Sorry for my typo. It should have been class 2 = shadow of the “well” not week. I made line selections through the black-grey area representing the shadow to segment out the well edges and corresponding shadow.
Jacqueline Ross Lead Technologist Optical Microscopy & Image Analysis Biomedical Imaging Research Unit (BIRU) Faculty of Medical & Health Sciences Waipapa Taumata Rau | The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Telephone: Ext 87438; DDI: +64 9 923 7438 Website: Biomedical Imaging Research Unit - The University of Auckland<https://www.fmhs.auckland.ac.nz/en/sms/about/our-departments/biomedical-imaging-research-unit.html> SHIPPING ADDRESS Waipapa Taumata Rau | The University of Auckland M&HS BUILDING 505 - Bldg 505 Level B, Room B36 85 PARK RD/Loading Dock, Park Avenue Grafton, Auckland 1023 NEW ZEALAND ORCID ID https://orcid.org/0000-0001-5578-6651 From: Jacqueline Ross <[email protected]> Sent: Friday, March 8, 2024 3:26 PM To: [email protected] Subject: Re: help to segment spheroids Sensitivity: Confidential Caution - Forged Internal Domain! This e-mail cannot be validated and may not have been sent by the sender shown in the 'From' field. If you were not expecting to receive this e-mail we recommend you contact the sender to confirm that they sent it. If you believe this email was legitimately sent, we suggest the sender notify the Staff Service Centre that it has been received as a forged (fake) e-mail. Please contact the Staff Service Centre on extension 86000 if you require further assistance. Hi Patricia, I used WEKA segmentation for your Cell2 image and it worked well. I suggest trying that. I had 3 classes, class 1 = spheroid, class 2 = shadow of the week and class 3 = in between the wells (white area). I've attached a PNG version of the classified image and the probability maps looked good. If the spheroids become more dense (darker), you may have to have 2 separate classifiers but I think it's worth a try. Kind regards, Jacqui Jacqueline Ross Lead Technologist Optical Microscopy & Image Analysis Biomedical Imaging Research Unit (BIRU) Faculty of Medical & Health Sciences Waipapa Taumata Rau | The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Telephone: Ext 87438; DDI: +64 9 923 7438 Website: Biomedical Imaging Research Unit - The University of Auckland<https://www.fmhs.auckland.ac.nz/en/sms/about/our-departments/biomedical-imaging-research-unit.html<https://www.fmhs.auckland.ac.nz/en/sms/about/our-departments/biomedical-imaging-research-unit.html>> SHIPPING ADDRESS Waipapa Taumata Rau | The University of Auckland M&HS BUILDING 505 - Bldg 505 Level B, Room B36 85 PARK RD/Loading Dock, Park Avenue Grafton, Auckland 1023 NEW ZEALAND ORCID ID https://orcid.org/0000-0001-5578-6651<https://orcid.org/0000-0001-5578-6651> From: OBEID Patricia <[email protected]<mailto:[email protected]>> Sent: Monday, March 4, 2024 9:36 PM To: [email protected]<mailto:[email protected]> Subject: help to segment spheroids Sensitivity: Confidential Hello, I would like to segment spheroids that are in microcavities. For the first cell, all is ok. Here are a few lines from my macro: run("Duplicate...", " "); run("Invert LUT"); setAutoThreshold("Moments dark"); setOption("BlackBackground", true); run("Convert to Mask"); run("Invert LUT"); run("Analyze Particles...", "size=6000-80000 display summarize add"); For the second cell, my problem is that I'm working in white light and the edges of the wells are also detected .... One solution might be to do a threshold on the edges of the wells and the outside and remove these areas, then do a new threshold to detect spheroids, but I don't know how to write these lines of code ... :-( Thanks for any help and/or suggestions you can give me. 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