Cyto 2017 Image Analysis Challenge

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Cyto 2017 Image Analysis Challenge

Silas Leavesley
Hi All,

Some of you may be interested in the Image Data Analysis Challenge that we are hosting this year in conjunction with the Cyto Conference.  If interested, please see the information below.  Thanks!

Best regards,


Take the CYTO 2017 Image Analysis Challenge

In a time when vast amounts of bio-imaging data are produced in labs around the globe every day, effectively extracting salient information from this growing resource is paramount to understanding complex biological questions.

The CYTO 2017 Image Analysis Challenge proposes four tasks where the aim is to classify fluorescence microscopy images from the Human Protein Atlas database based on subcellular protein localization, and present your findings during the final platform session at CYTO 2017.

The Dataset
The image data provided in this challenge were generated by the Cell Atlas (ref Science to be published), part of the Human Protein Atlas database (Uhlen et al. 2010). The images visualize immunostaining of human proteins and the aim of this challenge is to recognize the patterns of protein subcellular distribution to major organelles and fine substructures.

All images were acquired in a standardized manner using Leica SP5 confocal microscopes using a 63x/1.2 NA oil objective and Nyquist sampling rate in 4 fluorescence channels. Each field of view is comprised of 4 images. This includes 3 reference channels; DAPI for the nucleus (“blue”), antibody based staining of microtubules (“red”), and endoplasmic reticulum (“yellow”). These can be used to aid you in predicting localizations of the protein of interest (“green”).

Four Challenges + Bonus Challenge
The input images for all sub-challenges will be .tif format with separate images for each of the channels from a given field of view. A brief description of the dataset contained in each sub-challenge:

Challenge 1
1,802 fields of view containing multi-label data for 2 protein localizations

Challenge 2
20,000 fields of view containing multi-label data for 13 protein localizations

Challenge 3
870 fields of view containing multi-label data for an additional 3 classes to be combined with the dataset from Challenge 2

Challenge 4
There are no new images in Challenge 4. Solution keys for this challenge reveal patterns that were merged in previous challenges and should replace the solution keys from those challenges.

Bonus Challenge
There are no new images for this challenge. Solution keys for this challenge specify a binary value indicating whether the field of view has been labeled as “variable”. Further background information and specifications can be found HERE.

Presentation of results at CYTO 2017
The leader board and presentation submissions will close 24 hours prior to presentations (June 13 15:30 EDT). Top teams present at the CYTO conference should prepare a five minute presentation of their approaches and email them to [hidden email]. Teams not present that still wish to present results should submit a two-slide presentation.

All presentations will take place on June 14, from 15:30-16:00 in Ballroom B of the Hynes Convention Center.  Teams will be notified by 17:00 on June 13 if they are presenting.

In addition to the satisfaction of besting the challenges, prizes for winners may include complimentary registration to CYTO 2018 in Prague, complimentary ISAC membership and the possibility of participating in a paper published on the challenge in Cytometry Part A.

Silas J. Leavesley, Ph.D.
Associate Professor
Department of Chemical and Biomolecular Engineering
Department of Pharmacology
Center for Lung Biology
University of South Alabama
150 Jaguar Drive, SH4129
Mobile, AL 36688
ph: (251)-460-6160
fax: (251)-461-1485
google scholar:


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