FIJI (ImageJ): Automating Analysis with Macros (II. Batch Analysis of Images in a Folder)

[@alineroberta6545]

You are not a human, you are an ANGEL! Thanks so much, u saved my sanity this month

[@SoleneVacher]

Thank you so much ! You made me understand 6 hours of class in 2 videos !

[@johanna.m.dela-cruz]

Glad this helped, @SoleneVacher. Thanks for watching.

[@cristianrod7341]

THIS HELPED ME SO MUCH I HAVE 1200 IMAGES TO DO AND WITHOUT THISNI WOULDVE HAD TO DO IT ALL MANUALLY

[@jhanirawittingchavarria151]

The best videos about image j, thanks so much for sharing!

[@johanna.m.dela-cruz]

Thanks so much, Jhanira. I’m happy to help.

[@taystevens6009]

You are a true hero, may you live a blessed and fruitful life!!

[@johanna.m.dela-cruz]

Thank you so much, Tay (@taystevens6009).

[@_catonwner9204]

very good illustration on how batch process work!

[@johanna.m.dela-cruz]

Thanks for the nice comment.

[@gingerpietka8426]

Super helpful video. I am having a problem with an ROI that I use for every image. When I record, I click on the Roi name in the manager, then the roi appears on my image. When I run the macro it inserts a rectangle instead of the roi. I'm very new at this and dont know what I'm doing wrong.

[@johanna.m.dela-cruz]

Hi @gingerpietka8426. Thanks for watching. I'm curious...how do you create your ROIs.

[@gingerpietka8426]

Hi ​@@johanna.m.dela-cruz. Yeah I've watched a few. I have to slow them down so I can catch everything but they really help me so far. I use 'make band' to make the ROI. it worked the first time i tried it but not since. I see you put the setup in your macro and close everything between images so I will try that next. If I want to have a wait, is it 'waitForUser'?

[@johanna.m.dela-cruz]

@@gingerpietka8426 It must be something with your script. The ROI with a band works for me. Yes, waitForUser can be used if you want to do something yorself before the macro runs completely.

[@gingerpietka8426]

@@johanna.m.dela-cruz Okay thanks so much for all your help and videos!

[@antoniogarciajimenez2533]

I am getting the pop up window that my list of results is empty? Does anyone know how to solve this?

[@johanna.m.dela-cruz]

Hi Antonio. Have you tried running the macro a few lines at a time to check if it is doing what you want it to do? Perhaps your script 'Clears' your results table before saving it?

[@kevinn1534]

I have a problem with my saving of plot data, it is not saving my csv z axis profile, only if I run the code several times I can see half or less of the overall data

[@kevinn1534]

and adding "wait" steps doesn't work

[@johanna.m.dela-cruz]

@kevinn1534 Perhaps there’s something missing in your code.

[@kevinn1534]

@@johanna.m.dela-cruz thanks for your reply... can I show it to you? I don't think is missing something, I literally use the macro recorder and I verify it.

[@johanna.m.dela-cruz]

@kevinn1534 you can email me. I’m not an expert in macros, but I can take a look at it.

[@kevinn1534]

@johanna.m.dela-cruz thanks a lot 🙏 Can you share me your email pls

[@johanna.m.dela-cruz]

@microscopyra6961 I saw a notification about your comment, but somehow, can't find it here. Thank you for suggesting and introducing me to Github Gist. I'll look into it.

[@dangothilf1171]

thanks for the many videos! I'm now trying to do it but with constructing 3D model (avi videao). sadly i dont manage to make a macro which saves the models into a folder, only results and so. is there a solution?

[@johanna.m.dela-cruz]

@dangothilf1171 Have you tried using the macro recorder first while saving the reconstructed image?

[@dangothilf1171]

@@johanna.m.dela-cruz ​ thanks for the quick answer! yes. but the recorder than records the path and name, does not work with input and output folder, and saves all results by the same name

[@johanna.m.dela-cruz]

@@dangothilf1171 What exactly do you want to automate? Do you just want to create a 3D reconstruction from images in a folder? Are they single slices?

[@dangothilf1171]

@@johanna.m.dela-cruz create a 3D reconstructions from LSM files with varying amount of slices (images from confocal microscopy if it matters) in a folder, naming them after the original file and placing them in a folder of choice

[@johanna.m.dela-cruz]

@@dangothilf1171 So you have image stacks in a folder? Perhaps you could send me an email and we could discuss your needs further.

[@mritunjayhiremath7942]

Good tutorial and helpful on time.

[@johanna.m.dela-cruz]

Thanks 😊.

[@mritunjayhiremath7942]

@@johanna.m.dela-cruz However, I am getting an error like "The list is empty" after processing only two images out of 30 images. What could be the problem in the code?

[@johanna.m.dela-cruz]

@@mritunjayhiremath7942 Hard to say, but perhaps, check how the path (directory) is written.

[@marinataylor836]

Hi! Thanks for the video, it is super clear and helpful! Nevertheless, I don't know why I am having some trouble to loop the analysis macros. I think I don"t have the function list.lenght Is it possible I have another function instead? This is the following error I get: Error: Array or string expected in line 18: for ( i = 0 ; i < list . ; i ++ ) { when I change list.lenght for 10 I get another error in the following command: Error: Empty array in line 19: open ( input , list [ i ) ; Do you know how can I make it work? Many thanks in advance!

[@johanna.m.dela-cruz]

Hi Marina. I think you misspelled length.

[@marinataylor836]

@@johanna.m.dela-cruz Oh god, true. Sorry for that. Now it is perfectly running, but I have another question if you don't mind helping me... When I run the macros separately for every picture, the cuantification is okay. Then, when I run the autimatization of that macros in the whole folder of images, I only get 5 results per image. Do you have any idea why would this be? Thanks in advance!

[@johanna.m.dela-cruz]

@Marina Taylor. Does the threshold you use work on all your images? Are you counting particles in your images? Perhaps there is a small error in your code? If you like, you can email me your code and a copy of one of your images, so I can troubleshoot.

[@marinataylor836]

@@johanna.m.dela-cruz many thanks! I sent you an email.

[@greyge4799]

Thanks !!!

[@johanna.m.dela-cruz]

My pleasure.

[@melaniep.117]

Good tutorial. It might be helpful if you posted the code too.

[@melaniep.117]

Unless you did and I missed it somehow

[@johanna.m.dela-cruz]

@@melaniep.117 Hi there. Thanks for watching. I tried copy-pasting my code but there are certain restrictions regarding the characters that can be used in KZbin. I can email you the code I used if you would like to have it.