Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2024
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2024
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
versions View all 4 versions
addClaim

Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues - Data processing manual

Authors: Kylies, Dominik; Heil, Hannah S.; Vesga, Arturo G.; Del Rosario, Mario; Schwerk, Maria; Kuehl, Malte; Wong, Milagros N.; +2 Authors

Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues - Data processing manual

Abstract

Here we provide test datasets and a training manual for the parameter optimization with eSRRF. The training manual will guide users through an eSRRF paramenter optimization routine and quantiative image quality assesment with both, the ImagJ-Plugin NanoJ-eSRRF (Chapter 1) and the python implementation NanoPyx-eSRRF (Chapter 2). By showcasing the optimization routine on three differnt test dataset (Chapter 3), providing intermediate results and expected outcome, the users can eaisily learn how to find the optimal processing parameters for eSRRF processing. Three samples are provided to showcase the eSRRF reconstruction process: 1. Microtubules sample: Set01_DNA-PAINT_Microtubules.tif DNA-PAINT microscopy measurement of immunolabeled microtubules in fixed COS-7 cells, showing 0.121 localizations per frame and µm^2 (data published in Laine and Heil et al.) 108x90 pixels, 500 frames, pixel size: 160 nm 2. Kidney sample: Set02_KidneySDNephrinExM.tif ExM of human kidney biopsies stained with nephrin (data published in Kylies et al.) 150x150 pixels, 200 frames, pixel size: 102 nm 3. Single emitters simulation: Set03_simulation_groundTruth_2p5Sigma - Fluorescence stack_Avg5.tif Simulated individual molecules emitting placed on concentric rings with radii increasing by 220 nm steps. On each ring the molecules are separated by 57.5, 115, 173, 230, 288 and 345 nm, respectively (data published in Laine and Heil et al.) 33x33 pixels, 100 frames, pixel size: 100 nm 4. Test dataset for drift/vibration correction: Set04_ExSRRF_eSRRF_vibration_correction_practice_dataset.tif EsM of human kidney biopsies stained with nephrin (data published in Kylies et al.) 100x100 pixels, 200 frames, pixel size: 102 nm 5. Test dataset for photobleaching: Set05_Photobleaching.tif ExM of 120 nm Nanorulers (data published in Kylies et al.) 150x150 pixels, 75 frames, pixel size: 64 nm Jupyter-Notebook: ridge_detection.ipynb With this notebook qantitative image analyis of sturctures resolved with ExSRRF can be performed. Such as: calculation of the target structure density. identifying areas with high inter-ridge spacing by maping the distance to the nearest ridge based on Euclidean distance transform. measuring the spatial uniformity of the structure of interest by examining the distribution of the local densities and the distances to the nearest ridge. 

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    1
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
1
Average
Average
Average
Related to Research communities