Feature request: option to output manifold in ImageJ plugin

[tlambert03]

Would be nice to have an option to output the manifold z map (i.e. the Manifold array provided in the output of the Matlab functions) in the ImageJ plugin. Perhaps just a checkbox that, if checked, outputs the manifold as an additional image?

[erexhepa]

Hi,

Yeah no problems with that. It was a feature of earlier version for debugging purposes. We also had as feature the save locally as a tiff the zmap. I can activate it and put it through my github account to leave the official version as it was described in the publication.
you have to be careful when manipulating it as depending on number of Z planes you need to adjust the format of the image so that it can be visualized optimally. Although till 256 z-levels it should be ok.

[tlambert03]

yeah, that'd be great thanks! so, just keep an eye on https://github.com/erexhepa/SME?

[erexhepa]

yes keep an eye my local rep. I will post a comment here too so that you get notified.

[SoleneW]

Hello,
I am also interested by this feature. Did you have time to implement it? I

Thanks,
Solène

[erexhepa]

No and I have to apologize because it is actually easily done and I can see it helping you guys out. I will do it today or tomorrow and let you guys know. Apologies again.

[SoleneW]

Thank you very much. It will indeed help me saving a time for further analysis.

[erexhepa]

Hi,

I uploaded the changes with regard to the interface.

I modified the interface and introduced two new text editable fields (at the bottom). One for the file name and the second one for the folder. Both fields are initialised with 1) the folder where the input image is located and the output image constructed as follow <smeprojection.tiff>. However you can this fields by adding text before the "". The "smeprojection.tiff" extention however should be left unchanged because it is replace with "_smeprojectionImage.tiff" and "_smeprojectionIndex.tiff". The first image is the 2D projection and the second one is the index (depth) of the manifold.

The plugin you can find it here :

https://github.com/erexhepa/IJ_PROJECTION_PLUGIN/tree/master/IJ2
(SME_stacking.jar)

I have put also two examples images in the folder above to illustrate the outputs:
Centriole1_smeprojectionImage.tiff
Centriole1_smeprojectionIndex.tiff

I did some test but please let me know if there is something not working.

[SoleneW]

Thank you, I will try it today an give you some feedbacks. 2018-04-21 19:36 GMT+02:00 Elton Rexhepaj <[email protected]>:

…

Hi, I uploaded the changes with regard to the interface changes. I modified the interface and introduced two new text editable fields (at the bottom). One for the file name and the second one for the folder. Both fields are initialised with 1) the folder where the input image is located and the output image constructed as follow <*smeprojection.tiff>. However you can this fields by adding text before the "*". The "smeprojection.tiff" extention however should be left unchanged because it is replace with "_smeprojectionImage.tiff" and "_smeprojectionIndex.tiff". The first image is the 2D projection and the second one is the index (depth) of the manifold. The plugin you can find it here : https://github.com/erexhepa/IJ_PROJECTION_PLUGIN/tree/master/IJ2 (SME_stacking.jar) I have put also two examples images in the folder above to illustrate the outputs: Centriole1_smeprojectionImage.tiff Centriole1_smeprojectionIndex.tiff I did some test but please let me know if there is something not working. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMAx7jzMwiExjNdeNEom5n160PDAq9z3ks5tq24kgaJpZM4QSbDu> .

[SoleneW]

Hi,
I tried to use the plugin with the updated functionality several time but I always end up with the same error which is related to imput/output permission denied. (see below). I tried changing the permission of the folder in which the image is and also the permission of the image but it didn't worked.
Do you have any idea?

Thank you,
Solène

[erexhepa]

Hi,

Sorry, I had forgot to retrieve the paths from the GUI so it was writing to the same folder where the input image is, hence the error as it seems the folder you have only read access.

I have updated the plugin and it should be OK now. Please download it and try again. Just be careful with the / (Linux & Mac) and \ (Windows) (just check the path displayed by default on the GUI to be sure which one you should use).

Elton

[SoleneW]

Thanks, it's working. 2018-04-25 7:33 GMT+02:00 Elton Rexhepaj <[email protected]>:

…

Hi, Sorry, I had forgot to retrieve the paths from the GUI so it was writing to the same folder where the input image is, hence the error as it seems the folder you have only read access. I have updated the plugin and it should be OK now. Please download it and try again. Just be careful with the / (Linux & Mac) and \ (Windows) (just check the path displayed by default on the GUI to be sure which one you should use). Elton — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMAx7tKsm2dvtcYCo-OvDIuOjz3rQDfeks5tsAqpgaJpZM4QSbDu> .