ISBI eurobioimaging
Open Bio Image Alliance

Deconvolution — Making the Most of Fluorescence Microscopy

Deconvolution is one of the most common image-reconstruction tasks that arise in 3D fluorescence microscopy. The aim of this challenge is to benchmark existing deconvolution algorithms and to stimulate the community to look for novel, global and practical approaches to this problem.

The challenge will be divided into two stages: a training phase and a competition (testing) phase. It will primarily be based on realistic-looking synthetic data sets representing various sub-cellular structures. In addition it will rely on a number of common and advanced performance metrics to objectively assess the quality of the results.

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Deconvolution results

The minimum requirement for each participant is to upload four files, corresponding to the deconvolution results he/she obtained for the four channels of the qualification-stage data.

For a given channel, the result must be stored in an uncompressed 32-bit floating-point TIFF file. It must have the same size as the original data stack (that is, 192 x 192 x 64 pixels along the X, Y and Z dimensions respectively).

In addition, the result files must comply with the following naming convention: the result for channel 0 must be named Result0.tif, the result for channel 1 must be named Result1.tif, etc.

Technical documentation

Apart from the deconvolution results each participant is also expected to upload a brief technical description of the employed method. This description should include the steps involved in the deconvolution method and the approach of the participant for tuning the parameters of the algorithm.

We ask you, if possible, to provide this document in Latex format based on the template and instructions available here; it must be between one and two pages in length. If you need assistance with Latex, please contact us by e-mail.


The aforementioned files must be uploaded by January 6, 2014, 23:59 (GMT+1).

Registered participants will receive a personalized upload link by e-mail.

Important Dates

Deadline for submission

The registered participants will receive soon a personalized upload link.

January 6, 2014

Beginning of evaluation stage

The evaluation stage of the second edition of the challenge has started.

November 6, 2013

Evaluation stage

The official stage of the challenge will last around 2 months.

November/December, 2013

Beginning of training stage

The training stage of the second edition of the challenge has started. Follow this link to register and receive e-mail updates.

July 17, 2013