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BlobFinder specifications

Information


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

Versioning


No version available

Maintainers


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

Additional information


http://www.cb.uu.se/~amin/BlobFinder/HelpBlobFinder.html

Publication for BlobFinder

BlobFinder citations

 (56)
library_books

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

2018
Haematologica
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 […]

library_books

KSRP specifies monocytic and granulocytic differentiation through regulating miR 129 biogenesis and RUNX1 expression

2017
Nat Commun
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, http://svi.nl). 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 […]

library_books

Glucose regulated protein 75 determines ER–mitochondrial coupling and sensitivity to oxidative stress in neuronal cells

2017
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 […]

library_books

GABARAPL1 tumor suppressive function is independent of its conjugation to autophagosomes in MCF 7 breast cancer cells

2017
Oncotarget
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) […]

library_books

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

2017
Sci Rep
PMCID: 5524754
PMID: 28740178
DOI: 10.1038/s41598-017-05869-x

[…] 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)., chip and re-chip were performed as previously described, . all primer pairs used are presented in supplementary table ., […]

library_books

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

2017
Oncogene
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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