I get an obscure script instead of an image, can you help please?

Dear ImageJ community,

I need to open an “.edf” file with imageJ on my MacOS Sierra Version10.12.6.
I installed in ImageJ the plugins required to open the .edf file.

But when I drag and drop the .edf file in ImageJ I get this (see attached) and I have no clue what to do next to get an image. Is this Java related? Does anyone have an idea what I should do?

Thanks a lot if you can help me, besos

Chloé

@chlochou

I don’t think the drag-and-drop method will work for this type of image file. In general, we don’t recommend users opening image files that way - we usually advise people to open image files via Bio-Formats - that comes with Fiji ( NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. If you are just getting started, we recommend downloading/using Fiji.). However, I don’t believe .edf files are listed in Bio-Format’s supported files list. You could check about submitting this file format: see their Bug Reports Page.

There also appears to be some ImageJ Plugins for opening .edf files here. Let us know if any of this is helpful! If you have more questions… just let us know too!

eta

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Hello Eta,

Thank you for your answer. I tried to open my file with Fiji but it is not successful. I also installed the Plugins for opening .edf files as I mentionned in my first message.

On my mac computer at work it works but not on my personal computer and I need to use my personal computer for this.

Do you have any other idea I should try?

Thanks

Chloé

@chlochou Can you attach the original file so I could give it a try? Perhaps others here on the Forum might respond as well with some insight in the meantime…

eta

1 Like

yes, good idea. I get this error message though “Sorry, new users can not upload attachments.”
:s is there a way to send it to you?

@chlochou

Can you try once again? I just upgraded your user status … so should work now.

eta :slight_smile:

Thanks a lot, here is the file :slight_smile:

0002_cap1_s43382.edf.zip (8.7 MB)

Thanks for posting the image file that opens perfectly when using the plugin “EdfRead_.class” from:
http://www.esrf.eu/UsersAndScience/Experiments/Imaging/ID19/Software/imagej-plugins

Please open your image file from the plugin, i.e. after putting the plugin in the ImageJ plugin folder, restart ImageJ, and go to “Plugins >> EdfRead”. A file dialog opens where you should select your image file.

HTH

Herbie

PS: It appears that the image size is not correctly reported

2 Likes

What @anon96376101 said is correct… just drag/drop that Edf_Read.class file after downloading into your ‘plugins’ folder within your Fiji/ImageJ package. Then restart Fiji/ImageJ - and you’ll see EdfRead in your Plugins dropdown menu - will open it up just fine!

eta :slight_smile:

Here is a downsized version of your image:

Happy processing

Herbie

Thanks a lot for your help and ideas, but I suspect I have an issue with java…(see attached) I don’t know which one

Could you please tell us exactly what you’ve done — step by step — to install the plugin and to open your image?

Curious

Herbie

PS:
I fear you tried to launch the plugin by double-clicking it which is not what I’ve proposed and won’t work.

1 Like

@chlochou

Can you provide some more information?

Are you using Fiji? What version are you using? Where exactly did you place the EdfRead_.class file? Did you restart Fiji/ImageJ?

what is the other way to open it without double-clicking?

As I’ve written:

Please open your image file from the plugin, i.e. after putting the plugin in the ImageJ plugin folder, restart ImageJ, and go to “Plugins >> EdfRead”. A file dialog opens where you should select your image file.

Of course, in ImageJ go to “Plugins >> EdfRead”

HTH

Herbie

it is working!!! thank you for you great help and patience guys!!! :kissing_heart:
so the plugin… I was clicking right on the Fiji icon then I clicked “show package contents” then “plugins” then I dragged and drop the plugins right there. And doing it this way it doesn’t work and made me so crazy I didn’t see the Plugin tab at the top of my screen when the Fiji app was open!!!

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In the old ImageJ version I had to drag and drop the plugins in the folder plugins then Input-Output. That’s why I was doing it the same way with Fiji

Nice to hear that you’ve finally noticed the plugin menu item of imageJ and please
don’t forget to thank the ominpresent gals on this forum !

Regards

Herbie

sorry I am a French speaker, female myself, and I thought “guys” was not gender specific. Thanks for letting me know! Thanks everybody!!!