The question of the worm-align

[hello-lei]

Hi,I am interested in the worm-align. I can't success it in my data. So should I process the pictures ? I succeed it in the example from github Thank you very much!

[hello-lei]

My data is tif format,

[hannekeo]

Hi Lei Sorry to hear that you have issues. Could you elaborate a bit on what goes wrong? Where does the pipeline crash? Without seeing your data it is a little tricky to know what the issue is.

[berk1835]

Hi Lei,

I had to convert all my images to PNG (using ImageJ) and then they worked fine.

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Rebekah J White (she/her)

Evolutionary Biology PhD Student

College of Life and Environmental Sciences, Streatham Campus, University of Exeter

Twitter @rebekah_jwhitehttps://twitter.com/rebekah_jwhite

Latest paper: Anthropogenic land-use change and emerging zoonotic diseaseshttps://onlinelibrary.wiley.com/doi/epdf/10.1111/mam.12201

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From: Hanneke Okkenhaug @.> Sent: Friday, May 6, 2022 10:30:29 AM To: hannekeo/Worm-align @.> Cc: Subscribed @.***> Subject: Re: [hannekeo/Worm-align] The question of the worm-align (Issue #2)

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Hi Lei Sorry to hear that you have issues. Could you elaborate a bit on what goes wrong? Where does the pipeline crash? Without seeing your data it is a little tricky to know what the issue is.

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhannekeo%2FWorm-align%2Fissues%2F2%23issuecomment-1119428888&data=05%7C01%7Crw617%40exeter.ac.uk%7Cb266902ed8004fa76fb208da2f431fcb%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637874262582538936%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jaqYea761zPnx3WM4nWRfuavS6aGvvo4qLFSgTm1ZTI%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAYESQD2KOZXXUNRUMVGWB3DVITRDLANCNFSM5VHRDNHA&data=05%7C01%7Crw617%40exeter.ac.uk%7Cb266902ed8004fa76fb208da2f431fcb%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637874262582538936%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GfaubBNGfdOL4piXvE7wk0tHMb8mRseGg3ALGKa5L%2Fc%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[hello-lei]

Ok, I will try it in PNG

[hello-lei]

Hi， If the number of worms is different from various groups. Could the length of the worms be change because of the number of worms?Such as one group is 5,another 8. Thank you! And may I use the result of worm aglin to measure the length of worms.

[berk1835]

Hi Lei,

Do you mean you have a different number of worms in each image? If so, this has worked fine for me. As for measuring worm length, this has worked for me too. As you are using PNG, try the solution here: https://github.com/hannekeo/Worm-align/issues/3

All the best, B

[hannekeo]

Hi Lei Really, a different number of worms in images should not be a problem. The analysis and montage (if selected) will only be done on those worms that are traced during execution of the macro. As far as I am aware the pipeline should work on different file formats. The original files I started with (provided to me by the people who wanted the analysis done) were from a Nikon microscope, so in nd2 format, but the pipeline should work as well on tif, jpeg or png. It can however be the case that those formats do not preserve the pixel scaling, so measurements might end up being pixels, rather than microns. As long as all images are captured with the same system/settings, i.e. magnification, this should not be problematic.