WGSMART Guidelines for Image Quality in SmartDots exchanges

[JCoadDavies]

In response to recommendations for an image taking workshop/seminar (to both WGBIOP and WGSMART) it was agreed that guidelines would be drafted to ensure image quality of samples in SmartDots it at the standard needed to ensure the users can give a reliable estimation of age/maturity...etc..

[JCoadDavies]

Guidelines have been drafted but only for otolith image capture. Sections are needed for maturity staging images and egg and larvae image capture

WGSMART Guidelines for Image Quality in SmartDots exchanges V2.docx

[JCoadDavies]

very important to add image specifications to the document https://github.com/ices-eg/SmartDots/projects/3?card_filter_query=295

[rellebo]

@JCoadDavies I'm going to set a point next Wednesday to work on this, if it can wait until then.

[JCoadDavies]

We discussed this at WGSMART yesterday and the plan is to have these guidelines ready for the Q1 meeting on Feb 9th 2023 @rellebo that is fine Romain, thank you. What is need is some good and bad quality images and any text suggestions you have. @MKAlbisua thanks for offering to contribute also

[rellebo]

I worked on the doc in pj for the age part of the colleagues working on the maturity and on the fish larva will recommend me protocols to add to the doc soon Do not hesitate if needed WGSMART.Guidelines.for.Image.Quality.in.SmartDots.exchanges.V2.docx

[JCoadDavies]

WKMaturityReportsReview_ImageAdquisitionGuidelines_Maria.docx

Hi all,

I have been reviewing the maturity Wks reports as to what they might contain in relation to image acquisition, and it is not much..

In AZTI there is not a protocol as such either..

I will include the sharepoint file draft some pictures then to illustrate the guidelines …

Cheers, maria

[ComeDenechaud]

Hi all,

I did some early work on the guidelines for maturity following Maria's review of the WK maturity reports. Please find them in this latest version. I think we need someone working closely with maturity to fill in the part on common issues to avoid, as I don't have any material for it. WGSMART_Guidelines_for_image_quality_V3.docx

[JCoadDavies]

Thanks @ComeDenechaud and @rellebo I have updated a little and tried to clarify the text on image naming. Honestly, I am lost in the ICES vocabs, it feels like they are changing them often. Anyway....have a look...

@MKAlbisua there is space there for some maturity images of you have them under "Issues to avoid when preparing and imaging maturity samples: INSERT IMAGES AND LIST OF SPECIFIC ISSUES"

WGSMART_Guidelines_for_image_quality_V3.docx

[JCoadDavies]

ooops...I never renamed the file d to V4, sorry! I hope it is not confusing

[JCoadDavies]

Now with scale bar text corrected and renamed V4

[Uploading WGSMART_Guidelines_for_image_quality_V4.docx…]()

[rellebo]

With the help of colleagues on other subjects here is a new version. WGSMART_Guidelines_for_image_quality_V5.docx

[CindyvanDamme]

Thanks all for the work so far. Updated maturity images with recommendations from maturity staging workshops and added information from Vivian on images for larvae. Created version 6 WGSMART_Guidelines_for_image_quality_V6.docx

[MKAlbisua]

A few more comments. Thank you!

WGSMART_Guidelines_for_image_quality_V7.docx

[JCoadDavies]

WGSMART_Guidelines_for_image_quality_V9.docx

This version has the comment from Maik and Matthias incorporated. I am following up on the question of formatting of the scale bars on the images so SmartDots can detect them and also on the characters to avoid when naming images.

There are still comments to be addressed for maturity, eggs and larvae

[ComeDenechaud]

WGSMART_Guidelines_for_image_quality_V10.docx

I added a few comments myself and cleaned up some of the structure in the document. Seems like the current bottleneck is the missing images for the maturity guidelines (elasmobranchs) and egg&larvae?

[JCoadDavies]

I have just written to the chairs of the upcoming ICES Working group on Ageing and Maturity in Elasmobranch Species (WKARMSE). Hopefully they have some images to share

[JCoadDavies]

Still waiting on some images, see comment above, I have written and asked @Follesac

I have clarified the text on image naming and scale bar specifications and cannot do anymore without the final images WGSMART_Guidelines_for_image_quality_V11.docx

[JCoadDavies]

WGSMART_Guidelines_for_image_quality_V12.docx

@CindyvanDamme There are answers to comments for you

I think if we do not have all the image examples then we should get these Guidelines out there as a DRAFT asap

[JCoadDavies]

MISSING:

1. image example of fish gonads’ photoshoot workbench - homogenous background, not white, ID tag and ruler
2. 2 flatfish images and image text
3. roundfish - Picture of a longitudinally cut of the gonad
4. MISSING INFO ON USE OF MICROSCOPES for larval ID WGSMART_Guidelines_for_image_quality_V13.docx

I had to reduce the size of the images so that i could upload a word doc here but the quality should still be fine

We have agreed with Neil that a direct link to this can be put on the SmartDots landing page as soon as we have this draft final.

[JCoadDavies]

@ComeDenechaud can you please give a final check so we can make this available WGSMART_Guidelines_for_image_quality_DRAFT.docx

[ComeDenechaud]

WGSMART_Guidelines_for_image_quality.docx Did a final pass on the file with some small wording correction and editing issues with image or text placement. Still missing something on use of microscopes for larval ID but it might not be needed since this is guidelines for taking pictures only.

[rellebo]

A small suggestion: on page 7 of the document, we could associate this table with the image "Image with a standardized image field for this Trachurus trachurus species in x ~7mm and y ~5mm". See how to modify the image to match the table?

[JCoadDavies]

Guidelines available under GUIDES and STANDARDS here https://www.ices.dk/data/tools/Pages/smartdots.aspx and sent out via mail to age & maturity national coordinators and a list of ichtyoplankton experts

ICES secretariat are asking that this be made an official handbook end of 2023/early 2024 so feedback has been requested with a deadline of October 6th so that WGBIOP can evaluate

[JCoadDavies]

See https://github.com/ices-eg/SmartDots/issues/295 and https://github.com/ices-eg/SmartDots/issues/298 for comments on stress size and file size and type