Cyto 2017 Image Analysis Challenge

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Cyto 2017 Image Analysis Challenge

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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

*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]
<mailto:[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