Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot: Difference between revisions

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Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot (view source)

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→‎Digitization TCN: Capturing California's Flowers: Using Digital Images to Investigate Phenological Change in a Biodiversity Hotspot (CAP)
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''Project Manager:'' [mailto:kdpearso@calpoly.edu Katie Pearson]<br>
''Project Manager:'' [mailto:kdpearso@calpoly.edu Katie Pearson]<br>
''Data Manager:'' Jason Alexander<br>
''Data Manager:'' Jason Alexander<br>
=== Protocols & Workflows ===
The CAP Network has created a semi-comprehensive digitization manual that aggregates documentation from the digitization process, from imaging to image processing to transcription and georeferencing. This document is available here: [[File:CAP Digitization Manual.pdf]]
The Network also developed a manual for using their Symbiota data portal, CCH2, than can be generalized for users of other Symbiota portals: [[File:CAP Symbiota Guide.pdf]]
Additional protocols, workflows, and other documentation can be found on the project website: http://www.capturingcaliforniasflowers.org
=== Publications ===
Goëau H, Mora-Fallas A, Champ J, Love NLR, Mazer SJ, Mata-Montero E, Joly A, Bonnet P. 2020. A new fine-grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction. ''Applications in Plant Sciences'' 8(6):e11368. doi:10.1002/aps3.11368
Pearson KD, Nelson G, Aronson MFJ, Bonnet P, Brenskelle L, Davis CC, Denny EG, Ellwood ER, Goëau H, Heberling JM, Joly A, Lorieul T, Mazer SJ,
Meineke EK, Stucky BJ, Sweeney P, White AE, Soltis PS. 2020. Machine learning using digitized herbarium specimens to advance phenological research. ''BioScience''. 70(7):610-620. doi:[https://academic.oup.com/bioscience/article/70/7/610/5825721 10.1093/biosci/biaa044]
Love NLR, Park IW, Mazer SJ. 2019. A new phenological metric for use in pheno‐climatic models: A case study using herbarium specimens of Streptanthus tortuosus. Applications in Plant Sciences 7(7): e11276. doi:[https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11276 10.1002/aps3.11276]
Yost JM, Pearson KD, Alexander J, Gilbert E, et al. 2019. The California Phenology Collections Network: Using digital images to investigate phenological change in a biodiversity hotspot. ''Madroño''. 66(4):130-141. doi:[https://bioone.org/journals/madro%C3%B1o/volume-66/issue-4/0024-9637-66.4.130/THE-CALIFORNIA-PHENOLOGY-COLLECTIONS-NETWORK--USING-DIGITAL-IMAGES-TO/10.3120/0024-9637-66.4.130.full 10.3120/0024-9637-66.4.130]
Lorieul T, Pearson KD, Ellwood ER, Goëau H, Molino J-F, Sweeney PW, Yost JM, Sachs J, Mata-Montero E, Nelson G, Soltis PS, Bonnet P, Joly A. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: case studies from temperate, tropical, and equatorial floras. ''Applications in Plant Sciences''. 7(3):e1233. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426157/ doi:10.1002/aps3.1233]
Alexander, Jason A. 2019. Upcoming changes in the Consortium of California Herbaria. ''Madroño'', 66(1):37-38. [https://doi.org/10.3120/0024-9637-66.1.37 doi:10.3120/0024-9637-66.1.37]
=== Professional Presentations ===
====Conference Talks====
*Pearson KD, Yost J. The California Phenology Network: Building capacity for sharing specimen-based phenological data. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://youtu.be/YO65BPO2MIY [https://youtu.be/YO65BPO2MIY Recording]
*Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists: A new phenology-focused CURE using herbarium specimen data. Botany 2020.  [Virtual]. July 2020. https://youtu.be/Le1zewbdOXs [https://youtu.be/Le1zewbdOXs Recording]
*Yost J, Pearson KD, Alexander J, Love N, Mazer S, Mishler B. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2020. [Virtual]. July 2020. https://youtu.be/rYVm5XAIQvI [Recording https://youtu.be/rYVm5XAIQvI]
*Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists. 4th Annual Digital Data in Biodiversity Research Conference. [Virtual].  June 2, 2020. [https://drive.google.com/file/d/1NDFVNYzgwF3WTm13NNWgQEDulZd4_cUv/view Recording]
*Pearson KD. Using Notes from Nature to digitize California herbaria. Northern California Botanists Symposium, Chico, CA. January 13, 2020. [https://www.youtube.com/watch?v=AQv3EXy03r8&feature=youtu.be&t=1528 Recording]
*Yost J, Pearson KD. California Phenology TCN: Starting Year 2. ADBC Summit 2019. October 2019. Gainesville, FL. [https://www.idigbio.org/wiki/images/d/d7/CAP_ADBCSummit2019.pdf Slides]
*Pearson KD. Old plants, new tricks: Phenological revelations from herbarium specimens. Southern California Botanists Symposium, Claremont, CA. October 5, 2019.
*Alexander J. Upcoming changes in the Consortium of California Herbaria. Northern California Botanists Symposium. January 2019. Chico, CA.
*Yost J. Introducing the California Phenology TCN. ADBC Summit 2018. October 2019. Gainesville, FL. [https://mediasite.video.ufl.edu/Mediasite/Play/1efdcec7f4414a7783798fc2b88ebe5e1d?catalog=588bdfbb38134fac83c6ef66a7c59e4e21 Recording]
====Posters====
*Pearson KD, Yost JM. Creating and mobilizing specimen-based plant phenological data: The California Phenology Network. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/cap_tcn_esa2020_v2.pdf
*Waselkov K, Riley R, Peña M, Pearson K, Yost J. Capturing the flowers of the Sierra Nevada Mountains: The Contribution of the Fresno State Herbarium (FSC) to the California Phenology Network. Society for the Preservation of Natural History Collections. [Virtual]. June 2020. https://spnhc.biowikifarm.net/wiki/Posters#/media/File:Waselkov_spnhc_2020_optimized.jpg
*Cazares J, Carter BE. Capturing phenology from herbarium specimens to understand flowering period in Winecup Clarkia (Clarkia purpurea ssp. quadrivulnera, Onagraceae).  Northern California Botanists Symposium, Chico, CA. January 13-14, 2020. http://www.norcalbotanists.org/files/NCB_2020_Poster34_Cazares.pdf
*Crowe RE, Bowler PA. Reopening the UCI Herbarium (IRVC). Southern California Botanists Symposium, Claremont, CA. October 2, 2019.
*McGowan H, Fisher AE. A Flora of the Chiquito Basin, Santa Ana Mountains, Peninsular Ranges of Southern California. Botany 2019. Tucson, AZ. July 2019.
*Olmeda BL, Cuadra S, Barnett A, Rice M, Fisher AE. Capturing California’s Flowers at the Beach: Herbarium Specimen Imaging at Long Beach State (LOB). Botany 2019. Tucson, Arizona. July 2019.
*Tang K, Fisher AE. A Visual Guide and Morphometric Analysis of Leaf Shapes of Common Shrubs of the Santa Ana Mountains of Southern California. Botany 2019. Tucson, AZ. July 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2019, Tucson, AZ. July 28, 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Digital Data in Biodiversity Research Conference, New Haven, CT. June 11, 2019.
*Pearson KD, Yost JM. (Presented by A Ayers). Capturing flowering time data from herbarium specimens: The California Phenology TCN. California Botanical Society Graduate Student Symposium. San Luis Obispo, CA. April 6, 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Southern California Botanists Symposium, Claremont, CA. November 3, 2018.
=== Education and Outreach ===


=== Project Collaborators  ===
=== Project Collaborators  ===
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=====University of Nevada, Las Vegas (UNLV)=====
=====University of Nevada, Las Vegas (UNLV)=====
Lloyd Stark, associate professor [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
Lloyd Stark, associate professor [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2001644 (NSF Award #2001644)]
=== Protocols & Workflows ===
The CAP Network has created a semi-comprehensive digitization manual that aggregates documentation from the digitization process, from imaging to image processing to transcription and georeferencing. This document is available here: [[File:CAP Digitization Manual.pdf]]
The Network also developed a manual for using their Symbiota data portal, CCH2, than can be generalized for users of other Symbiota portals: [[File:CAP Symbiota Guide.pdf]]
Additional protocols, workflows, and other documentation can be found on the project website: http://www.capturingcaliforniasflowers.org
=== Publications ===
Goëau H, Mora-Fallas A, Champ J, Love NLR, Mazer SJ, Mata-Montero E, Joly A, Bonnet P. 2020. A new fine-grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction. ''Applications in Plant Sciences'' 8(6):e11368. doi:10.1002/aps3.11368
Pearson KD, Nelson G, Aronson MFJ, Bonnet P, Brenskelle L, Davis CC, Denny EG, Ellwood ER, Goëau H, Heberling JM, Joly A, Lorieul T, Mazer SJ,
Meineke EK, Stucky BJ, Sweeney P, White AE, Soltis PS. 2020. Machine learning using digitized herbarium specimens to advance phenological research. ''BioScience''. 70(7):610-620. doi:[https://academic.oup.com/bioscience/article/70/7/610/5825721 10.1093/biosci/biaa044]
Love NLR, Park IW, Mazer SJ. 2019. A new phenological metric for use in pheno‐climatic models: A case study using herbarium specimens of Streptanthus tortuosus. Applications in Plant Sciences 7(7): e11276. doi:[https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11276 10.1002/aps3.11276]
Yost JM, Pearson KD, Alexander J, Gilbert E, et al. 2019. The California Phenology Collections Network: Using digital images to investigate phenological change in a biodiversity hotspot. ''Madroño''. 66(4):130-141. doi:[https://bioone.org/journals/madro%C3%B1o/volume-66/issue-4/0024-9637-66.4.130/THE-CALIFORNIA-PHENOLOGY-COLLECTIONS-NETWORK--USING-DIGITAL-IMAGES-TO/10.3120/0024-9637-66.4.130.full 10.3120/0024-9637-66.4.130]
Lorieul T, Pearson KD, Ellwood ER, Goëau H, Molino J-F, Sweeney PW, Yost JM, Sachs J, Mata-Montero E, Nelson G, Soltis PS, Bonnet P, Joly A. 2019. Toward a large-scale and deep phenological stage annotation of herbarium specimens: case studies from temperate, tropical, and equatorial floras. ''Applications in Plant Sciences''. 7(3):e1233. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426157/ doi:10.1002/aps3.1233]
Alexander, Jason A. 2019. Upcoming changes in the Consortium of California Herbaria. ''Madroño'', 66(1):37-38. [https://doi.org/10.3120/0024-9637-66.1.37 doi:10.3120/0024-9637-66.1.37]
=== Professional Presentations ===
====Conference Talks====
*Pearson KD, Yost J. The California Phenology Network: Building capacity for sharing specimen-based phenological data. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://youtu.be/YO65BPO2MIY [https://youtu.be/YO65BPO2MIY Recording]
*Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists: A new phenology-focused CURE using herbarium specimen data. Botany 2020.  [Virtual]. July 2020. https://youtu.be/Le1zewbdOXs [https://youtu.be/Le1zewbdOXs Recording]
*Yost J, Pearson KD, Alexander J, Love N, Mazer S, Mishler B. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2020. [Virtual]. July 2020. https://youtu.be/rYVm5XAIQvI [Recording https://youtu.be/rYVm5XAIQvI]
*Pearson KD, Yost J, Ramirez Parada T, Love N. Creating new data, questions, and scientists. 4th Annual Digital Data in Biodiversity Research Conference. [Virtual].  June 2, 2020. [https://drive.google.com/file/d/1NDFVNYzgwF3WTm13NNWgQEDulZd4_cUv/view Recording]
*Pearson KD. Using Notes from Nature to digitize California herbaria. Northern California Botanists Symposium, Chico, CA. January 13, 2020. [https://www.youtube.com/watch?v=AQv3EXy03r8&feature=youtu.be&t=1528 Recording]
*Yost J, Pearson KD. California Phenology TCN: Starting Year 2. ADBC Summit 2019. October 2019. Gainesville, FL. [https://www.idigbio.org/wiki/images/d/d7/CAP_ADBCSummit2019.pdf Slides]
*Pearson KD. Old plants, new tricks: Phenological revelations from herbarium specimens. Southern California Botanists Symposium, Claremont, CA. October 5, 2019.
*Alexander J. Upcoming changes in the Consortium of California Herbaria. Northern California Botanists Symposium. January 2019. Chico, CA.
*Yost J. Introducing the California Phenology TCN. ADBC Summit 2018. October 2019. Gainesville, FL. [https://mediasite.video.ufl.edu/Mediasite/Play/1efdcec7f4414a7783798fc2b88ebe5e1d?catalog=588bdfbb38134fac83c6ef66a7c59e4e21 Recording]
====Posters====
*Pearson KD, Yost JM. Creating and mobilizing specimen-based plant phenological data: The California Phenology Network. Ecological Society of America Annual Meeting. [Virtual]. August 2020. https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/cap_tcn_esa2020_v2.pdf
*Waselkov K, Riley R, Peña M, Pearson K, Yost J. Capturing the flowers of the Sierra Nevada Mountains: The Contribution of the Fresno State Herbarium (FSC) to the California Phenology Network. Society for the Preservation of Natural History Collections. [Virtual]. June 2020. https://spnhc.biowikifarm.net/wiki/Posters#/media/File:Waselkov_spnhc_2020_optimized.jpg
*Cazares J, Carter BE. Capturing phenology from herbarium specimens to understand flowering period in Winecup Clarkia (Clarkia purpurea ssp. quadrivulnera, Onagraceae).  Northern California Botanists Symposium, Chico, CA. January 13-14, 2020. http://www.norcalbotanists.org/files/NCB_2020_Poster34_Cazares.pdf
*Crowe RE, Bowler PA. Reopening the UCI Herbarium (IRVC). Southern California Botanists Symposium, Claremont, CA. October 2, 2019.
*McGowan H, Fisher AE. A Flora of the Chiquito Basin, Santa Ana Mountains, Peninsular Ranges of Southern California. Botany 2019. Tucson, AZ. July 2019.
*Olmeda BL, Cuadra S, Barnett A, Rice M, Fisher AE. Capturing California’s Flowers at the Beach: Herbarium Specimen Imaging at Long Beach State (LOB). Botany 2019. Tucson, Arizona. July 2019.
*Tang K, Fisher AE. A Visual Guide and Morphometric Analysis of Leaf Shapes of Common Shrubs of the Santa Ana Mountains of Southern California. Botany 2019. Tucson, AZ. July 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Botany 2019, Tucson, AZ. July 28, 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Digital Data in Biodiversity Research Conference, New Haven, CT. June 11, 2019.
*Pearson KD, Yost JM. (Presented by A Ayers). Capturing flowering time data from herbarium specimens: The California Phenology TCN. California Botanical Society Graduate Student Symposium. San Luis Obispo, CA. April 6, 2019.
*Pearson KD, Yost JM. Capturing flowering time data from herbarium specimens: The California Phenology TCN. Southern California Botanists Symposium, Claremont, CA. November 3, 2018.
=== Education and Outreach ===


== PENs ==
== PENs ==
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