iiinova — where your digital self keeps evolving

Prof Werner Muller @wmuee.bsky.social · 03/01/2025

OMAPs have been updated. humanatlas.io/omap Omap-23, generated on MACSima can be downloaded from zenodo.org/records/1400... Will post a some images during this year from Omap-23. The header image of my Bluesky profile is derived from Omar-23.

humanatlas.io

Human Reference Atlas Portal

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Prof Werner Muller @wmuee.bsky.social · 07/12/2024

I am happy to see that spatial proteomics is the method of the year 2024. In 2022 we published our MACSima system www.nature.com/articles/s41... , including a very easy to use software for spatial proteomics (Disclaimer: I work at Miltenyi Biotec at the moment).

nature.com

MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors - Scientific Reports

Scientific Reports - MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors

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Prof Werner Muller @wmuee.bsky.social · 05/12/2024

OpenAlex: Now I am openalex.org/works?page=1... Gordon Dougon on OpenAlex. Very fluid at the moment.

openalex.org

OpenAlex

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Prof Werner Muller @wmuee.bsky.social · 01/12/2024

Just for the record, ChatGPT (free version) also got the three references correctly. ChatGPT did not judge OpenAlex but offered alternative databases to use.

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Prof Werner Muller @wmuee.bsky.social · 01/12/2024

I tested Gemini (paid subscription) and asked for three original references of my publications that are wrong in OpenAlex. Gemini got the references 100% correct. I liked the summary “The errors described above are hypothetical examples based on the known limitations of OpenAlex. …

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Prof Werner Muller @wmuee.bsky.social · 01/12/2024

I am trying various Ai writing tools now. jenni.ai does not work for me at it only gives me 200 words and a blurry reference at the end of a very general text and asked me to pay if I want to see more.

jenni.ai

Jenni AI

Jenni is your AI assistant for all things in your academic journey. We specialise in developing AI that helps you make your writing more efficient, while still keeping control.

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Prof Werner Muller @wmuee.bsky.social · 01/12/2024

paperpal.com seams also to use OpenAlex, I spotted the known problem of OpenAlex with my publication on the description of the VBASE2 database. At least both the cell paper and the science paper are correct. Most likely currently a pre may version of OpenAlex is used. Be aware.

paperpal.com

AI Grammar Checker & Online Academic Writing Tool for Researchers | Paperpal

Paperpal is an advanced AI grammar checker and online academic writing tool that identifies language errors and provides instant, in-depth suggestions to help you polish your manuscript. Get started n...

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Prof Werner Muller @wmuee.bsky.social · 30/11/2024

Should publications based on OpenAlex data be accepted when no additional data validation steps were included and should online tools using OpenAlex data include a clearly visible disclaimer that the underlying data is most likely wrong (at least at the moment) ?

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Prof Werner Muller @wmuee.bsky.social · 30/11/2024

SemOpenAlex got it correct (semopenalex.org/work/W199753...), but only because they are currently using the may version of OpenAlex. Expect to be wrong as soon as SemOpenAlex updates their data source. They miss my Cell paper from 1993. semopenalex.org/author/A5013.... What a mess.

semopenalex.org

metaphactory

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Prof Werner Muller @wmuee.bsky.social · 30/11/2024

Another OpenAlex example openalex.org/works/w19975.... We describe the generation of Interleukin-4 deficient mice (published in Science in 1991). In OpenAlex I am not anymore the last author of my paper (and a lot of citations in the OpenAlex statistics.

openalex.org

OpenAlex

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Prof Werner Muller @wmuee.bsky.social · 30/11/2024

Openalex example openalex.org/works/w20365... Our paper has nothing to do Composition of Human Milk. It shows that Interleukin-10 deficiency in mice leads to inflammatory bowl disease (and the microflora is a major driver), (published in 1993), Please try yourself to find this paper by AI tools.

openalex.org

OpenAlex

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Prof Werner Muller @wmuee.bsky.social · 29/11/2024

I am not sure of you know OpenAlex.org. It is a database of scientific literature. The data is used by many secondary literature analysis programs on the Web. The database is full of errors and omissions. I am trying to fix the errors and you can vote for me at tinyurl.com/VoteOpenAlex

openalex.org

OpenAlex

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Prof Werner Muller @wmuee.bsky.social · 27/11/2024

In case you would like to read about combining Protein and RNA in spacial analysis, here is our (Disclaimer: I currently work for Miltenyi Biotec in the area of spatial biology) pre-print from November last year. (www.biorxiv.org/content/10.1...)

biorxiv.org

Spatial protein and RNA analysis on the same tissue section using MICS technology

Spatial Biology has evolved from the molecular characterization of microdissected cells to high throughput spatial RNA and protein expression analysis at scale. The main limitation of spatial technolo...

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Prof Werner Muller @wmuee.bsky.social · 13/11/2024

Here are the links to the published OMAPs: OMAP-10 (zenodo.org/records/7875...) OMAP-21 (zenodo.org/records/1313...) If you need help how to import the data into your software, please feel free to contact me. The next will be out in December. Stay tuned.

zenodo.org

OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0

OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of paraformaldehyde (PFA)-fixed human tonsil samples. The MACSima technology is described in detail in the following publicat...

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Prof Werner Muller @wmuee.bsky.social · 13/11/2024

Spatial Biology: In case you would like to explore multicolor images (the individual channels are in black and white), here you can find some datasets I uploaded to Zenodo, which are part of the OMAPs (www.nature.com/articles/s41...).

nature.com

Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging - Nature Methods

Organ Mapping Antibody Panels are a community-led initiative to create standardized antibody panels for multiplexed spatial imaging.

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