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

May 2023 Genome Biol

Synopsis of Social media discussions

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.

A
Agreement
 Moderate agreement

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

I
Interest
 High level of 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.

E
Engagement
 Moderate level of engagement

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

I
Impact
 High level of impact

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

Social Mentions

YouTube

1 Videos

Twitter

62 Posts

Blogs

2 Articles

Metrics

Video Views

15

Total Likes

129

Extended Reach

701,381

Social Features

65

Timeline: Posts about article

Top Social Media Posts

Posts referencing the article

Social RTCL TV

September 7, 2023

15 views

  • Ahmad Majed
    @2c817a7338f14a3 (Twitter)

    RT @public4safety: @2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model…
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    January 17, 2025

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  • @public4safety (Twitter)

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

    January 17, 2025

    2


  • @public4safety (Twitter)

    @2c817a7338f14a3 Correct spelling Oscilloscope التهجئة الصحيحة ~~~~~~~~~~~~~~~~~~~~~~ Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
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    January 17, 2025

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  • Charles Dussiau
    @DussiauC (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    November 4, 2024

    17

  • Taco Jesse
    @TJesse62 (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    October 30, 2024

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  • Karol Kaiser
    @KarolKaiser1 (Twitter)

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

    October 30, 2024

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  • antisense.
    @razoralign (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    October 30, 2024

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  • Max von Hades
    @Densifiy (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    July 13, 2024

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  • antisense.
    @razoralign (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    July 13, 2024

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  • Mar Muñiz Moreno
    @marmmmoreno (Twitter)

    RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…
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    May 27, 2023

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  • Startup Or Scaleup
    @StartupNScaleup (Twitter)

    RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…
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    May 26, 2023

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  • A Coffee with Technology
    @CoffeTechnology (Twitter)

    RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…
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    May 26, 2023

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  • Techie Girl
    @CandyTech1 (Twitter)

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

    May 26, 2023

    10

  • Ciso Online Club
    @CisoOnlineClub (Twitter)

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

    May 26, 2023

    10

  • DATA DAVE
    @Dare2Digitize (Twitter)

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

    May 26, 2023

    10

  • Digi Biz Insight
    @digibizinsight (Twitter)

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

    May 26, 2023

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  • Karol Kaiser
    @KarolKaiser1 (Twitter)

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

    May 26, 2023

    10

  • CIO Connection
    @CIOConnection (Twitter)

    RT @RNASeqBlog: Researchers from the @PW_edu propose an innovative #probabilisticmodel, Celloscope, that utilizes established prior knowled…
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    May 26, 2023

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  • Vince Beltran, Ph.D.
    @levin_beltran (Twitter)

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

    May 26, 2023

    10

  • RNA-Seq Blog
    @RNASeqBlog (Twitter)

    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
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    May 26, 2023

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  • wook
    @wook20120711 (Twitter)

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

    May 26, 2023

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  • BioDecoded
    @BioDecoded (Twitter)

    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
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    May 25, 2023

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  • Alexis Lomakin, Ph.D. (אל) אַלעקסיס לאָמאַקין
    @Alexis_Lomakin (Twitter)

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

    May 22, 2023

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  • AiiHC International Ltd.
    @AiihcLtd2022 (Twitter)

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

    May 22, 2023

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  • antisense.
    @razoralign (Twitter)

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

    May 22, 2023

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  • choiLab
    @jungminchoilab (Twitter)

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

    May 22, 2023

    3

  • Phenomics
    @Phenomics_J (Twitter)

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

    May 22, 2023

    3

  • Lukas Valihrach
    @LukasValihrach (Twitter)

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

    May 22, 2023

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  • Sevenn
    @renxwise (Twitter)

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

    May 19, 2023

    17

  • Hamim Zafar
    @Quasarzafar (Twitter)

    RT @razoralign: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.…
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    May 19, 2023

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  • Transcriptomes
    @transcriptomes (Twitter)

    Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial t... https://t.co/atA4sngv2Z
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    May 18, 2023

  • Ewa Szczurek
    @ewa_szczurek (Twitter)

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

    May 18, 2023

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  • Genome Biology
    @GenomeBiology (Twitter)

    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
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    May 18, 2023

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  • Paolo Devanna
    @PaoloDevanna (Twitter)

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

    May 18, 2023

    5

  • ashley
    @notashleel (Twitter)

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

    May 18, 2023

    5

  • Marcel Schulz - @marcelschulz@genomic.social
    @TheMarcelSchulz (Twitter)

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

    May 18, 2023

    5

  • Michael Love
    @mikelove (Twitter)

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

    May 18, 2023

    5

  • Francisco J Ruiz-Ruano
    @fjruizruano (Twitter)

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

    May 18, 2023

    17

  • Szu Shuo Lee
    @ShuoSzu (Twitter)

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

    May 17, 2023

    17

  • Brian Dean
    @bdean_ (Twitter)

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

    May 17, 2023

    17

  • Toyota_Group_Komaba
    @KomaToug (Twitter)

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

    May 17, 2023

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  • Leiy
    @leur123 (Twitter)

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

    May 17, 2023

    17

  • Gerard Baquer
    @GerardBaquer (Twitter)

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

    May 17, 2023

    17

  • Nils Eling
    @NilsEling (Twitter)

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

    May 17, 2023

    5

  • Yiran Meng
    @YRMeng (Twitter)

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

    May 17, 2023

    17

  • priya joseph
    @ayirpelle (Twitter)

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

    May 17, 2023

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  • MyJournals
    @myjournals (Twitter)

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

    May 17, 2023

  • AL'AM KATAM
    @BULLWTI (Twitter)

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

    May 17, 2023

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  • antisense.
    @razoralign (Twitter)

    Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data https://t.co/yp5zVZCssq https://t.co/sMBJ3bgNkQ
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    May 17, 2023

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  • Ewa Szczurek
    @ewa_szczurek (Twitter)

    Link to the paper: https://t.co/wJDj9t5bAT
    view full post

    May 17, 2023

  • Ewa Szczurek
    @ewa_szczurek (Twitter)

    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!
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    May 17, 2023

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  • Sandy Anderson
    @ara_anderson (Twitter)

    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
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    September 15, 2022

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  • antisense.
    @razoralign (Twitter)

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

    May 30, 2022

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  • antisense.
    @razoralign (Twitter)

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

    May 26, 2022

  • Alex
    @Alex_WU_Biology (Twitter)

    RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…
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    May 26, 2022

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  • Dake Zhang
    @dakezhang (Twitter)

    RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…
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    May 26, 2022

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  • CompChemBio Bot
    @CompChemBioBot (Twitter)

    RT @SeqComplete: #BioIT #BioInformatics Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcr…
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    May 26, 2022

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  • SeqComplete
    @SeqComplete (Twitter)

    #BioIT #BioInformatics Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data [NEW RESULTS] https://t.co/Pcv90XTBhf
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    May 26, 2022

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  • Helio Rocha
    @_elioRocha (Twitter)

    #bioRxiv Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data #bioinfo https://t.co/LlCboZNHqk
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    May 26, 2022

  • Dr. Shashank Joshi
    @AskDrShashank (Twitter)

    RT @biorxivpreprint: Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data http…
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    May 26, 2022

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  • bioRxiv Bioinfo
    @biorxiv_bioinfo (Twitter)

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

    May 25, 2022

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  • bioRxiv
    @biorxivpreprint (Twitter)

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

    May 25, 2022

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Abstract Synopsis

  • 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.