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Review
. 2024 Feb;21(2):170-181.
doi: 10.1038/s41592-023-01987-9. Epub 2023 Sep 14.

Community-developed checklists for publishing images and image analyses

Christopher Schmied  1   2 , Michael S Nelson  3 , Sergiy Avilov  4 , Gert-Jan Bakker  5 , Cristina Bertocchi  6   7 , Johanna Bischof  8 , Ulrike Boehm  9 , Jan Brocher  10 , Mariana T Carvalho  11 , Catalin Chiritescu  12 , Jana Christopher  13 , Beth A Cimini  14 , Eduardo Conde-Sousa  15 , Michael Ebner  16 , Rupert Ecker  17   18   19 , Kevin Eliceiri  20 , Julia Fernandez-Rodriguez  21 , Nathalie Gaudreault  22 , Laurent Gelman  23 , David Grunwald  24 , Tingting Gu  25 , Nadia Halidi  26 , Mathias Hammer  24 , Matthew Hartley  27 , Marie Held  28 , Florian Jug  29 , Varun Kapoor  30 , Ayse Aslihan Koksoy  31 , Judith Lacoste  32 , Sylvia Le Dévédec  33 , Sylvie Le Guyader  34 , Penghuan Liu  35 , Gabriel G Martins  36 , Aastha Mathur  8 , Kota Miura  37 , Paula Montero Llopis  38 , Roland Nitschke  39 , Alison North  40 , Adam C Parslow  41 , Alex Payne-Dwyer  42 , Laure Plantard  23 , Rizwan Ali  43 , Britta Schroth-Diez  44 , Lucas Schütz  45 , Ryan T Scott  46 , Arne Seitz  47 , Olaf Selchow  48 , Ved P Sharma  40 , Martin Spitaler  49 , Sathya Srinivasan  50 , Caterina Strambio-De-Castillia  51 , Douglas Taatjes  52 , Christian Tischer  53 , Helena Klara Jambor  54
Affiliations
Review

Community-developed checklists for publishing images and image analyses

Christopher Schmied et al. Nat Methods. 2024 Feb.

Abstract

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

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Figures

Extended Data figure 1.
Extended Data figure 1.
Overview of current repositories that accept image data.
Fig. 1.
Fig. 1.. Scope of the checklists.
The checklists present easy-to-use guidelines for publishing microscopy image figures and image analysis workflows.
Fig. 2.
Fig. 2.. Checklist for image publication.
Includes points to be addressed on image format, image colors and channels, image annotations, and image availability.
Fig. 3.
Fig. 3.
Image formatting may include (A) image cropping, rotation, and resizing, (B) image spacing in the figure, and (C) presenting several magnifications (zoom, inset) of images. Image colors and channels. (D) Adjust brightness/contrast to achieve good visibility of the imaging signal. (E) Channel information should be annotated and visible to audiences (high contrast to background color, visible to color-blind audiences). (F) Image details are most unbiased in grayscale. (G) It is best practice to publish legends to color intensities (intensity/calibration scales) with images, and recommended for pseudo-color scales.
Fig. 4.
Fig. 4.. Image Annotation.
(A) Possible ways to provide scale information. (B) Features in images can be annotated with symbols, letters, or region-of-interest. (C, D) For advanced image publication, information on anatomical view or intervals in time-lapses may be required. Image Availability. (A) Currently, image data is often shared ‘upon request’. (B) More images along with the image metadata should be available for download in public databases, and in the future (C) also archived in dedicated, added-value databases, in which images are machine searchable or curated.
Fig. 5.
Fig. 5.. Image analysis.
(A) An established workflow template is applied on new image data to produce a result (plot). (B) A new sequence of existing image analysis components is assembled into a novel workflow for a specific analysis (image segmentation). (C) Machine learning workflows learn specific tasks from data, and the resulting model is applied to obtain results.
Fig. 6.
Fig. 6.
Checklist for publication of image analysis workflows.
See this image and copyright information in PMC

Update of

  • Community-developed checklists for publishing images and image analyses.
    Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Schmied C, et al. ArXiv [Preprint]. 2023 Sep 14:arXiv:2302.07005v2. ArXiv. 2023. Update in: Nat Methods. 2024 Feb;21(2):170-181. doi: 10.1038/s41592-023-01987-9. PMID: 36824427 Free PMC article. Updated. Preprint.

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    2. This paper provides an nicely detailed breakdown of both why complete reporting of methods in microscopy are important, who the stakeholders are, and where the changes and motivation needs to come from.

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