Reviewer name and names of any other individual's who aided in reviewer	Zhaowei Wang
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published manuscript. (If no, please inform the editor that you cannot review this manuscript.)	Yes
Is the language of sufficient quality?	Yes
Please add additional comments on language quality to clarify if needed
Is there a clear statement of need explaining what problems the software is designed to solve and who the target audience is?	Yes
Additional Comments
Is the source code available, and has an appropriate Open Source Initiative license <a href="https://opensource.org/licenses" target="_blank">(https://opensource.org/licenses)</a> been assigned to the code?	Yes
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As Open Source Software are there guidelines on how to contribute, report issues or seek support on the code?	Yes
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Is the code executable?	Yes
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Is installation/deployment sufficiently outlined in the paper and documentation, and does it proceed as outlined?	Yes
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Is the documentation provided clear and user friendly?	Yes
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Is there enough clear information in the documentation to install, run and test this tool, including information on where to seek help if required?	Yes
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Is there a clearly-stated list of dependencies, and is the core functionality of the software documented to a satisfactory level?	Yes
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Have any claims of performance been sufficiently tested and compared to other commonly-used packages?	Yes
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Are there (ideally real world) examples demonstrating use of the software?	Yes
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Additional Comments
Any Additional Overall Comments to the Author	In this manuscript, the authors propose STCellbin to generate single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images. The experiment results on mouse liver and Arabidopsis seed datasets prove the good performance of STCellbin. The topic is significant and the proposed method is feasible. However, there are still some concerns and problems to be improved and clarified. (1) STCellbin is an update version of StereoCell, but the explanation of StereoCell is not sufficient. The authors should give a more detailed explanation of StereoCell, such as its input and main process. (2) The authors list some existing dyeing methods in Lines 52-53, Page 3. They should clarify that these methods are used for nuclei staining, which differentiate them from the cell membrane/wall staining methods of following content. It can provide a more accurate explanation for readers and users. (3) The authors share the GitHub repository of STCellbin, and I noticed that when executing STCellbin, the input only requires the path of image data and spatial gene expression data, the path of the output results, and the chip number. Are there other adjustable parameters? (4) In Page 5, Line 85, “steps” should be “step”, and in Page 8, Line 145, “must” would be better revised to “should”. Moreover, the writing of “stained image” and “staining image” should be consistent.
Recommendation	Minor Revisions