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BFPTool: a software tool for analysis of Biomembrane Force Probe experiments

View Article: PubMed Central - PubMed

ABSTRACT

Background: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available.

Results: This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form.

Conclusions: An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

Electronic supplementary material: The online version of this article (doi:10.1186/s13628-016-0033-2) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Outputs of quick analysis. Results of simple case analysis of good quality video. a Frame from the video, t=5.0 s, contrast is sufficiently high and stable. The bead is marked by the red ring, the point tracked on the pipette in blue, the pipette tip pattern outlined by the white dashed box. b Tracking quality metrics of the bead (red) and correlation coefficient of the pipette (blue). Note that the bead detection quality is very volatile as compared to the pipette. c Tracks of the bead centre (red) and the pipette anchor point (blue) during the experiment time course. In the inset, part of the bead track is magnified; the last second of the path, delimited by the time points 6 s and 7 s, is highlighted (rest is faded). The time point 6.6 s denotes the probe rupture—see panel D. Fluctuations of the bead along the Y-coordinate (perpendicular to the pipette movements) are of order 10 nm. d Deformation of the RBC (Δx) and the force exerted by the probe during the experiment. Red dashed line indicates the zero force, the red mark indicates a separation of the RBC and bead. Total computational CPU time 105 s. The video file used for this analysis, basic.avi, is included in the program repository
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Fig3: Outputs of quick analysis. Results of simple case analysis of good quality video. a Frame from the video, t=5.0 s, contrast is sufficiently high and stable. The bead is marked by the red ring, the point tracked on the pipette in blue, the pipette tip pattern outlined by the white dashed box. b Tracking quality metrics of the bead (red) and correlation coefficient of the pipette (blue). Note that the bead detection quality is very volatile as compared to the pipette. c Tracks of the bead centre (red) and the pipette anchor point (blue) during the experiment time course. In the inset, part of the bead track is magnified; the last second of the path, delimited by the time points 6 s and 7 s, is highlighted (rest is faded). The time point 6.6 s denotes the probe rupture—see panel D. Fluctuations of the bead along the Y-coordinate (perpendicular to the pipette movements) are of order 10 nm. d Deformation of the RBC (Δx) and the force exerted by the probe during the experiment. Red dashed line indicates the zero force, the red mark indicates a separation of the RBC and bead. Total computational CPU time 105 s. The video file used for this analysis, basic.avi, is included in the program repository

Mentions: Figure 3a shows a screenshot of the video overlaid with the tracking results, the bead delineated in red, the reference point (anchor) on the pipette in blue. In this example, the analysed video was 456 frames long (7.0 s at 65 fps), and the whole interval was treated in a single run. After opening the video, the bead was click-selected, and a tight delineating rectangle was drawn around the pipette tip (white dashed in Fig. 3a) to delimit the pattern for matching. The tracking procedure could be started immediately.Fig. 3


BFPTool: a software tool for analysis of Biomembrane Force Probe experiments
Outputs of quick analysis. Results of simple case analysis of good quality video. a Frame from the video, t=5.0 s, contrast is sufficiently high and stable. The bead is marked by the red ring, the point tracked on the pipette in blue, the pipette tip pattern outlined by the white dashed box. b Tracking quality metrics of the bead (red) and correlation coefficient of the pipette (blue). Note that the bead detection quality is very volatile as compared to the pipette. c Tracks of the bead centre (red) and the pipette anchor point (blue) during the experiment time course. In the inset, part of the bead track is magnified; the last second of the path, delimited by the time points 6 s and 7 s, is highlighted (rest is faded). The time point 6.6 s denotes the probe rupture—see panel D. Fluctuations of the bead along the Y-coordinate (perpendicular to the pipette movements) are of order 10 nm. d Deformation of the RBC (Δx) and the force exerted by the probe during the experiment. Red dashed line indicates the zero force, the red mark indicates a separation of the RBC and bead. Total computational CPU time 105 s. The video file used for this analysis, basic.avi, is included in the program repository
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5304404&req=5

Fig3: Outputs of quick analysis. Results of simple case analysis of good quality video. a Frame from the video, t=5.0 s, contrast is sufficiently high and stable. The bead is marked by the red ring, the point tracked on the pipette in blue, the pipette tip pattern outlined by the white dashed box. b Tracking quality metrics of the bead (red) and correlation coefficient of the pipette (blue). Note that the bead detection quality is very volatile as compared to the pipette. c Tracks of the bead centre (red) and the pipette anchor point (blue) during the experiment time course. In the inset, part of the bead track is magnified; the last second of the path, delimited by the time points 6 s and 7 s, is highlighted (rest is faded). The time point 6.6 s denotes the probe rupture—see panel D. Fluctuations of the bead along the Y-coordinate (perpendicular to the pipette movements) are of order 10 nm. d Deformation of the RBC (Δx) and the force exerted by the probe during the experiment. Red dashed line indicates the zero force, the red mark indicates a separation of the RBC and bead. Total computational CPU time 105 s. The video file used for this analysis, basic.avi, is included in the program repository
Mentions: Figure 3a shows a screenshot of the video overlaid with the tracking results, the bead delineated in red, the reference point (anchor) on the pipette in blue. In this example, the analysed video was 456 frames long (7.0 s at 65 fps), and the whole interval was treated in a single run. After opening the video, the bead was click-selected, and a tight delineating rectangle was drawn around the pipette tip (white dashed in Fig. 3a) to delimit the pattern for matching. The tracking procedure could be started immediately.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: The Biomembrane Force Probe is an approachable experimental technique commonly used for single-molecule force spectroscopy and experiments on biological interfaces. The technique operates in the range of forces from 0.1 pN to 1000 pN. Experiments are typically repeated many times, conditions are often not optimal, the captured video can be unstable and lose focus; this makes efficient analysis challenging, while out-of-the-box non-proprietary solutions are not freely available.

Results: This dedicated tool was developed to integrate and simplify the image processing and analysis of videomicroscopy recordings from BFP experiments. A novel processing feature, allowing the tracking of the pipette, was incorporated to address a limitation of preceding methods. Emphasis was placed on versatility and comprehensible user interface implemented in a graphical form.

Conclusions: An integrated analytical tool was implemented to provide a faster, simpler and more convenient way to process and analyse BFP experiments.

Electronic supplementary material: The online version of this article (doi:10.1186/s13628-016-0033-2) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus