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Turku-BioImaging / ColonyArea

ImageJ-plugin that performs standard analysis of colony formation assays conducted in 6- to 24-well dishes.
GNU General Public License v3.0
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Failed to obtain correct threshold #1

Closed koeic closed 3 months ago

koeic commented 4 months ago

Hi,

I have performed colony-forming assay using MDA-MB-231 cancer cells, which have a tendency to spread out during growth to form a monolayer, with a doubling time of around 36 hours. The assay lasted for 2 weeks and majority of the surface of the wells were occupied. The wells were then stained with crystal violet.

I tried using the automatic "Colony thresholder" plug-in and the thresholds for some of the wells were not satisfactory. I then tried determining the ideal threshold using "image > adjust > threshold" then apply the threshold number onto "manual thresholder". The results were better but some of the wells still do not show accurate results.

May I know if there is a solution to this problem please?

Picture of the original plate, results obtained using "colony thresholder" and "manual colony thresholder" are in the link: https://drive.google.com/drive/folders/1iREyz8UjfAuXQEZB6nnDdtWwaPG2R9mU?usp=share_link

Thank you very much.

junelsolis commented 3 months ago

@koeic I believe that you have been in touch with one of the authors already. Have you been able to resolve this issue?

koeic commented 3 months ago

Dear Junel,

Indeed, I have received an email from Camilo. I tried shortening the duration of the assay, a smaller surface was covered and the analysis was able to detect the correct threshold. Thank you so much for your help.

Best regards, Koei

From: Junel Solis @.> Sent: Friday, 28 June 2024 2:20 pm To: Turku-BioImaging/ColonyArea @.> Cc: Ho Lam Cheung @.>; Mention @.> Subject: Re: [Turku-BioImaging/ColonyArea] Failed to obtain correct threshold (Issue #1)

@koeichttps://github.com/koeic I believe that you have been in touch with one of the authors already. Have you been able to resolve this issue?

— Reply to this email directly, view it on GitHubhttps://github.com/Turku-BioImaging/ColonyArea/issues/1#issuecomment-2196221784, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BI3LZLKAUU35K56ZOJIV4R3ZJT6CHAVCNFSM6AAAAABIS7VULCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJWGIZDCNZYGQ. You are receiving this because you were mentioned.Message ID: @.***>

junelsolis commented 3 months ago

Thanks for the feedback! If you have any ideas about how to make this plugin better, please do feel free to open another issue.