If you choose to participate, you will be asked to segment fluorescence z-stack images of nuclei in 3D cell culture or FISH staining in C. elegans and then complete a survey to report your results and describe your analysis strategy. The goal of this study is not to identify novel segmentation strategies, but to compare the ways in which diverse individuals approach a common image analysis problem. You do not need to be an image analysis expert to participate! We seek a broad range of participants.

The links, below, will guide you through the steps in participating in this study. Thank you in advance!

If you have already completed the study and/or are interested in the ground truth data and information for how we produced the images, please see here: https://github.com/ABRFLMRG/image-analysis-study. The page contains links to the ground-truth images corresponding to the study images, as well as the program and configuration files that were used to produce the datasets.

-The ABRF Light Microscopy Research Group (LMRG)

Note: Regarding the issue with the mismatch between the dimensions reported and apparent PSF for the nuclei images, you can find updates here as well as on the github page, above. We have identified the source of the problem and determined that, in addition to making deconvolution problematic, it reduced the blur of the nuclei making the images easier to segment. We have also determined that the issue did not affect the FISH images.

1. Image download

You may download and analyze as many of the images that you like. If you aren't sure how many you want to analyze, please prioritize image #1 in each set (the easiest ones) and then image #4 (the most difficult). The more times an image is analyzed by different people, the more useful the data are for our study, so please analyze as many as you can. Thank you, in advance!

Calibration Image: When you have completed your analysis of an image, please run the calibration image through the same protocol. Your analysis of the image will provide a reference for the coordinate system (location of the origin) as defined by your analysis program, and possibly altered by your analysis (e.g. image is flipped/rotated). The image is a simple, z-stack containing four spheres. Although the image only needs the most minimal segmentation (it is essentially binary, objects are 255, background 0), it should be processed through any analysis steps that affect the orientation or location of the origin. If your analysis protocol is essentially the same for all images in a set (e.g. all nuclei images), you only need to analyze the calibration image once for the set.

Note for ImageJ/FIJI users: We recommend opening the images through the Bio-Formats Importer Plugin. Dragging-and-dropping the file on the ImageJ control window to open it may prevent some of the metatdata from loading (specifically the voxel dimensions).

Note: If you want to download all the images in a set, hover your pointer over the file list, and a gray box with an arrow will appear in the upper-right corner. Click on the box to open the files in Google Drive.

3. Data and Metadata Submission

This Qualtrics survey will lead you through the submission process, including uploading your data, reporting your analysis strategy, and collecting demographic information. Please complete all your analyses before starting the survey; this will allow you to enter all your data at once and prevent you from having to reenter your demographic information. Please do NOT change your analyses after viewing the survey.

By completing the survey, you are granting us permission to use all of the information you provide for our study. Identifiable information will only be used to match records (i.e. if you complete the survey more than once). All data will be de-identified prior to downloading and analysis. We may quote short sections of your written responses anonymously in public presentations and publications, but will not reproduce your response in its entirety. Your name or identifiable information will not be associated with any public presentation or publication of this study unless you wish to have your name included in a list of volunteers in the acknowledgements.