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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


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

Additional information

Publication for BlobFinder

BlobFinder in publications

PMCID: 5865439
PMID: 29326120
DOI: 10.3324/haematol.2017.175216

[…] 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., binding experiments are described in detail […]

PMCID: 5681548
PMID: 29127290
DOI: 10.1038/s41467-017-01425-3

[…] microscopy (zeiss, germany) followed by deconvolution with huygens essential version 16.05 (scientific volume imaging, the netherlands, pla dots per cell were quantified with blobfinder v3.2 image analysis software (uppsala university, stockholm, sweden) and the mean number of pla dots per cell was calculated by analyzing a minimum of 100 cells., all paired-end reads […]

PMCID: 5672593
PMID: 29367884
DOI: 10.1038/cddiscovery.2017.76

[…] medium containing dapi 18 (sigma-aldrich) and analyzed with a zeiss inversed fluorescent microscope at 63× magnification. quantification of signals (number of red dots per cell) was done using the blobfinder software. experiments were performed in triplicate, n=10 pictures per conditions., cell viability was assessed in real-time using the xcelligence system (roche, munich, germany). ht22 […]

PMCID: 5593540
PMID: 28915569
DOI: 10.18632/oncotarget.19639

[…] recommendations using duolink® in situ detection reagents red kit (sigma-aldrich, duo92008) and as previously described []. the number of red dots and the intensity per dots were counted using the blobfinder software. 200 cells were randomly selected in 5 fields., mcf-7 cells were washed in 0.1m sörensen buffer, ph 7.3. then, cells were fixed with 2% glutaraldehyde (sigma aldrich, g5882) […]

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

[…] 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., for immunoprecipitation, at the indicated time points after treatments, cells were lysed using ip lysis buffer (25 mm tris-hcl ph7.4, 150 mm nacl, 1% np-40, 1 mm edta). […]

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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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