Merge pull request #106 from CsatiZoltan/master

How to cite Skan, and publications that use it

doc/citing.rst

@@ -0,0 +1,14 @@
+Citing Skan
+===========
+
+If you use Skan in your work, please cite it as
+
+.. bibliography::
+    :filter: key % "NunezIglesias2018"
+
+So far, the following publications rely on Skan:
+
+.. bibliography::
+    :list: bullet
+    :filter: not key % "NunezIglesias2018"
+

doc/conf.py

@@ -39,6 +39,7 @@
     'sphinx.ext.githubpages',
     'sphinx.ext.napoleon',
     'nb2plots',
+    'sphinxcontrib.bibtex'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -86,6 +87,9 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
+# List of publications
+bibtex_bibfiles = ['publications.bib']
+
 
 # -- Options for HTML output ----------------------------------------------
 

doc/index.rst

@@ -18,6 +18,7 @@ Skan is a pure Python library to analyse skeleton images.
    getting_started
    gui
    complete_analysis
+   citing
    api/api
 
 

doc/publications.bib

@@ -0,0 +1,137 @@
+% Encoding: UTF-8
+
+@Article{NunezIglesias2018,
+  author       = {Nunez-Iglesias, Juan and Blanch, Adam J. and Looker, Oliver and Dixon, Matthew W. and Tilley, Leann},
+  journal      = {PeerJ},
+  title        = {A new {P}ython library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton},
+  year         = {2018},
+  issn         = {2167-8359},
+  pages        = {e4312},
+  volume       = {6},
+  abstract     = {We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the "analyse skeletons" plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan's measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.},
+  country      = {United States},
+  doi          = {10.7717/peerj.4312},
+  issn-linking = {2167-8359},
+  keywords     = {Cytoskeleton; Malaria; Python; Red blood cell; Skeleton analysis},
+  nlm-id       = {101603425},
+  owner        = {NLM},
+  pii          = {4312},
+  pmc          = {PMC5816961},
+  pmid         = {29472997},
+  pubmodel     = {Electronic-eCollection},
+  pubstate     = {epublish},
+  revised      = {2019-11-20},
+}
+
+@Article{Hoffseth2021,
+  author    = {Kevin F. Hoffseth and Jennifer Simkin and Emily Busse and Kennon Stewart and James Watt and Andrew Chapple and Aaron Hargrove and Mimi C. Sammarco},
+  journal   = {Bone},
+  title     = {A new approach to analyzing regenerated bone quality in the mouse digit amputation model using semi-automatic processing of {microCT} data},
+  year      = {2021},
+  month     = mar,
+  pages     = {115776},
+  volume    = {144},
+  doi       = {10.1016/j.bone.2020.115776},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Csati2021,
+  author    = {Zoltan Csati and Jean-Fran{\c{c}}ois Witz and Vincent Magnier and Ahmed El Bartali and Nathalie Limodin and Denis Najjar},
+  journal   = {{SoftwareX}},
+  title     = {{CristalX}: {F}acilitating simulations for experimentally obtained grain-based microstructures},
+  year      = {2021},
+  month     = jun,
+  pages     = {100669},
+  volume    = {14},
+  doi       = {10.1016/j.softx.2021.100669},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Pfister2021,
+  author    = {Martin Pfister and Hannes Stegmann and Kornelia Sch\"utzenberger and Bhavapriya Jasmin Sch\"afer and Christine Hohenadl and Leopold Schmetterer and Martin Gr\"oschl and Ren{\'{e}} M. Werkmeister},
+  journal   = {Annals of the New York Academy of Sciences},
+  title     = {Deep learning differentiates between healthy and diabetic mouse ears from optical coherence tomography angiography images},
+  year      = {2021},
+  month     = feb,
+  doi       = {10.1111/nyas.14582},
+  publisher = {Wiley},
+}
+
+@Article{Paone2020,
+  author    = {Silvio Paone and Sarah D'Alessandro and Silvia Parapini and Francesco Celani and Valentina Tirelli and Manoochehr Pourshaban and Anna Olivieri},
+  journal   = {Scientific Reports},
+  title     = {Characterization of the erythrocyte {GTPase} {Rac1} in relation to {P}lasmodium falciparum invasion},
+  year      = {2020},
+  month     = dec,
+  number    = {1},
+  volume    = {10},
+  doi       = {10.1038/s41598-020-79052-0},
+  publisher = {Springer Science and Business Media {LLC}},
+}
+
+@Article{Looker2019,
+  author    = {Oliver Looker and Adam J. Blanch and Boyin Liu and Juan Nunez-Iglesias and Paul J. McMillan and Leann Tilley and Matthew W. A. Dixon},
+  journal   = {{PLOS} Pathogens},
+  title     = {The knob protein {KAHRP} assembles into a ring-shaped structure that underpins virulence complex assembly},
+  year      = {2019},
+  month     = may,
+  number    = {5},
+  pages     = {e1007761},
+  volume    = {15},
+  doi       = {10.1371/journal.ppat.1007761},
+  editor    = {Michael J. Blackman},
+  publisher = {Public Library of Science ({PLoS})},
+}
+
+@Article{Liu2019,
+  author    = {Boyin Liu and Adam J. Blanch and Arman Namvar and Olivia Carmo and Snigdha Tiash and Dean Andrew and Eric Hanssen and Vijay Rajagopal and Matthew W. A. Dixon and Leann Tilley},
+  journal   = {Cellular Microbiology},
+  title     = {Multimodal analysis of {P}lasmodium knowlesi-infected erythrocytes reveals large invaginations, swelling of the host cell, and rheological defects},
+  year      = {2019},
+  month     = feb,
+  number    = {5},
+  pages     = {e13005},
+  volume    = {21},
+  doi       = {10.1111/cmi.13005},
+  publisher = {Wiley},
+}
+
+@Article{Weinkamer2019,
+  author    = {Richard Weinkamer and Philip Kollmannsberger and Peter Fratzl},
+  journal   = {Current Osteoporosis Reports},
+  title     = {Towards a {C}onnectomic {D}escription of the {O}steocyte {L}acunocanalicular {N}etwork in {B}one},
+  year      = {2019},
+  month     = sep,
+  number    = {4},
+  pages     = {186--194},
+  volume    = {17},
+  doi       = {10.1007/s11914-019-00515-z},
+  publisher = {Springer Science and Business Media {LLC}},
+}
+
+@Article{Walt2019,
+  author    = {St{\'{e}}fan van der Walt},
+  journal   = {Microscopy and Microanalysis},
+  title     = {Scientific {P}ython: {A} {M}ature {C}omputational {E}cosystem for {M}icroscopy},
+  year      = {2019},
+  month     = aug,
+  number    = {S2},
+  pages     = {132--133},
+  volume    = {25},
+  doi       = {10.1017/s1431927619001399},
+  publisher = {Cambridge University Press ({CUP})},
+}
+
+@Article{Warncke2019,
+  author    = {Jan D. Warncke and Hans-Peter Beck},
+  journal   = {Microbiology and Molecular Biology Reviews},
+  title     = {Host {C}ytoskeleton {R}emodeling throughout the {B}lood {S}tages of {P}lasmodium falciparum},
+  year      = {2019},
+  month     = sep,
+  number    = {4},
+  volume    = {83},
+  doi       = {10.1128/mmbr.00013-19},
+  publisher = {American Society for Microbiology},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}

requirements/doc.txt

@@ -3,6 +3,7 @@ jupyter
 imageio>=2.0
 tqdm>=4.11
 nb2plots>=0.5
+sphinxcontrib-bibtex
 sphinx<2
 sphinx_rtd_theme
 seaborn>=0.9

test-environment.yml

@@ -23,5 +23,6 @@ dependencies:
   - tqdm>=4.11
   - nose>=1.3
   - nb2plots>=0.5
+  - sphinxcontrib-bibtex
   - sphinx_rtd_theme
   - seaborn>=0.9