2017 Program Image Analysis Challenge

In a time when vast amounts of bioimaging 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 www.proteinatlas.org 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 (Thul et al. Science 2017), part of the Human Protein Atlas database www.proteinatlas.org (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”).

The official test data is now up on the downloads site (http://www.proteinatlas.org/CYTO_challenge2017/)

Solution submission can be performed by following the instructions here: 
https://cellprofiling.github.io/cyto-challenge/ or by email to cytochallenge2017@gmail.com
Deadline for submission of results is June 13 15:30


4 Challenges and a 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: 1802 fields of view containing multilabel data for 2 protein localizations
Challenge 2: 20,000 fields of view containing multilabel data for 13 protein localizations
Challenge 3: 870 fields of view containing multilabel 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”.

Background Information and Further Specifications:

Further background information and specifications can be found online at:

Presentation of results at CYTO 2017 (June 14 15:30-16:00  Ballroom B):

The leader board and presentation submissions will close 24 hours prior to presentations (June 13 15:30 EDT). The top teams present at the CYTO conference should prepare a 5 minute presentation of their approaches and email them to cytochallenge2017@gmail.com. Teams not present that still wish to present results should submit a 2 slide presentation to cytochallenge2017@gmail.com. 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.