Required Files

TIFF formatted time-lapse image set of the puncta
TIFF formatted time-lapse image set of the ECM

Experiment Configuration

Amount of time, in minutes, between the images
Size of each side of the pixels, in µm.

Cell Detection

Apply a median filter before trying to find the cells

Puncta Detection

Puncta seed identification threshold
Puncta seed minimum size in pixels
Puncta seed expansion threshold

Puncta Size Options

Leave blank to remove the minimum puncta size limit
Leave blank to remove the maximum puncta size limit

Puncta Properties

Leave blank to remove the major/minor axis ratio limit

ECM Normalization

The ECM intensity not covered by cells will be normalized to this intensity.



TIFF formatted flat field correction image.

Notification Options

Your email address will only be used for notification purposes
Any text in this box will be returned with the results email.


Thank you for helping to test the invadopodia analysis webserver. If you encounter any problems, feel free to email me (matthew.berginski [AT]

Required Files

All files should be submitted as raw-data grayscale TIFF files. The processing pipeline also expects that the files submitted were taken simultaneously or as close as is possible with your imaging setup. Thus, the ECM imaged in the first frame of the time-lapse should be from the same region and time as the first frame of the puncta time-lapse.

Puncta Time-lapse

The puncta file should look something like the sample file linked from the home page. Namely, the bright regions of image should correspond to the potential invadopodia. The system has been tested with Lifeact-GFP images, but I expect that images of other invadopodia componenets will also be acceptable for processing.

ECM Time-lapse

The puncta file should look something like the sample file linked from the home page. Namely, the field of view should be uniformly bright, with the regions corresponding to invadopodia degradation appearing dim compared to the surronding area. The processing pipeline can deal with some variation in the uniformity of the labeled ECM.

Experiment Configuration

Median Filter:The cell outlines are idenfied from the puncta images, which occassionally require a median filtering step. Select this option if the cells in your images are not being detected.

Puncta Seed and Expansion Thresholds:Puncta identification uses two thresholds to determine where the puncta are located in each image. First a set of seeds pixels are identifed using the seed threshold and then those seeds are expanded based on the expansion threshold. You also have the option to eliminate seeds below a certain size using the puncta seed minimum size settings.

If you want to see what one of your images looks like when processed with a specific threshold try out the threshold tester available through the Focal Adhesion Analysis Server. The algorithm used to idenfity adhesions is very similar to the one used to identify the puncta, so the results from this service are a good guide as to how you should set these parameters.

Min/Max Size: These settings control the minimum or maximum puncta sizes allowed through the segmentation step, both are specified in pixels.

Max Major/Minor Axis Ratio: This setting controls maximum allowable ratio between the major and minor axes of an ellipse fit to a potential puncta. This filter allows very elongated structures to be automatically removed from consideration.

ECM Normalization

This value sets the average intensity of the ECM outside the cell bodies in your ECM images. Setting this value will allow comparisons to be made between the intensities of seperate fluorescent ECM preparations. You can remove the setting by leaving the box blank. When blank, the ECM will be photobleach corrected to the first image in the image set.


ECM Flat Field Correction File

If this image is submitted, it will be used to flat field correct the ECM image set.

Notification Options

Email Address

If an email address is provided, you will be notified via email when your job finishes processing. Your email address will only be used for notification purposes. If this is not provided, then the experiment status page returned on submission needs to bookmarked in order to retrieve your results.

Note to Self About Experiment

Whatever you put in this box will be send back to you in any email the system sends concerning your experiment. It is limited to 80 characters.
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