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jries / SMAP

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Impossible to build an image with the parameters for a sCMOS camera #6

Open xavpinson opened 2 years ago

xavpinson commented 2 years ago

Hi Jonas,

I contact you as I encounter a problem when I try to reconstruct a 3D image. Since my images are obtained with a sCMOS camera I ask for the sCMOS variance to be corrected in the "Peak finder" tab and check in the "fitter" tab I indicate that my camera is an sCMOS one. Unfortunately when I add this information I get these error msg and the image is not reconstructed. **Error using ./ Arrays have incompatible sizes for this operation.

Error in WorkflowModules.Filters.ImageFilter/run (line 138)

Error in interfaces.WorkflowInterface/input (line 77)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in WorkflowModules.Loaders.TifLoader/run (line 128)

Error in WorkflowModules.Loaders.LoaderGUI/run (line 34)

Error in interfaces.Workflow/run (line 250)

Error in gui.GuiLocalize>localize_callback (line 348)

Error while evaluating UIControl Callback.**

Also on the camera manager, unfortunately when I tried to add a camera to informe these informations I'm not able to modified the default settings proposed.

Thank you in advance for your help,

Best,

Eva Pinto

Rieslab commented 2 years ago

Hi Eva, Do you have the possibility to use the MATLAB version of SMAP and the develop branch? Could you try there? Best, Jonas

On 4. Mar 2022, at 11:45, xavpinson @.***> wrote:

Hi Jonas,

I contact you as I encounter a problem when I try to reconstruct a 3D image. Since my images are obtained with a sCMOS camera I ask for the sCMOS variance to be corrected in the "Peak finder" tab and check in the "fitter" tab I indicate that my camera is an sCMOS one. Unfortunately when I add this information I get these error msg and the image is not reconstructed. **Error using ./ Arrays have incompatible sizes for this operation.

Error in WorkflowModules.Filters.ImageFilter/run (line 138)

Error in interfaces.WorkflowInterface/input (line 77)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in WorkflowModules.Loaders.TifLoader/run (line 128)

Error in WorkflowModules.Loaders.LoaderGUI/run (line 34)

Error in interfaces.Workflow/run (line 250)

Error in gui.GuiLocalize>localize_callback (line 348)

Error while evaluating UIControl Callback.**

Also on the camera manager, unfortunately when I tried to add a camera to informe these informations I'm not able to modified the default settings proposed.

Thank you in advance for your help,

Best,

Eva Pinto

— Reply to this email directly, view it on GitHub https://github.com/jries/SMAP/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ52BWVIOQU7PFCCGAIIJLU6HSVHANCNFSM5P5F7YJA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you are subscribed to this thread.

Dr. Jonas Ries

Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany

Phone: +49 6221 3878199 Fax: +49 6221 387 8242 Mobile: +49 151 51040705 Email: @.*** http://www.embl.de/research/units/cbb/ries/index.html

Eva-pinto commented 2 years ago

Hi Jonas, We use the standalone Matlab as we don't have MATLAB. But as I identified that this issue appears when I check the sCMOS settings, we wonder what are their uses and if we don't check them, would it have impacts on the further analysis steps?

Best,

Eva

Rieslab commented 2 years ago

Hi Eva, I’ll compile SMAP again the next days. You could test with the new version. I’ll let you know once I am done. Best, Jonas

On 8. Mar 2022, at 13:00, Eva-pinto @.***> wrote:

Hi Jonas, We use the standalone Matlab as we don't have MATLAB. But as I identified that this issue appears when I check the sCMOS settings, we wonder what are their uses and if we don't check them, would it have impacts on the further analysis steps?

Best,

Eva

— Reply to this email directly, view it on GitHub https://github.com/jries/SMAP/issues/6#issuecomment-1061703166, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ52BXASRD463MNG4IWQPLU646MBANCNFSM5P5F7YJA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.

Dr. Jonas Ries

Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany

Phone: +49 6221 3878199 Fax: +49 6221 387 8242 Mobile: +49 151 51040705 Email: @.*** http://www.embl.de/research/units/cbb/ries/index.html

Eva-pinto commented 2 years ago

Hi Jonas,

Oh great, thank you very much.

Eva

Rieslab commented 2 years ago

And sure, you can do the entire analysis without using sCMOS statistics. For most experiments, you would not see much of a difference. Best, Jonas

On 8. Mar 2022, at 13:00, Eva-pinto @.***> wrote:

Hi Jonas, We use the standalone Matlab as we don't have MATLAB. But as I identified that this issue appears when I check the sCMOS settings, we wonder what are their uses and if we don't check them, would it have impacts on the further analysis steps?

Best,

Eva

— Reply to this email directly, view it on GitHub https://github.com/jries/SMAP/issues/6#issuecomment-1061703166, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ52BXASRD463MNG4IWQPLU646MBANCNFSM5P5F7YJA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.

Dr. Jonas Ries

Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany

Phone: +49 6221 3878199 Fax: +49 6221 387 8242 Mobile: +49 151 51040705 Email: @.*** http://www.embl.de/research/units/cbb/ries/index.html

Eva-pinto commented 2 years ago

Ok great, thank you !

Best, Eva

Rieslab commented 2 years ago

I now made a new compiled version of SMAP for Mac and PC. You can download it from www.rieslab.de http://www.rieslab.de/ Let me know if it doesn’t work. Best, Jonas

On 8. Mar 2022, at 13:09, Eva-pinto @.***> wrote:

Ok great, thank you !

Best, Eva

— Reply to this email directly, view it on GitHub https://github.com/jries/SMAP/issues/6#issuecomment-1061711130, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ52BS7F3DF67Z3H4D6G3LU647RHANCNFSM5P5F7YJA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.

Dr. Jonas Ries

Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany

Phone: +49 6221 3878199 Fax: +49 6221 387 8242 Mobile: +49 151 51040705 Email: @.*** http://www.embl.de/research/units/cbb/ries/index.html

Eva-pinto commented 2 years ago

Hi Jonas,

Thank you for your return. I just try your new compiled version of SMAP and unfortunately it still doesn't work. I copy paste the error messages as some errors are different than the first one.

"Arrays have incompatible sizes for this operation.

Error in WorkflowModules.Filters.ImageFilter/run (line 139)

Error in interfaces.WorkflowInterface/input (line 77)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in WorkflowModules.Loaders.TifLoader/run (line 133)

Error in WorkflowModules.Loaders.LoaderGUI/run (line 34)

Error in interfaces.Workflow/run (line 250)

Error in gui.GuiLocalize>localize_callback (line 348)

Error while evaluating UIControl Callback."

Best, Eva

Rieslab commented 2 years ago

Hi Eva, Can you check the following: Activate the checkmark ‘Correct Offset’ in the Localise…Input Image tab. It seems that without this, the sCMOS files are not loaded. If this does not work, push the ’set Camera Parameters’ button and see if the path to the CMOS calibration file is valid. Thanks, Jonas

On 11. Mar 2022, at 10:53, Eva-pinto @.***> wrote:

Hi Jonas,

Thank you for your return. I just try your new compiled version of SMAP and unfortunately it still doesn't work. I copy paste the error messages as some errors are different than the first one.

"Arrays have incompatible sizes for this operation.

Error in WorkflowModules.Filters.ImageFilter/run (line 139)

Error in interfaces.WorkflowInterface/input (line 77)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in interfaces.WorkflowInterface/input (line 79)

Error in interfaces.WorkflowInterface/output (line 68)

Error in WorkflowModules.Loaders.TifLoader/run (line 133)

Error in WorkflowModules.Loaders.LoaderGUI/run (line 34)

Error in interfaces.Workflow/run (line 250)

Error in gui.GuiLocalize>localize_callback (line 348)

Error while evaluating UIControl Callback."

Best, Eva

— Reply to this email directly, view it on GitHub https://github.com/jries/SMAP/issues/6#issuecomment-1064952399, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZ52BUBZMP4UBQGHFJDCQTU7MJ2ZANCNFSM5P5F7YJA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.

Dr. Jonas Ries

Cell Biology and Biophysics Unit European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg, Germany

Phone: +49 6221 3878199 Fax: +49 6221 387 8242 Mobile: +49 151 51040705 Email: @.*** http://www.embl.de/research/units/cbb/ries/index.html