Merging channels and not getting the first image I want to get the DAPI from

[andreevg04]

Dear Chandler,

I love VALIS. I wrote some extra code to generate multiplexed images.
registrar = registration.Valis(str(d), dst_dir, feature_detector_cls=OrbVggFD_low_fd, imgs_ordered=True)

In the docs its said that the channel to get the DAPI from will be the first ordered (Merge channels based on the position of each slide in the stack. This will be the same as the original order when imgs_ordered=True)
I do want my DAPI to be from the first image. I tried also with getting the image as reference but I always got the message that no series were selected and therefore the largest image will be selected. And for some reason it was not the first I wanted.

What I ended up doing is in the merging line to include drop_duplicates=False but that just made the image 2x larger which I dont actually need.

Also may I write you an email with a small request/proposal if you of course would give me the honor writing you and asking you?

Best regards

[andreevg04]

I processed them in batch and only the first image got the correct order. The others didnt and the code crashed after processing two images. On the third one after rigid registration was performed it crashed (JVM was killed)

[cdgatenbee]

Hi @andreevg04,
So happy to hear you're finding valis useful, but sorry you're running into these issues. I think I have figured out why the slides may not be in the same order when merging, and the fix will is in the next update. I can let you know when it is available, which I hope will be relatively soon. Regarding the other issues, if you could share the error messages I may be able to help figure out the reasons behind the crash.

Best,
-Chandler

[andreevg04]

I didnt get any error message. It was just killed.
Would love to get the new update. May I send you some images/question per Email?

[cdgatenbee]

Sure, I'd be happy to discuss over e-mail :) You can send images/questions to Chandler[dot]Gatenbee[at]moffitt[dot]org

Best,
-Chandler

[cdgatenbee]

Hi @andreevg04,

I just pushed the latest version of valis (1.1.0), which should have fixed the issue the images not being in the expected order. Please try it out and let me know if it resolves that particular issue for you.

Best,
-Chandler

[andreevg04]

Hi Chandler, thank you for letting me know!
I am not very familiar how to upload this version and also I have still the problem with the killing of the script because the images are still loaded in memory. I can give you 3 examples per email for you to check if you are willing to. If not I must do them single handed manually.

Looking forward to your answer
Best wishes

[cdgatenbee]

Hi @andreevg04,
Apologies for the delayed response. I'd be happy to take a look at your example images if you want to share them with me over e-mail (Chandler[dot]Gatenbee[at]moffitt[dot]org). If they are large, it may be possible to upload them to something like Dropbox, Google Drive, Onedrive, etc..., and then share the link with me using my e-mail address. WeTransfer used to be a good option, but unfortunately our institution has blocked it.

Best,
-Chandler