Imaging software

[Mary Barkworth]

I am wanting to provide instructions for preparing and uploading data for images for use with OpenHerbarium. Could someone send me a link to routines for a) renaming images to their barcodes, b) generating the three file sizes used by Symbiota, and c) uploading and linking/creating records on the server. The server will not be associated with iDigBio because the herbaria involved are outside the US. Currently, it is on an ASU server but not the same server as SEINet. I appreciate that it may be necessary to modify the routine for the last step to accommodate this aspect, but having a copy of current versions of the routines used in serving images via one of the SEINet portals would be very helpful. I tried Symbiota.org and was told the file could not be found – a timeout, not 404, message.

 

Mary

[Katelin Pearson]

Hi Mary,

The California Phenology TCN uses a camera tethering software that auto-renames our images for us, so I'm not sure if this completely addresses your question. Nevertheless, here are the links to our imaging and image processing protocols. We store our images on CyVerse and link them over, and our Symbiota portal creates the two other versions from the CyVerse link.

https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/2_imaging_protocol_aug2020.docx

https://www.capturingcaliforniasflowers.org/uploads/1/6/3/7/16372936/3_image_processing_protocol_aug4.docx

Best,

~Katie

On Thu, May 20, 2021 at 10:01 AM Mary Barkworth <Mary.Ba...@usu.edu> wrote:

I am wanting to provide instructions for preparing and uploading data for images for use with OpenHerbarium. Could someone send me a link to routines for a) renaming images to their barcodes, b) generating the three file sizes used by Symbiota, and c) uploading and linking/creating records on the server. The server will not be associated with iDigBio because the herbaria involved are outside the US. Currently, it is on an ASU server but not the same server as SEINet. I appreciate that it may be necessary to modify the routine for the last step to accommodate this aspect, but having a copy of current versions of the routines used in serving images via one of the SEINet portals would be very helpful. I tried Symbiota.org and was told the file could not be found – a timeout, not 404, message.

 

Mary

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Katelin (Katie) D. Pearson

Portal manager, CNABH & CNALH

Arizona State University

Project manager, California Phenology TCN

California Polytechnic State University, San Luis Obispo

[Mary Barkworth]

Thank you.

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[Herrick Brown]

Just fyi, if CyVerse is an option, the image derivatives can be created on the fly using the BisQue service. This option uses and API that points to a single resource (image file essentially), but a resize option is included in the URL to generate a 'full size', 'web friendly', and thumbnail so the only thing that is stored on the server are the three different URLs. On the Symbiota side, there's an iPlant image ingestor that works with the BisQue service to build these links and associate with your metadata by matching image filename to catalogNumber. Downside of this is that when CyVerse is down for maintenance, your images will appear as broken links.

Best,

Herrick

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[Mary Barkworth]

I forgot one item because it is so long since I worked with North American herbaria: many of the specimen images will be recorded using a cell phone – because that is what the herbaria concerned have. Cellphones images are not ideal for specimens, but they will be helpful. It has taken me about five years to appreciate this. There are very few, if any, herbaria where I work that foresee being able to purchase the equipment routinely used in North America.

 

Mary

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[Herrick Brown]

Mary,

FWIW, I think moving forward with the best option that is available is perfectly fine. Multiple images can be associated with a single record. If and when your colleagues can secure additional equipment (if desired), then new images can be added. I have yet to see guidance from NSF pertaining to biodiversity collections digitization suggesting an expected outcome of absolutely perfect, complete data...in fact quite the opposite.

Best,

Herrick

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[Mary Barkworth]

The collections are not in the US. The problem is more with me than the NSF.

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