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[PRE REVIEW]: Precision-medicine-toolbox: An open-source Python package for facilitation of quantitative medical imaging and radiomics analysis #4668

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@lavrovaliz<!--end-author-handle-- (Elizaveta Lavrova) Repository: https://github.com/primakov/precision-medicine-toolbox Branch with paper.md (empty if default branch): Version: 0.11 Editor: !--editor-->@cMadan<!--end-editor-- Reviewers: Pending Managing EiC: Daniel S. Katz

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Author instructions

Thanks for submitting your paper to JOSS @lavrovaliz. Currently, there isn't a JOSS editor assigned to your paper.

@lavrovaliz if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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editorialbot commented 2 years ago

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.28 s (136.7 files/s, 39250.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        13            584              0           2128
Python                           9            447            287           2011
TeX                              1             36              0           1242
Jupyter Notebook                 3              0           3727            156
YAML                             7             36             74            152
XML                              5              0              0             34
-------------------------------------------------------------------------------
SUM:                            38           1103           4088           5723
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 992

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1038/s41746-021-00438-z may be a valid DOI for title: Diagnostic accuracy of deep learning in medical imaging: a systematic review and meta-analysis
- 10.3389/fnins.2021.679941 may be a valid DOI for title: Exploratory Radiomic Analysis of Conventional vs. Quantitative Brain MRI: Toward Automatic Diagnosis of Early Multiple Sclerosis
- 10.1118/1.3611983 may be a valid DOI for title: SU-E-T-33: Pydicom: An Open Source DICOM Library
- 10.1109/mcse.2011.37 may be a valid DOI for title: The NumPy Array: A Structure for Efficient Numerical Computation
- 10.18502/fbt.v8i4.7754 may be a valid DOI for title: The Impact of Preprocessing on the PET-CT Radiomics Features in Non-small Cell Lung Cancer
- 10.1016/j.ejrad.2019.108735 may be a valid DOI for title: Potential feature exploration and model development based on 18F-FDG PET/CT images for differentiating benign and malignant lung lesions
- 10.3390/jcm10061327 may be a valid DOI for title: Special Issue: Emerging Technologies for Medical Imaging Diagnostics, Monitoring and Therapy of Cancers
- 10.1007/s10278-017-0037-8 may be a valid DOI for title: SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
- 10.1016/j.breast.2019.10.018 may be a valid DOI for title: Overview of radiomics in breast cancer diagnosis and prognostication
- 10.1002/cam4.2464 may be a valid DOI for title: Role of medical imaging for immune checkpoint blockade therapy: From response assessment to prognosis prediction
- 10.1186/1532-429x-11-s1-p100 may be a valid DOI for title: Intra-observer and interobserver variability of biventricular function, volumes and mass in patients with congenital heart disease measured by CMR imaging
- 10.1109/jproc.2021.3054390 may be a valid DOI for title: A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises
- 10.1016/s2589-7500(20)30160-6 may be a valid DOI for title: Artificial intelligence in medical imaging: switching from radiographic pathological data to clinically meaningful endpoints
- 10.21037/tcr.2016.07.11 may be a valid DOI for title: Impact of image preprocessing on the volume dependence and prognostic potential of radiomics features in non-small cell lung cancer
- 10.1016/j.cmpb.2020.105796 may be a valid DOI for title: pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis
- 10.1038/s41467-020-19116-x may be a valid DOI for title: Non-invasive decision support for NSCLC treatment using PET/CT radiomics
- 10.3389/fnins.2021.791776 may be a valid DOI for title: Radiomics Analysis Based on Magnetic Resonance Imaging for Preoperative Overall Survival Prediction in Isocitrate Dehydrogenase Wild-Type Glioblastoma
- 10.1158/0008-5472.can-17-0339 may be a valid DOI for title: Computational Radiomics System to Decode the Radiographic Phenotype
- 10.3389/fphy.2021.634693 may be a valid DOI for title: Medical Physics and Imaging–A Timely Perspective
- Errored finding suggestions for "Radiomics: extracting more information from medica...", please try later
- 10.1016/s0167-8140(21)06964-4 may be a valid DOI for title: OC-0557 AI-based NSCLC detection and segmentation: faster and more prognostic than manual segmentation
- Errored finding suggestions for "nipy/nibabel: 3.2.1", please try later
- Errored finding suggestions for "Radiomics: Enabling Factors Towards Precision Medi...", please try later
- 10.1201/9781351208277-12 may be a valid DOI for title: Pathways to radiomics-aided clinical decision-making for precision medicine

INVALID DOIs

- None
danielskatz commented 2 years ago

@lavrovaliz - Thanks for your submission.

Please work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

danielskatz commented 2 years ago

👋 @cMadan - would you be able to edit this submission?

danielskatz commented 2 years ago

@editorialbot invite @cMadan as editor

editorialbot commented 2 years ago

Invitation to edit this submission sent!

cMadan commented 2 years ago

@editorialbot assign @cMadan as editor

editorialbot commented 2 years ago

Assigned! @cMadan is now the editor

lavrovaliz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41746-021-00438-z is OK
- 10.3389/fnins.2021.679941 is OK
- 10.1118/1.3611983 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.5281/zenodo.6903385 is OK
- 10.1148/radiol.2020191145 is OK
- 10.18502/fbt.v8i4.7754 is OK
- 10.1016/j.ejrad.2019.108735 is OK
- 10.2214/ajr.175.1.1750035 is OK
- 10.1631/jzus.B1700260 is OK
- 10.3390/jcm10061327 is OK
- 10.1007/s10278-017-0037-8 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK
- 10.1038/srep46349 is OK
- 10.1002/jmri.28027 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1007/978-3-319-33383-0_5 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/j.breast.2019.10.018 is OK
- 10.1002/cam4.2464 is OK
- 10.1007/s10554-009-9501-y is OK
- 10.1109/JPROC.2021.3054390 is OK
- 10.1016/S2589-7500(20)30160-6 is OK
- 10.21037/tcr.2016.07.11 is OK
- 10.1016/j.cmpb.2020.105796 is OK
- 10.1038/s41467-020-19116-x is OK
- 10.3389/fnins.2021.791776 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fphy.2021.634693 is OK
- 10.1016/j.ejca.2011.11.036 is OK
- 10.1038/s41467-022-30841-3 is OK
- 10.5281/zenodo.4295521 is OK
- 10.1201/9781351208277-12 is OK

MISSING DOIs

- 10.21037/tcr.2016.07.11 may be a valid DOI for title: Impact of image preprocessing on the volume dependence and prognostic potential of radiomics features in non-small cell lung cancer

INVALID DOIs

- None
lavrovaliz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41746-021-00438-z is OK
- 10.3389/fnins.2021.679941 is OK
- 10.1118/1.3611983 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.5281/zenodo.6903385 is OK
- 10.1148/radiol.2020191145 is OK
- 10.18502/fbt.v8i4.7754 is OK
- 10.1016/j.ejrad.2019.108735 is OK
- 10.2214/ajr.175.1.1750035 is OK
- 10.1631/jzus.B1700260 is OK
- 10.3390/jcm10061327 is OK
- 10.1007/s10278-017-0037-8 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK
- 10.1038/srep46349 is OK
- 10.1002/jmri.28027 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1007/978-3-319-33383-0_5 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/j.breast.2019.10.018 is OK
- 10.1002/cam4.2464 is OK
- 10.1007/s10554-009-9501-y is OK
- 10.1109/JPROC.2021.3054390 is OK
- 10.1016/S2589-7500(20)30160-6 is OK
- 10.21037/tcr.2016.07.11 is OK
- 10.1016/j.neunet.2014.09.003 is OK
- 10.1016/j.cmpb.2020.105796 is OK
- 10.1038/s41467-020-19116-x is OK
- 10.3389/fnins.2021.791776 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fphy.2021.634693 is OK
- 10.1016/j.ejca.2011.11.036 is OK
- 10.1038/s41467-022-30841-3 is OK
- 10.5281/zenodo.4295521 is OK
- 10.1201/9781351208277-12 is OK

MISSING DOIs

- None

INVALID DOIs

- None
lavrovaliz commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lavrovaliz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41746-021-00438-z is OK
- 10.3389/fnins.2021.679941 is OK
- 10.1118/1.3611983 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.5281/zenodo.6903385 is OK
- 10.1148/radiol.2020191145 is OK
- 10.18502/fbt.v8i4.7754 is OK
- 10.1016/j.ejrad.2019.108735 is OK
- 10.2214/ajr.175.1.1750035 is OK
- 10.1631/jzus.B1700260 is OK
- 10.3390/jcm10061327 is OK
- 10.1007/s10278-017-0037-8 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.7717/peerj.453 is OK
- 10.1038/srep46349 is OK
- 10.1002/jmri.28027 is OK
- 10.1038/nrclinonc.2017.141 is OK
- 10.1007/978-3-319-33383-0_5 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1016/j.breast.2019.10.018 is OK
- 10.1002/cam4.2464 is OK
- 10.1007/s10554-009-9501-y is OK
- 10.1109/JPROC.2021.3054390 is OK
- 10.1016/S2589-7500(20)30160-6 is OK
- 10.21037/tcr.2016.07.11 is OK
- 10.1016/j.neunet.2014.09.003 is OK
- 10.1016/j.cmpb.2020.105796 is OK
- 10.1038/s41467-020-19116-x is OK
- 10.3389/fnins.2021.791776 is OK
- 10.1158/0008-5472.CAN-17-0339 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fphy.2021.634693 is OK
- 10.1016/j.ejca.2011.11.036 is OK
- 10.1038/s41467-022-30841-3 is OK
- 10.5281/zenodo.4295521 is OK
- 10.1201/9781351208277-12 is OK

MISSING DOIs

- None

INVALID DOIs

- None
lavrovaliz commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

lavrovaliz commented 2 years ago

Hi @danielskatz @cMadan ! Thank you for kindly reviewing our submission. I fixed the incorrect DOIs. From the reviewers list, I think any of these people could be asked to review: krother sealhuang nirum dpolychr GalenStocking Gweissman rlizzo daissi dirmeier jingpengw sahilseth grlee77 JonathanReardon SaumikDana

lavrovaliz commented 2 years ago

Dear @danielskatz @cMadan, could you please tell if there are any problems with the submission or there is anything pending from our side?

danielskatz commented 2 years ago

Sorry @lavrovaliz - It appears that @cMadan might have lost track of this after he accepted editing it. I hope this will bring it back to the top of his queue.

lavrovaliz commented 2 years ago

@danielskatz @cMadan hi, I just wanted to leave a kind reminder about this branch :-)

cMadan commented 2 years ago

@lavrovaliz, sorry!! I had gone on leave before the semester and then lost track here. I'll look through your reviewer suggestions and see who's available.

cMadan commented 2 years ago

@sealhuang @krother @sahilseth, would you be available and interested in reviewing this submission?

ghost commented 2 years ago

@cMadan @danielskatz are there any updates regarding this submission? While we would love to publish with you, @lavrovaliz has deadlines and time constrains, I hope you understand.

cMadan commented 2 years ago

@hwoodruff, unfortunately the current step is to find reviewers. I will ask a few more people now, but we can't advance further until reviewers have agreed to evaluate the submission.

cMadan commented 2 years ago

@dirmeier @jingpengw @grlee77, would you be available and interested in reviewing this submission?

lavrovaliz commented 2 years ago

Dear @cMadan, thank you very much for working on our manuscript and code! I understand that it is very hard to find the reviewers, but I just wanted to add that it's not necessary to invite users exclusively from the list I sent (I just picked the reviewers from the Journal's list based on the field of expertise) - please feel free to invite any person if you think they have expertise/interest in the field.

@hwoodruff @primakov @danielskatz

dirmeier commented 2 years ago

Hello, sorry for the late reply. I currently don't have much resources for reviewing. Sorry!

cMadan commented 2 years ago

@lavrovaliz, our hope is that you might have a better idea of who would have the expertise to review your submission than the editor would. It would be great if you could see if you have any additional suggestion (particularly those that seem to have been active on GitHub somewhat recently). I'll also try and think of some potential reviewers.

lavrovaliz commented 2 years ago

@editorialbot withdraw

editorialbot commented 2 years ago

I'm sorry @lavrovaliz, I'm afraid I can't do that. That's something only eics are allowed to do.

lavrovaliz commented 2 years ago

Dear EICs, please withdraw this submission.

danielskatz commented 2 years ago

@editorialbot withdraw

editorialbot commented 2 years ago

Paper withdrawn.