,377 followers View post →
Francisco J Ruiz-Ruano
@fjruizruano · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 18, 2023 · 17 shares · 679 followers View post →
Szu Shuo Lee
@ShuoSzu · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 155 followers View post →
Brian Dean
@bdean_ · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 562 followers View post →
Toyota_Group_Komaba
@KomaToug · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 669 followers View post →
Leiy
@leur123 · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 62 followers View post →
Gerard Baquer
@GerardBaquer · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 283 followers View post →
Nils Eling
@NilsEling · X

RT @ewa_szczurek: Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expressi…

May 17, 2023 · 5 shares · 581 followers View post →
Yiran Meng
@YRMeng · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 63 followers View post →
priya joseph
@ayirpelle · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 4,890 followers View post →
MyJournals
@myjournals · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/FccDXsTERe

May 17, 2023 · 556 followers View post →
AL'AM KATAM
@BULLWTI · X

RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…

May 17, 2023 · 17 shares · 115 followers View post →
antisense.
@razoralign · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/yp5zVZCssq https://t.co/sMBJ3bgNkQ

May 17, 2023 · 59 likes · 17 shares · 15,931 followers View post →
Ewa Szczurek
@ewa_szczurek · X

Link to the paper: https://t.co/wJDj9t5bAT

May 17, 2023 · 759 followers View post →
Ewa Szczurek
@ewa_szczurek · X

Our awesome Celloscope is out in Genome Biology! 10.1186/s13059-023-02951-8 . Spatial transcriptomics gives gene expression across tissues, but it does not specify which cell types are where. Celloscope uses marker genes to find them and to deconvolute mixtures of cells in spots!

May 17, 2023 · 17 likes · 5 shares · 759 followers View post →
Sandy Anderson
@ara_anderson · X

The penultimate talk of the meeting is by Agnieszka Geras presenting, Celloscope: A probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data #BCB22 https://t.co/tgQryJSZhM

Sep 15, 2022 · 2 likes · 5,369 followers View post →
antisense.
@razoralign · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/qPnEhW6k6m https://t.co/rM9ItJLXJY

May 30, 2022 · 3 likes · 15,931 followers View post →
antisense.
@razoralign · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/qPnEhW6k6m https://t.co/m4z0J3Cm3X

May 26, 2022 · 15,931 followers View post →
Alex
@Alex_WU_Biology · X

RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…

May 26, 2022 · 3 shares · 4 followers View post →
Dake Zhang
@dakezhang · X

RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…

May 26, 2022 · 3 shares · 111 followers View post →
CompChemBio Bot
@CompChemBioBot · X

RT @SeqComplete: #BioIT #BioInformatics Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcr…

May 26, 2022 · 1 share · 2,761 followers View post →
SeqComplete
@SeqComplete · X

#BioIT #BioInformatics Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data [NEW RESULTS] https://t.co/Pcv90XTBhf

May 26, 2022 · 1 like · 1 share · 4,413 followers View post →
Helio Rocha
@_elioRocha · X

#bioRxiv Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data #bioinfo https://t.co/LlCboZNHqk

May 26, 2022 · 609 followers View post →
Dr. Shashank Joshi
@AskDrShashank · X

RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…

May 26, 2022 · 3 shares · 32,534 followers View post →
bioRxiv Bioinfo
@biorxiv_bioinfo · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/kIAshapO7s #biorxiv_bioinfo

May 25, 2022 · 1 like · 18,070 followers View post →
bioRxiv
@biorxivpreprint · X

Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/oRYBU98J98 #bioRxiv

May 25, 2022 · 4 likes · 3 shares · 136,945 followers View post →