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Hyojung-Choo / Myosoft

automated muscle histology analysis using machine learning algorithm utilizing FIJI/Image J software
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'The list is empty' error #3

Open hus9301 opened 3 years ago

hus9301 commented 3 years ago

Hi.

I used v13. After the fiber gating (all of the fiber types), 'The list is empty' error occurs through ROI manager window.

I tried to follow up the whole step of the tutorial, but this error occurs again and again.

If you have any opinion or solution, please share.

thank you!

Hyojung-Choo commented 3 years ago

Sorry for late response. We updated a new version. Please try ver14. Thank you.

marvelouscandy commented 2 years ago

Hi Dr. Choo,

I have also run into "the list is empty" issue. I was trying v15 but failed when trying to quantify just 3 channels (one membrane, one type 2a and one type 2b). I wonder what should I do to avoid this issue? Thank you very much for your response and time. Best regards.

Hyojung-Choo commented 2 years ago

Hi,

Thank you for contacting me. I'm not sure you can get my response since email address is not clear, but Lucas may help you.

Lucas, could you please help?

Thank you.

Best regards,

Choo

Hyojung Choo, Ph.D. (she/her/hers)

Assistant Professor

Department of Cell Biology

School of Medicine

Emory University

Whitehead research building, Rm 542

615 Michael Street, Atlanta, GA 30322

Office) 404-727-3727

Lab) 404-727-3714

Cell) 864-633-7967

https://med.emory.edu/departments/cell-biology/choo-lab/index.html

https://twitter.com/choo_hyojunghttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2Fchoo_hyojung&data=05%7C01%7Chyojung.choo%40emory.edu%7C240d9d9ca4d04350732108da54501356%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637915000172547386%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9YoFwS25MEIjez4NRkC1eCI5XQThYdP%2F6%2FhPLdCQ6%2Fg%3D&reserved=0

From: marvelouscandy @.> Sent: Friday, August 5, 2022 12:22 AM To: Hyojung-Choo/Myosoft @.> Cc: Choo, Hyojung @.>; Comment @.> Subject: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3)

Hi Dr. Choo,

I have also run into "the list is empty" issue. I was trying v15 but failed when trying to quantify just 3 channels (one membrane, one type 2a and one type 2b). I wonder what should I do to avoid this issue? Thank you very much for your response and time. Best regards.

— Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHyojung-Choo%2FMyosoft%2Fissues%2F3%23issuecomment-1206026077&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nA5qQEJ7Lz9GaVe74fN0MlJAoTwuNvXAIZeTuz%2B6m38%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAMRFWN3ITZ653KNXFPZICOTVXSJHBANCNFSM4YU4OMWA&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yXersPr%2BvmqleNlENwz9LI4EWtbGr4vJHvfixqhn5aM%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

marvelouscandy commented 2 years ago

Hi, Thank you for contacting me. I'm not sure you can get my response since email address is not clear, but Lucas may help you. Lucas, could you please help? Thank you. Best regards, Choo Hyojung Choo, Ph.D. (she/her/hers) Assistant Professor Department of Cell Biology School of Medicine Emory University Whitehead research building, Rm 542 615 Michael Street, Atlanta, GA 30322 Office) 404-727-3727 Lab) 404-727-3714 Cell) 864-633-7967 https://med.emory.edu/departments/cell-biology/choo-lab/index.html https://twitter.com/choo_hyojunghttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2Fchoo_hyojung&data=05%7C01%7Chyojung.choo%40emory.edu%7C240d9d9ca4d04350732108da54501356%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637915000172547386%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9YoFwS25MEIjez4NRkC1eCI5XQThYdP%2F6%2FhPLdCQ6%2Fg%3D&reserved=0 … ____ From: marvelouscandy @.> Sent: Friday, August 5, 2022 12:22 AM To: Hyojung-Choo/Myosoft @.> Cc: Choo, Hyojung @.>; Comment @.> Subject: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3) Hi Dr. Choo, I have also run into "the list is empty" issue. I was trying v15 but failed when trying to quantify just 3 channels (one membrane, one type 2a and one type 2b). I wonder what should I do to avoid this issue? Thank you very much for your response and time. Best regards. — Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHyojung-Choo%2FMyosoft%2Fissues%2F3%23issuecomment-1206026077&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nA5qQEJ7Lz9GaVe74fN0MlJAoTwuNvXAIZeTuz%2B6m38%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAMRFWN3ITZ653KNXFPZICOTVXSJHBANCNFSM4YU4OMWA&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yXersPr%2BvmqleNlENwz9LI4EWtbGr4vJHvfixqhn5aM%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

Thank you very much! In the meantime, I also tried to use v14, it still didn't work and said "the list is empty" Please let me know if you would need more information to troubleshoot. Best regards

Hyojung-Choo commented 2 years ago

So sorry I missed this! This error is occurring because you are using only 3 channels. A simple fix is to use the duplicate function in imagej to create an equivalent image with an "extra" channel. This will allow you to run the program successfully. The duplicated image that occupies the fourth channel will be analyzed but that data can simply be discarded following data and ROI acquisition.

Best, -Lucas

From: Choo, Hyojung @.> Sent: Friday, August 5, 2022 1:32 PM To: Hyojung-Choo/Myosoft @.> Cc: Lucas Encarnacion-Rivera @.***> Subject: Re: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3)

Hi,

Thank you for contacting me. I'm not sure you can get my response since email address is not clear, but Lucas may help you.

Lucas, could you please help?

Thank you.

Best regards,

Choo

Hyojung Choo, Ph.D. (she/her/hers)

Assistant Professor

Department of Cell Biology

School of Medicine

Emory University

Whitehead research building, Rm 542

615 Michael Street, Atlanta, GA 30322

Office) 404-727-3727

Lab) 404-727-3714

Cell) 864-633-7967

https://med.emory.edu/departments/cell-biology/choo-lab/index.html

https://twitter.com/choo_hyojunghttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2Fchoo_hyojung&data=05%7C01%7Chyojung.choo%40emory.edu%7C240d9d9ca4d04350732108da54501356%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637915000172547386%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9YoFwS25MEIjez4NRkC1eCI5XQThYdP%2F6%2FhPLdCQ6%2Fg%3D&reserved=0

From: marvelouscandy @.> Sent: Friday, August 5, 2022 12:22 AM To: Hyojung-Choo/Myosoft @.> Cc: Choo, Hyojung @.>; Comment @.> Subject: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3)

Hi Dr. Choo,

I have also run into "the list is empty" issue. I was trying v15 but failed when trying to quantify just 3 channels (one membrane, one type 2a and one type 2b). I wonder what should I do to avoid this issue? Thank you very much for your response and time. Best regards.

— Reply to this email directly, view it on GitHubhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHyojung-Choo%2FMyosoft%2Fissues%2F3%23issuecomment-1206026077&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nA5qQEJ7Lz9GaVe74fN0MlJAoTwuNvXAIZeTuz%2B6m38%3D&reserved=0, or unsubscribehttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAMRFWN3ITZ653KNXFPZICOTVXSJHBANCNFSM4YU4OMWA&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yXersPr%2BvmqleNlENwz9LI4EWtbGr4vJHvfixqhn5aM%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

marvelouscandy commented 2 years ago

Hi Lucas,

Thank you so much for your reply. Here is what I did after your suggestion. my original image only has 3 channels, type 1 --Green; Type 2a--Red; Membrane--blue; in the merge channels option in imageJ, I assigned the Type 2a channel to 1 and 4; in this case, my new image has 4 channels; with 2a and 2b being the same source image. Then in Myosight, I assigned the channels respectively. membrane(blue)--3 Type1--2 Type2a--1 Type2b--4;

But I still get the "the list is empty" error. The program was able to give me some zip files of the ROI of individual fiber types and hybrid fibers before it ended with that error.

I am grateful for your help! Please let me know if you need additional information from me. Best regards,

On Tue, 16 Aug 2022 at 03:28, Hyojung-Choo @.***> wrote:

So sorry I missed this! This error is occurring because you are using only 3 channels. A simple fix is to use the duplicate function in imagej to create an equivalent image with an "extra" channel. This will allow you to run the program successfully. The duplicated image that occupies the fourth channel will be analyzed but that data can simply be discarded following data and ROI acquisition.

Best, -Lucas

From: Choo, Hyojung @.> Sent: Friday, August 5, 2022 1:32 PM To: Hyojung-Choo/Myosoft @.> Cc: Lucas Encarnacion-Rivera @.***> Subject: Re: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3)

Hi,

Thank you for contacting me. I'm not sure you can get my response since email address is not clear, but Lucas may help you.

Lucas, could you please help?

Thank you.

Best regards,

Choo

Hyojung Choo, Ph.D. (she/her/hers)

Assistant Professor

Department of Cell Biology

School of Medicine

Emory University

Whitehead research building, Rm 542

615 Michael Street, Atlanta, GA 30322

Office) 404-727-3727

Lab) 404-727-3714

Cell) 864-633-7967

https://med.emory.edu/departments/cell-biology/choo-lab/index.html

https://twitter.com/choo_hyojung< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2Fchoo_hyojung&data=05%7C01%7Chyojung.choo%40emory.edu%7C240d9d9ca4d04350732108da54501356%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637915000172547386%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=9YoFwS25MEIjez4NRkC1eCI5XQThYdP%2F6%2FhPLdCQ6%2Fg%3D&reserved=0

From: marvelouscandy @.> Sent: Friday, August 5, 2022 12:22 AM To: Hyojung-Choo/Myosoft @.> Cc: Choo, Hyojung @.>; Comment @.> Subject: [External] Re: [Hyojung-Choo/Myosoft] 'The list is empty' error (#3)

Hi Dr. Choo,

I have also run into "the list is empty" issue. I was trying v15 but failed when trying to quantify just 3 channels (one membrane, one type 2a and one type 2b). I wonder what should I do to avoid this issue? Thank you very much for your response and time. Best regards.

— Reply to this email directly, view it on GitHub< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHyojung-Choo%2FMyosoft%2Fissues%2F3%23issuecomment-1206026077&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nA5qQEJ7Lz9GaVe74fN0MlJAoTwuNvXAIZeTuz%2B6m38%3D&reserved=0>, or unsubscribe< https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAMRFWN3ITZ653KNXFPZICOTVXSJHBANCNFSM4YU4OMWA&data=05%7C01%7Chyojung.choo%40emory.edu%7Cd72792f4d87c4a106ec708da769a1014%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C637952701347800277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yXersPr%2BvmqleNlENwz9LI4EWtbGr4vJHvfixqhn5aM%3D&reserved=0

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— Reply to this email directly, view it on GitHub https://github.com/Hyojung-Choo/Myosoft/issues/3#issuecomment-1216251717, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALVKG3YDI27DK5EFEQHYK7TVZM7I7ANCNFSM4YU4OMWA . You are receiving this because you commented.Message ID: @.***>