If you publish data analyzed with Cytely, please include Cytely in your Methods, include a Cytely publication link in your Data Availability statement, and briefly describe the analysis workflow used.
1. Cite Cytely in your Methods section
Please describe that the image analysis was performed using Cytely and include enough detail for readers to understand the main analysis steps. Example Methods text:
"Image analysis was performed using Cytely. Individual cells/nuclei were segmented from the [channel/stain] channel using [segmentation method]. Fluorescence intensity, morphology, and spatial features were quantified at single-cell resolution. Cells were filtered and gated based on [briefly describe criteria, e.g. size, nuclear intensity, marker intensity, morphology, or manually defined gates]. The resulting single-cell measurements were used for downstream analysis of [briefly describe biological readout]."
You do not need to describe every internal implementation detail. Instead, describe the major steps of the workflow, including: which images/channels were analyzed how cells, nuclei, or other parent objects were segmented which child objects or subcellular features were quantified, if applicable which measurements were used how filtering, gating, or classification was performed
2. Include a Cytely publication link
Please include a Cytely publication link for the data analyzed in the publication. The Cytely publication link allows readers and reviewers to open the analyzed dataset, inspect gates and plots, click individual data points, view the corresponding cell images, and verify the analysis without altering the original data. To prepare a Cytely publication link, press Share in Cytely to generate a read-only link for each relevant dataset. Send the link or links together with some context to your Cytely contact or to support@cytely.io. Cytely will then prepare the final publication link and make sure the associated dataset record is properly locked for publication. This applies whether your publication uses one Cytely dataset or several. For publications with several Cytely datasets, Cytely can produce a single publication link that lists all relevant datasets.
See an example shared dataset here: https://app.cytely.io/essential/c4a8fe20-e879-47db-b202-e790c0e5fb14/results/shared
Recommended Data Availability text:
"The Cytely datasets generated and/or analyzed during the current study are available at: [Cytely publication link]"
3. Where should the Cytely link be placed?
At minimum, include the Cytely publication link in the Data Availability statement. When useful, you may also include Cytely links in figure legends, the Results section, or the Methods section, especially when a specific dataset directly supports a specific figure or claim.
4. Make sure the dataset is locked for publication
Before submitting your manuscript, contact Cytely so that the dataset can be locked properly for publication. To start this process, send your Cytely Share link or links to your Cytely contact or to support@cytely.io.