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Upload datasets

1. Select format

Input format
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2. Parameters

Input additional parameters

No additional parameters are required for this file format


Fill in all parameters to display the upload box (make this an info box).

3. Select datasets


Drag And Drop your file here

Uploaded datasets

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No dataset has been uploaded yet.
  • Number of uploaded files: {{successfullyUploaded}}/{{successfullyUploaded+$flow.files.length}}
id File name Description Status Options
{{$index+1}} {{file.name}} Uploading
{{$flow.files.length+$index+1}} {{data.name}} (uploaded, parsed, import report). {{data.description}} {{data.preanalysis_status}}

Editing dataset: {{editedDataset.name}}

Name:
Description:
 

Information about a dataset

Selected dataset: {{shownStatistics.name}}

Framerate (s) {{shownStatistics.dt | number : 5}}
Number of traces {{shownStatistics.pre_ntraces}}
Number of frames {{shownStatistics.pre_nframes}}
Number of detections {{shownStatistics.pre_npoints}}
Longest gap (frames) {{shownStatistics.pre_ngaps}}
Number of traces with ≥3 detections {{shownStatistics.pre_ntraces3}}
Number of jumps {{shownStatistics.pre_njumps}}
Length of trajectories (in number of frames) median: {{shownStatistics.pre_median_length_of_trajectories}}, mean: {{shownStatistics.pre_mean_length_of_trajectories | number}}
Particles per frame median: {{shownStatistics.pre_median_particles_per_frame}}, mean: {{shownStatistics.pre_mean_particles_per_frame | number}}
Jump length (µm) median: {{shownStatistics.pre_median_jump_length | number}}, Mean: {{shownStatistics.pre_mean_jump_length | number}}

Global statistics

Please wait while the dataset is preprocessed...
Datasets with incompatible framerates have been uploaded. Click on the symbol next to each dataset to display the inferred framerate.
Number of traces {{statistics.pre_ntraces}}
Number of frames {{statistics.pre_nframes}}
Number of detections {{statistics.pre_npoints}}
Longest gap (frames) {{statistics.pre_ngaps}}
Number of traces with ≥3 detections {{statistics.pre_ntraces3}}
Number of jumps {{statistics.pre_njumps}}
Length of trajectories (in number of frames) median: {{statistics.pre_median_length_of_trajectories | number}}, mean: {{statistics.pre_mean_length_of_trajectories | number}}
Particles per frame median: {{statistics.pre_median_particles_per_frame}}, mean: {{statistics.pre_mean_particles_per_frame | number}}
Jump length (µm) median: {{statistics.pre_median_jump_length | number}}, Mean: {{statistics.pre_mean_jump_length | number}}
Make sure that you have uploaded datasets.

In this tab, you can perform a kinetic modeling of your data

Please wait until all the datasets have been preprocessed.

Dataset selection

Id File name Description Status Include (all/none)
{{$index+1}} {{data.name}} {{data.description}}

Parameters

Jump length distribution

Bin width (µm)
Number of timepoints
Jumps to consider
Use entire trajectories?
Max jump (µm)

It seems that your dataset contains at most {{jldParameters.GapsAllowed}} gap(s), but defocalization (z) correction is not precomputed for that number of gaps. Thus z-correction will not be possible during model fitting.
It seems that your dataset contains at most {{jldParameters.GapsAllowed}} gap(s), so the algorithm has been set accordingly

Model fitting

Datasets with different framerates are selected. You can only fit a pool of datasets with the same framerate.
Kinetic model:
Dbound (µm²/s): min: max:
Dfree (µm²/s): min: max:
Fbound: min: max:
Dslow (µm²/s): min: max:
Dfast (µm²/s): min: max:
Fbound: min: max:
Ffast: min: max:
Localization error (µm): Fit it from data
  min: max:
dZ (µm): Use Z correction Your dataset contains at most {{jldParameters.GapsAllowed}} gap(s), but defocalization (z) correction is not precomputed for that number of gaps. z-correction will not be possible during model fitting.
(using (dZ={{modelingParameters.dZfit}} µm, dT={{modelingParameters.dTfit*1000.}} ms) for the z correction) ?.
Model Fit:
Perform single cell fit: (long)
Iterations:
  {{getNumberFittedDatasets()}}/{{getNumberDatasetsToFit()}}

Jump length histograms

Fit parameters for cell {{ce}}.
  • Dbound : {{jlfit[ce-1].fitparams.D_bound | number}} ± {{jlfit[ce-1].fitparams.D_bound_std | number:4}}
  • Dfree : {{jlfit[ce-1].fitparams.D_free | number}} ± {{jlfit[ce-1].fitparams.D_free_std | number:4}}
  • Dslow : {{jlfit[ce-1].fitparams.D_med | number}} ± {{jlfit[ce-1].fitparams.D_med_std | number:4}}
  • Dfast : {{jlfit[ce-1].fitparams.D_fast | number}} ± {{jlfit[ce-1].fitparams.D_fast_std | number:4}}
  • Fbound : {{jlfit[ce-1].fitparams.F_bound | number}} ± {{jlfit[ce-1].fitparams.F_bound_std | number:4}}
  • Fslow : {{1-jlfit[ce-1].fitparams.F_fast-jlfit[ce-1].fitparams.F_bound | number}}
  • Ffast : {{jlfit[ce-1].fitparams.F_fast | number}} ± {{jlfit[ce-1].fitparams.F_fast_std | number:4}}
  • σ (µm): {{jlfit[ce-1].fitparams.sigma| number}} ± {{jlfit[ce-1].fitparams.sigma_std| number : 4}}
  • l2 error: {{jlfit[ce-1].fitparams.l2| number : 8}}
  • AIC: {{jlfit[ce-1].fitparams.aic | number : 2}}, BIC: {{jlfit[ce-1].fitparams.bic | number : 2}}
Global fit parameters for cells {{getSelectedIds()}}.
  • Dbound : {{jlpfit.fitparams.D_bound | number}} ± {{jlpfit.fitparams.D_bound_std | number:4}}
  • Dfree : {{jlpfit.fitparams.D_free | number}} ± {{jlpfit.fitparams.D_free_std | number:4}}
  • Dslow : {{jlpfit.fitparams.D_med | number}} ± {{jlpfit.fitparams.D_med_std | number:4}}
  • Dfast : {{jlpfit.fitparams.D_fast | number}} ± {{jlpfit.fitparams.D_fast_std | number:4}}
  • Fbound : {{jlpfit.fitparams.F_bound | number}} ± {{jlpfit.fitparams.F_bound_std | number:4}}
  • Fslow : {{1-jlpfit.fitparams.F_fast-jlpfit.fitparams.F_bound | number}}
  • Ffast : {{jlpfit.fitparams.F_fast | number}} ± {{jlpfit.fitparams.F_fast_std | number:4}}
  • l2 error: {{jlpfit.fitparams.l2| number : 8}}
  • σ (µm) {{jlpfit.fitparams.sigma | number}} ± {{jlpfit.fitparams.sigma_std | number:4}}
  • AIC: {{jlpfit.fitparams.aic | number : 2}}, BIC: {{jlpfit.fitparams.bic | number : 2}}
Max jump displayed (µm)
Display PDF/CDF
Display dataset
Displayed group {{getSelectedIds()}}
Show pooled jump length distribution: Please wait...
Show pooled fit:
Display residuals:

In this tab, you can download the results of your analysis. To do so, you need to click the "Mark for download" button in the "Kinetic modeling" tab.

To download all the fitted coefficients, together with the raw data, choose the ZIP export. The archive contains a README.md file that details the content and organization of all the files.

id Created Name Description Dataset(s) Display Download Delete
{{$index+1}} {{dwl.date}} {{dwl.name}} {{dwl.description}} {{getDatasetInfo(incl, 'i')+1}}  P C f JP F d{{dwl.display.displayedDataset}} SVG, PDF, PNG, EPS, ZIP
Please wait...

 

Erase this analysis ( you are entering the danger zone)

All your uploaded datasets and analyses will be deleted. There is no way back!

Spot-On version v0.11.5a using the fastspt backend version 16.1, an open source software released under the AGPL license, 2017.