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BlobFinder specifications


Unique identifier OMICS_26135
Name BlobFinder
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data Some fluorescent images of cells.
Input format TIF
Output data TXT
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.2
Stability Stable
Maintained Yes


No version available


  • person_outline Amin Allalou
  • person_outline Carolina Wahlby
  • person_outline BlobFinder Team

Additional information

Publication for BlobFinder

BlobFinder citations


Macrophage scavenger receptor SR AI contributes to the clearance of von Willebrand factor

PMCID: 5865439
PMID: 29326120
DOI: 10.3324/haematol.2017.175216
call_split See protocol

[…] antigens is less than 40 nm.Images were analyzed using ImageJ software for quantification of fluorescence by measuring the total pixel intensity per cell. Duolink-PLA experiments were analyzed using BlobFinder software (Uppsala University, Sweden) to quantify the number of fluorescent spots per cell. All images were assembled using ImageJ software. […]


Andy’s Algorithms: new automated digital image analysis pipelines for FIJI

Sci Rep
PMCID: 5691210
PMID: 29146920
DOI: 10.1038/s41598-017-15885-6

[…] undled plugins for scientific image processing and analysis, and is widely used by the scientific community. Other image processing and analysis programs include ImmunoRatio, and ilastik, Icy, Daime, BlobFinder, CellProfiler, MATLAB, MetaMorph, Duolink® ImageTool and Imaris (Supp. Table ). The latter four are commercially available programs requiring a subscription fee and additional application-s […]


Angiopoietin like 4 induces a β catenin mediated upregulation of ID3 in fibroblasts to reduce scar collagen expression

Sci Rep
PMCID: 5524754
PMID: 28740178
DOI: 10.1038/s41598-017-05869-x

[…] erference contrast objective. Analyses were performed with ZEN 2012 Light Edition software (Carl Zeiss, Germany) and PLA signals per nucleus (50 nuclei per experiment condition) were quantified using Blobfinder software (Centre for Image Analysis, Uppsala University). […]


Elevation of adenylate energy charge by angiopoietin like 4 enhances epithelial–mesenchymal transition by inducing 14 3 3γ expression

PMCID: 5701092
PMID: 28745316
DOI: 10.1038/onc.2017.244

[…] l Zeiss confocal microscope LSM710 using a Plan-APOCHROMAT 63 × /1.4 oil DIC objective, and ZEN2012 LE software with constant exposure and gain. Number of protein interaction was quantified using the BlobFinder software. […]


Molecular requirements of the B‐cell antigen receptor for sensing monovalent antigens

PMCID: 5090217
PMID: 27634959
DOI: 10.15252/embj.201694177

[…] Carl Zeiss), equipped with a Zeiss Plan‐Apochromat 63× oil immersion objective lens. For each sample, several images were captured from randomly chosen regions. All recorded images were analysed with BlobFinder software (Centre for Image Analysis, Uppsala University). PLA signals (dots/cells) were counted from at least 100 cells for each sample. […]


Identification of FRA 1 as a novel player in pancreatic cancer in cooperation with a MUC1: ERK signaling axis

PMCID: 5129987
PMID: 27220889
DOI: 10.18632/oncotarget.9557
call_split See protocol

[…] e in 1X PLA wash buffer B then once in 0.1X buffer B. Coverslips were mounted with Fluoromount G with DAPI. Results were visualized with confocal microscopy and the interactions were quantified using Blobfinder. All experimental groups were performed in quadruplicate and multiple independent fields per slide were used for quantification. […]


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BlobFinder institution(s)
Uppsala University, Centre for Image Analysis, Uppsala, Sweden
BlobFinder funding source(s)
Supported by the EU FP6 Project ENLIGHT and Olink Bioscience.

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