Motility analysis returning "NAN",too!
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genji grace
Oct 22, 2023, 9:05:35 AM10/22/23
to OpenCASA Mailing List
Dear all.
I have a little problem using the software.
I click the motility,and choose the .avi file. but returning NAN!
I wonder why? I don't know where is wrong ,can somebody tell me?
genji grace
Oct 22, 2023, 9:08:32 AM10/22/23
to OpenCASA Mailing List
Here is details.
genji grace
Oct 22, 2023, 9:12:37 AM10/22/23
to OpenCASA Mailing List
Here is the .avi sample .
genji grace
Oct 22, 2023, 9:16:46 AM10/22/23
to OpenCASA Mailing List
Here is the original mp4 file.
I really don't know what to do next , i try three days . But I still can't work it out. Can Someone teach me how to do?
Sincere thanks.
jyaniz
Oct 22, 2023, 4:07:43 PM10/22/23
to genji grace, OpenCASA Mailing List
Dear Genji Grace,
Firstly, I would appreciate it if you could introduce yourself and
briefly explain the purpose for which you intend to use OpenCASA,
specifying the animal species involved.
With regard to the video, I believe there are several aspects that need
improvement.
1. I recommend utilizing the second version of OpenCASA (v2) as
described in the following study, as it incorporates additional
functionalities:
https://www.mdpi.com/2079-7737/9/8/207
2. Video capture should be performed using negative phase contrast
microscopy (not positive), or alternatively, you should invert the
image.
3. The spermatozoa appear quite small; perhaps you could consider using
higher magnification.
4. Finally, the video you've captured is too lengthy; it is recommended
to capture 1-second videos for more effective analysis.
There may also be issues with some program settings, but I believe it's
essential to address the capture issues first.
Best regards,
Jesús.
El 2023-10-22 15:16, 'genji grace' via OpenCASA Mailing List escribió:
> Here is the original mp4 file.
> https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link
> [2]
>
> --
> You received this message because you are subscribed to the Google
> Groups "OpenCASA Mailing List" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to opencasa_mailing...@googlegroups.com.
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> https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n%40googlegroups.com
> [3].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-nzaP7_df$
> [2]
> https://urldefense.com/v3/__https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n8IOqJSF$
> [3]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n*40googlegroups.com?utm_medium=email&utm_source=footer__;JQ!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n4HNp8Z0$
--
Jesús Yániz Pérez de Albéniz
Catedrático de Universidad (Full Professor in Animal Science)
Dpto. Producción Animal y CC. de los Alimentos
Escuela Politécnica Superior de Huesca
Universidad de Zaragoza
Ctra. Cuarte s/n, 22071, Huesca
email: jya...@unizar.es
Phone: 34 974 239 312
Firstly, I would appreciate it if you could introduce yourself and
briefly explain the purpose for which you intend to use OpenCASA,
specifying the animal species involved.
With regard to the video, I believe there are several aspects that need
improvement.
1. I recommend utilizing the second version of OpenCASA (v2) as
described in the following study, as it incorporates additional
functionalities:
https://www.mdpi.com/2079-7737/9/8/207
2. Video capture should be performed using negative phase contrast
microscopy (not positive), or alternatively, you should invert the
image.
3. The spermatozoa appear quite small; perhaps you could consider using
higher magnification.
4. Finally, the video you've captured is too lengthy; it is recommended
to capture 1-second videos for more effective analysis.
There may also be issues with some program settings, but I believe it's
essential to address the capture issues first.
Best regards,
Jesús.
El 2023-10-22 15:16, 'genji grace' via OpenCASA Mailing List escribió:
> Here is the original mp4 file.
> https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link
> I really don't know what to do next , i try three days . But I still
> can't work it out. Can Someone teach me how to do?
> Sincere thanks.
>
> 在2023年10月22日星期日 UTC+8 21:12:37<genji grace> 写道：
>
>> Here is the .avi sample .
>>
> https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing
>> [1]
> can't work it out. Can Someone teach me how to do?
> Sincere thanks.
>
> 在2023年10月22日星期日 UTC+8 21:12:37<genji grace> 写道：
>
>> Here is the .avi sample .
>>
> https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing
>
> --
> You received this message because you are subscribed to the Google
> Groups "OpenCASA Mailing List" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to opencasa_mailing...@googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n%40googlegroups.com
> [3].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-nzaP7_df$
> [2]
> https://urldefense.com/v3/__https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n8IOqJSF$
> [3]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n*40googlegroups.com?utm_medium=email&utm_source=footer__;JQ!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n4HNp8Z0$
--
Jesús Yániz Pérez de Albéniz
Catedrático de Universidad (Full Professor in Animal Science)
Dpto. Producción Animal y CC. de los Alimentos
Escuela Politécnica Superior de Huesca
Universidad de Zaragoza
Ctra. Cuarte s/n, 22071, Huesca
email: jya...@unizar.es
Phone: 34 974 239 312
genji grace
Oct 22, 2023, 9:24:34 PM10/22/23
to OpenCASA Mailing List
Dear jesus
Thank you very much for the help you provided me！
I'm a first year graduate student form xiamen university ，China.
I just want to use the Motility function to quantify the kelp zoospores. It's the reproductive cell of brown algae.It's Latin name is Laminaria japonica
These are kelp zoospores. They can move when environmental conditions are good.
They have two flagella of unequal length. My teacher wants to know if the procedure that tests sperm motility can also be used to test it.So the last few days I've been trying to opencasa.
I still have some question about details.
I still have some question about details.
1.To use the molitity function , Do I need to use a video of about 30 seconds or 1 second is enough?
2.Any suggestions for invert videos?（Because ,recently i just have the mp4 file. Materials for the next experiment will be available in a few weeks. We only have a microscope with an iPad that can record video, and the video is recorded by the screen recording function of the iPad. I'm not sure I can borrow another microscope either.So it's important for me to learn to reverse video, and I'd be grateful if you could give me a little advice.）
3.Can the problem of cells that are too small be solved by cropping the video and enlarging it?
FInal，I will attach the video i invert， I think I did not well is there any parameter is wrong？
genji grace
Oct 22, 2023, 9:46:30 PM10/22/23
to OpenCASA Mailing List
Dear jesus ，
This time I use the 1s video, but i still got NaN.
Here is the avi I use.
Best regards,
Genji grace.
jyaniz
Oct 23, 2023, 2:26:14 AM10/23/23
to genji grace, OpenCASA Mailing List
Dear Genji,
The simplest way to invert the image is by using ImageJ. You just need
to open the video with the program, go to Edit, select Invert, and then
save it as an AVI file. It is also advisable to convert it to black and
white in Image>Type.
However, you also need to clarify some aspects, such as the scale. You
need a reference to establish it, such as calibrated slides or a
chamber.
Regarding the length of the video, you can record it for any duration
you prefer, but if it's too long, it can pose issues with cell tracking.
Typically, 1-second videos are used for spermatozoa. In your case,
you'll need to experiment with different durations. I recommend
recording long videos and then, with ImageJ, selecting different frames
numbers when opening the video to test.
You should also clearify the frame rate, which can be selected in the
camera settings of the iPad.
Nevertheless, I believe these images have insufficient quality for
OpenCASA analysis; the cells appear very small, pixelated, and blurry. I
have attempted image inversion and other adjustments, but it hasn't
yielded successful results either.
All the best,
Jesús
El 2023-10-23 03:46, 'genji grace' via OpenCASA Mailing List escribió:
> Dear jesus ，
> This time I use the 1s video, but i still got NaN.
> Here is the avi I use.
> https://drive.google.com/file/d/1GD0WX_CqHKeu5Xc3ksF1Iraswcx2l8F-/view?usp=share_link
> [6]
>>> [3]
> [7].
>
>
> Links:
> ------
> [1]
> https://urldefense.com/v3/__https://www.mdpi.com/2079-7737/9/8/207__;!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeJb96pj3$
> [2]
> https://urldefense.com/v3/__https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link__;!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeKXEhpHv$
> [3]
> https://urldefense.com/v3/__https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing__;!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeFrr1rp8$
> [4]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n*40googlegroups.com__;JQ!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeBjccBed$
> [5]
> https://urldefense.com/v3/__https://drive.google.com/file/d/1H4qohjuXw2CasJMw7wwYaxLOQ7A5RKH1/view?usp=share_link__;!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeCIRKhEB$
> [6]
> https://urldefense.com/v3/__https://drive.google.com/file/d/1GD0WX_CqHKeu5Xc3ksF1Iraswcx2l8F-/view?usp=share_link__;!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeCfgY67n$
> [7]
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/ac1d3e4e-4624-4684-bab3-af02101505fcn*40googlegroups.com?utm_medium=email&utm_source=footer__;JQ!!D9dNQwwGXtA!V5PixDFOmM7kVgpJumLvEp1Wj1geg2AFk25zasty5_iGLxctuZxsY6rFZmOVj2zN0z_xiQQaJjRbqJ6pVhNE5FKMeFSBXp9S$
The simplest way to invert the image is by using ImageJ. You just need
to open the video with the program, go to Edit, select Invert, and then
save it as an AVI file. It is also advisable to convert it to black and
white in Image>Type.
However, you also need to clarify some aspects, such as the scale. You
need a reference to establish it, such as calibrated slides or a
chamber.
Regarding the length of the video, you can record it for any duration
you prefer, but if it's too long, it can pose issues with cell tracking.
Typically, 1-second videos are used for spermatozoa. In your case,
you'll need to experiment with different durations. I recommend
recording long videos and then, with ImageJ, selecting different frames
numbers when opening the video to test.
You should also clearify the frame rate, which can be selected in the
camera settings of the iPad.
Nevertheless, I believe these images have insufficient quality for
OpenCASA analysis; the cells appear very small, pixelated, and blurry. I
have attempted image inversion and other adjustments, but it hasn't
yielded successful results either.
All the best,
Jesús
El 2023-10-23 03:46, 'genji grace' via OpenCASA Mailing List escribió:
> Dear jesus ，
> This time I use the 1s video, but i still got NaN.
> Here is the avi I use.
> https://drive.google.com/file/d/1GD0WX_CqHKeu5Xc3ksF1Iraswcx2l8F-/view?usp=share_link
>
> Best regards,
> Genji grace.
>
> 在2023年10月23日星期一 UTC+8 09:24:34<genji grace> 写道：
>
>> Dear jesus
>> Thank you very much for the help you provided me！
>> I'm a first year graduate student form xiamen university ，China.
>> I just want to use the Motility function to quantify the kelp
>> zoospores. It's the reproductive cell of brown algae.It's Latin
>> name is _Laminaria japonica_
> Best regards,
> Genji grace.
>
> 在2023年10月23日星期一 UTC+8 09:24:34<genji grace> 写道：
>
>> Dear jesus
>> Thank you very much for the help you provided me！
>> I'm a first year graduate student form xiamen university ，China.
>> I just want to use the Motility function to quantify the kelp
>> zoospores. It's the reproductive cell of brown algae.It's Latin
>> These are kelp zoospores. They can move when environmental
>> conditions are good.
>> They have two flagella of unequal length. My teacher wants to know
>> if the procedure that tests sperm motility can also be used to test
>> it.So the last few days I've been trying to opencasa.
>> I still have some question about details.
>> 1.To use the molitity function , Do I need to use a video of about
>> 30 seconds or 1 second is enough?
>> 2.Any suggestions for invert videos?（Because ,recently i just have
>> the mp4 file. Materials for the next experiment will be available in
>> a few weeks. We only have a microscope with an iPad that can record
>> video, and the video is recorded by the screen recording function of
>> the iPad. I'm not sure I can borrow another microscope either.So
>> it's important for me to learn to reverse video, and I'd be grateful
>> if you could give me a little advice.）
>> 3.Can the problem of cells that are too small be solved by cropping
>> the video and enlarging it?
>> FInal，I will attach the video i invert， I think I did not well
>> is there any parameter is wrong？
>>
> https://drive.google.com/file/d/1H4qohjuXw2CasJMw7wwYaxLOQ7A5RKH1/view?usp=share_link
>> [5]
>> conditions are good.
>> They have two flagella of unequal length. My teacher wants to know
>> if the procedure that tests sperm motility can also be used to test
>> it.So the last few days I've been trying to opencasa.
>> I still have some question about details.
>> 1.To use the molitity function , Do I need to use a video of about
>> 30 seconds or 1 second is enough?
>> 2.Any suggestions for invert videos?（Because ,recently i just have
>> the mp4 file. Materials for the next experiment will be available in
>> a few weeks. We only have a microscope with an iPad that can record
>> video, and the video is recorded by the screen recording function of
>> the iPad. I'm not sure I can borrow another microscope either.So
>> it's important for me to learn to reverse video, and I'd be grateful
>> if you could give me a little advice.）
>> 3.Can the problem of cells that are too small be solved by cropping
>> the video and enlarging it?
>> FInal，I will attach the video i invert， I think I did not well
>> is there any parameter is wrong？
>>
> https://drive.google.com/file/d/1H4qohjuXw2CasJMw7wwYaxLOQ7A5RKH1/view?usp=share_link
>>
>> 在2023年10月23日星期一 UTC+8 04:07:43<jya...@unizar.es>
>> 写道：
>>
>>> Dear Genji Grace,
>>>
>>> Firstly, I would appreciate it if you could introduce yourself and
>>>
>>> briefly explain the purpose for which you intend to use OpenCASA,
>>> specifying the animal species involved.
>>>
>>> With regard to the video, I believe there are several aspects that
>>> need
>>> improvement.
>>>
>>> 1. I recommend utilizing the second version of OpenCASA (v2) as
>>> described in the following study, as it incorporates additional
>>> functionalities:
>>> https://www.mdpi.com/2079-7737/9/8/207 [1]
>> 在2023年10月23日星期一 UTC+8 04:07:43<jya...@unizar.es>
>> 写道：
>>
>>> Dear Genji Grace,
>>>
>>> Firstly, I would appreciate it if you could introduce yourself and
>>>
>>> briefly explain the purpose for which you intend to use OpenCASA,
>>> specifying the animal species involved.
>>>
>>> With regard to the video, I believe there are several aspects that
>>> need
>>> improvement.
>>>
>>> 1. I recommend utilizing the second version of OpenCASA (v2) as
>>> described in the following study, as it incorporates additional
>>> functionalities:
>>>>> [1]
>>>>
>>>> --
>>>> You received this message because you are subscribed to the
>>> Google
>>>> Groups "OpenCASA Mailing List" group.
>>>> To unsubscribe from this group and stop receiving emails from
>>> it, send
>>>> an email to opencasa_mailing...@googlegroups.com.
>>>> To view this discussion on the web, visit
>>>>
>>>
>>
> https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n%40googlegroups.com
>>> [4]
>>>>
>>>> --
>>>> You received this message because you are subscribed to the
>>>> Groups "OpenCASA Mailing List" group.
>>>> To unsubscribe from this group and stop receiving emails from
>>> it, send
>>>> an email to opencasa_mailing...@googlegroups.com.
>>>> To view this discussion on the web, visit
>>>>
>>>
>>
> https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n%40googlegroups.com
>>>> [3].
>>>>
>>>>
>>>> Links:
>>>> ------
>>>> [1]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-nzaP7_df$
>>>
>>>> [2]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n8IOqJSF$
>>>
>>>> [3]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n*40googlegroups.com?utm_medium=email&utm_source=footer__;JQ!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n4HNp8Z0$
>>>
>>>
>>> --
>>> Jesús Yániz Pérez de Albéniz
>>> Catedrático de Universidad (Full Professor in Animal Science)
>>> Dpto. Producción Animal y CC. de los Alimentos
>>> Escuela Politécnica Superior de Huesca
>>> Universidad de Zaragoza
>>> Ctra. Cuarte s/n, 22071, Huesca
>>> email: jya...@unizar.es
>>> Phone: 34 974 239 312
>
>>>>
>>>>
>>>> Links:
>>>> ------
>>>> [1]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://drive.google.com/file/d/1ABHT0gcZtHYccimkVQBgAIXWBqI_VR1J/view?usp=sharing__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-nzaP7_df$
>>>
>>>> [2]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://drive.google.com/file/d/19OvpsTVvstkROXCZ9SnBm3T7z-Kb1Jz_/view?usp=share_link__;!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n8IOqJSF$
>>>
>>>> [3]
>>>>
>>>
>>
> https://urldefense.com/v3/__https://groups.google.com/d/msgid/opencasa_mailinglist/dc37d3fd-a82c-40e8-be5e-5897f79edc06n*40googlegroups.com?utm_medium=email&utm_source=footer__;JQ!!D9dNQwwGXtA!Q5gRBacEztO3LaD3F4_DZhmrOG92Mni6em_Xk7345vQMd9_wYmh5XNNRTikML9Ykx_Mrad0yQ2T2011UpLb0rLV-n4HNp8Z0$
>>>
>>>
>>> --
>>> Jesús Yániz Pérez de Albéniz
>>> Catedrático de Universidad (Full Professor in Animal Science)
>>> Dpto. Producción Animal y CC. de los Alimentos
>>> Escuela Politécnica Superior de Huesca
>>> Universidad de Zaragoza
>>> Ctra. Cuarte s/n, 22071, Huesca
>>> email: jya...@unizar.es
>>> Phone: 34 974 239 312
>
> --
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genji grace
Oct 23, 2023, 2:45:18 AM10/23/23
to OpenCASA Mailing List
Dear jesus,
Thank you very much!
I will try to capture another videos next week.
Thank you very much for letting me know how to solve the problem.
Best wishes,
Genji grace
genji grace
Oct 25, 2023, 4:27:18 AM10/25/23
to OpenCASA Mailing List
Dear all，
Yesterday ， I borrow a microscope to capture a new video.I try to test the motility, but i'm still failed.
I think might be the problem in process the video.
I invert the video and cut it to 1s , then run the program but it still return the NAN.
I invert the video and cut it to 1s , then run the program but it still return the NAN.
The image size under the 10x objective lens this time is 1024*768，the real size provided on the computer is 11077.82*8308.36μm.
So the microns per pixel is 10.81.
And the kelp zoospores diameter is 1-3μm measure by a microscope.(The parameter i used is below, in fact I think it might be wrong because it didn't bring me a result)
Can you please teach me how to do it or is it impossible for my species to measure his sperm motility?Is there still something wrong with the video I recorded?
This time I recorded the video under the 4X 10X 40X objective lens. The 20X video was not recorded because there is no such objective lens.
Below is the link to the video I provided
3.40x videos (Because there was very little swimming in a field of view after the cover glass was applied, two videos were taken.） https://drive.google.com/drive/folders/12_74ILj_ALaf2ZUuFUortmXiQdJI82eK?usp=sharing
And here is the video I processed ， I think it might be bad.
Sincerely,
Genji Grace.
Felipe Martínez Pastor
Oct 25, 2023, 5:54:43 AM10/25/23
to opencasa_m...@googlegroups.com
Hi Genji,
I see many problems with your video, Jesús mentioned some of them. The
background is too "heavy," for instance.
However, I opened your 40x1.avi video (images 100 to 200 only), saved
and I was able to analyse it, even without image inversion. Not great,
but playing with the settings I was able to get trajectories only from
the zoospores. If you could get a cleaner image (maybe more contrast or
lighting?) it would be much better.
Another technical problem is the framerate. It is too low for your
cells. These cells are too fast, and the images in individual frames are
blurry. This is an indication that you should go for much higher framerates.
In any case, check your scale. I used 0.8 to 0.4 µm/px, just by chance,
and it worked. You should use a microscopic scale or maybe (inaccurate,
but it could help you) the grid of a Neubauer chamber or similar. You
need to measure a scale in your image to be sure of the actual one. For
the other settings, I set area from 10 to 200 µm, maximum displacement
50. Maybe your scale and area settings are good, but you should check.
Finally, you might check the last messages in the group. Many users
(including myself) were having this problem in which ImageJ gave up
trying to analyse the images and returnin NAN or nothing at all. We
found that, rather misteriously, the problem solved if we installed an
older version (for instance, I believe last one is 1.53t, then you
download and run 1.53a with OpenCASA), then the problem is solved and
you can go back to the last version. Give it a try just in case.
Good luck!
Felipe
El 25/10/23 a las 10:27, 'genji grace' via OpenCASA Mailing List escribió:
> And the kelp zoospores diameter is *1-3μm* measure by a microscope.(The
----------------------------oOo----------------------------
Felipe Martínez Pastor
Research in Biology of Reproduction
Biología Celular
Facultad de CC. Biológicas y Ambientales
Universidad de León
Campus de Vegazana
24071-León
Tfno.: +34 987 291 491
Móvil: +34 687 365 362
e-mail: felipe....@unileon.es
web: http://reprobio.unileon.es
profiles:
https://www.researchgate.net/profile/Felipe_Martinez-Pastor
http://orcid.org/0000-0001-9184-8581
http://www.researcherid.com/rid/B-4277-2008
------------------------------------------------------------
Aviso de confidencialidad https://www.unileon.es/mail-disclaimer/20180525
Confidentiality Notice https://www.unileon.es/mail-disclaimer/20180525
I see many problems with your video, Jesús mentioned some of them. The
background is too "heavy," for instance.
However, I opened your 40x1.avi video (images 100 to 200 only), saved
and I was able to analyse it, even without image inversion. Not great,
but playing with the settings I was able to get trajectories only from
the zoospores. If you could get a cleaner image (maybe more contrast or
lighting?) it would be much better.
Another technical problem is the framerate. It is too low for your
cells. These cells are too fast, and the images in individual frames are
blurry. This is an indication that you should go for much higher framerates.
In any case, check your scale. I used 0.8 to 0.4 µm/px, just by chance,
and it worked. You should use a microscopic scale or maybe (inaccurate,
but it could help you) the grid of a Neubauer chamber or similar. You
need to measure a scale in your image to be sure of the actual one. For
the other settings, I set area from 10 to 200 µm, maximum displacement
50. Maybe your scale and area settings are good, but you should check.
Finally, you might check the last messages in the group. Many users
(including myself) were having this problem in which ImageJ gave up
trying to analyse the images and returnin NAN or nothing at all. We
found that, rather misteriously, the problem solved if we installed an
older version (for instance, I believe last one is 1.53t, then you
download and run 1.53a with OpenCASA), then the problem is solved and
you can go back to the last version. Give it a try just in case.
Good luck!
Felipe
El 25/10/23 a las 10:27, 'genji grace' via OpenCASA Mailing List escribió:
> Dear all，
> Yesterday ， I borrow a microscope to capture a new video.I try to test the
> motility, but i'm still failed.
> I think might be the problem in process the video.
> I invert the video and cut it to 1s , then run the program but it still
> return the NAN.
> The image size under the 10x objective lens this time is 1024*768，the real
> size provided on the computer is 11077.82*8308.36μm.
> So the *microns per pixel is 10.81*.
> Yesterday ， I borrow a microscope to capture a new video.I try to test the
> motility, but i'm still failed.
> I think might be the problem in process the video.
> I invert the video and cut it to 1s , then run the program but it still
> return the NAN.
> The image size under the 10x objective lens this time is 1024*768，the real
> size provided on the computer is 11077.82*8308.36μm.
> And the kelp zoospores diameter is *1-3μm* measure by a microscope.(The
Felipe Martínez Pastor
Research in Biology of Reproduction
Biología Celular
Facultad de CC. Biológicas y Ambientales
Universidad de León
Campus de Vegazana
24071-León
Tfno.: +34 987 291 491
Móvil: +34 687 365 362
e-mail: felipe....@unileon.es
web: http://reprobio.unileon.es
profiles:
https://www.researchgate.net/profile/Felipe_Martinez-Pastor
http://orcid.org/0000-0001-9184-8581
http://www.researcherid.com/rid/B-4277-2008
------------------------------------------------------------
Aviso de confidencialidad https://www.unileon.es/mail-disclaimer/20180525
Confidentiality Notice https://www.unileon.es/mail-disclaimer/20180525
genji grace
Oct 25, 2023, 9:11:07 AM10/25/23
to OpenCASA Mailing List
Dear Filipe,
I’m extremely grateful for your help. I will follow your advice and capture videos with a higher frame rate and a simpler background in next experiment.
I still have a question about the Set scale . Should I set it in imagej or just in the setting of the openCASA's Microns per Pixel?(I haven't do it in imagej)
Best wishes
Genji grace
genji grace
Oct 25, 2023, 9:15:01 AM10/25/23
to OpenCASA Mailing List
I forgot to attach this picture.
Felipe Martínez Pastor
Oct 25, 2023, 4:13:09 PM10/25/23
to opencasa_m...@googlegroups.com
Hi,
It is enough if you enter that in the OpenCASA settings. However, you
should use imageJ to measure a grid in an image of the same
characteristics than your videos (size and resolution). You'll get the
distance in pixel, and, if you know the distance between lines, you can
get an accurate µm/px ratio.
Best wishes,
Felipe
El 25/10/23 a las 15:11, 'genji grace' via OpenCASA Mailing List escribió:
> or just in the setting of the *openCASA*'s Microns per Pixel?(I haven't do
>> Tfno.: +34 987 291 491 <+34%20987%2029%2014%2091>
>> Móvil: +34 687 365 362 <+34%20687%2036%2053%2062>
It is enough if you enter that in the OpenCASA settings. However, you
should use imageJ to measure a grid in an image of the same
characteristics than your videos (size and resolution). You'll get the
distance in pixel, and, if you know the distance between lines, you can
get an accurate µm/px ratio.
Best wishes,
Felipe
El 25/10/23 a las 15:11, 'genji grace' via OpenCASA Mailing List escribió:
> Dear Filipe,
> I’m extremely grateful for your help. I will follow your advice and capture
> videos with a higher frame rate and a simpler background in next experiment.
> I still have a question about the *Set scale . *Should I set it in imagej
> I’m extremely grateful for your help. I will follow your advice and capture
> videos with a higher frame rate and a simpler background in next experiment.
> or just in the setting of the *openCASA*'s Microns per Pixel?(I haven't do
>> Móvil: +34 687 365 362 <+34%20687%2036%2053%2062>
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