A first look at ChatGPT. Is it a game changer for Image Analysis? Can it write an ImageJ Macro? If you cant get on to ChatGPT right now (cos its too busy) then this video might help.
The issue is that the macro includes placeholder text to load an image, you would want to replace "path/to/image.tif" with your image path and then it will work (need to also replace save path if you want it to save to local directory). Alternatively if you just delete/comment out that line it will work on an open image.
I agree that is the exact issue with GPT written macro. Craig needs to ask GPT for a macro on an already open image or have to comment out opening and saving commands. Otherwise, it will do what is expected. Or he needs to adapt file paths as you suggest. As GPT noted, it is an example macro code that needs some adaptations.
hello. I have a question.would you please help me?I want to count the number of grafts inside the plates with the Fiji (filament detector). how can i do that(can i have your email address i want to send photos of analysis)
Hey Craig, I have been using chatgpt to enhance marco functionality instead of writing it from scratch and that is where I think it shines. For example I would record my work flow in Fiji with the macro recorder. Then I would give the code to ChatGPT and tell it I want to do this analysis in all files of a single folder. That works like magic
Hello sir, I have a question. I have a macro(that gives me the output of an.csv excel sheet with columns of 1)number of cells 2)Total transcripts 3) Cytoplasm only transcripts and their fraction) upon using DAPI IMAGE AND CALCOFLOR IMAGE. My questionis how to modify my macro to get “transcripts only in nucleus”. Or can I use GUI to do that in imageJ? Please reply.
Hi, sorry for the delay. This one is too difficult to answer without seeing the image. Send me an example if you want. I'm easy to find - but prefer not to leave an email address here for the spam-bots.
Yes, disappointing. The workaround might be to get Python code from ChatGPT and use PyImageJ (which I haven't tried yet - but should probably investigate).
Hi, have you tried using the 'colour threshold' option? You image needs to be in RGB format to work. You could use the colour threshold to identify your region of interest and make a mask. Then use that mask to extract the intensity information from the R, G & B channels (if you 'split'' the image).
@@CraigDaly Yeah. After doing some research i figured that after masking, from set measurement i need to select area fraction and this will give me painted area to region of interest ratio. Then i need to compare slides based on this value. i think the hard part will be calibrating slides' brightness. Cause mostly dyed pixel's brightness will differ from slide to slide. I need to work one by one on those RGB values. Thank you for your answer. Your videos are so educative and inspiring.
The issue is that the macro includes placeholder text to load an image, you would want to replace "path/to/image.tif" with your image path and then it will work (need to also replace save path if you want it to save to local directory).
Alternatively if you just delete/comment out that line it will work on an open image.
I agree that is the exact issue with GPT written macro. Craig needs to ask GPT for a macro on an already open image or have to comment out opening and saving commands. Otherwise, it will do what is expected. Or he needs to adapt file paths as you suggest. As GPT noted, it is an example macro code that needs some adaptations.
hello. I have a question.would you please help me?I want to count the number of grafts inside the plates with the Fiji (filament detector). how can i do that(can i have your email address i want to send photos of analysis)
Hi I'm from Argentina. Thank for your videos are very good they help me
Hey Craig,
I have been using chatgpt to enhance marco functionality instead of writing it from scratch and that is where I think it shines.
For example I would record my work flow in Fiji with the macro recorder. Then I would give the code to ChatGPT and tell it I want to do this analysis in all files of a single folder.
That works like magic
That’s a great idea. Thanks for sharing. Cheers. C
ChatGPT is a great tool for napari too
Nice video~~ it seems promising but I need to refresh my python skills. Thanks for your suggestions 😊 waiting for next video
Hello sir, I have a question.
I have a macro(that gives me the output of an.csv excel sheet with columns of 1)number of cells 2)Total transcripts 3) Cytoplasm only transcripts and their fraction) upon using DAPI IMAGE AND CALCOFLOR IMAGE.
My questionis how to modify my macro to get “transcripts only in nucleus”. Or can I use GUI to do that in imageJ?
Please reply.
Hi, sorry for the delay. This one is too difficult to answer without seeing the image. Send me an example if you want. I'm easy to find - but prefer not to leave an email address here for the spam-bots.
One of the first question I asked on chatgpt was can you write imagej script. Seemed really promising!
Yes, disappointing. The workaround might be to get Python code from ChatGPT and use PyImageJ (which I haven't tried yet - but should probably investigate).
Could you please show how to measure color intensity for the immunohistochemistry slides?
Hi, have you tried using the 'colour threshold' option? You image needs to be in RGB format to work. You could use the colour threshold to identify your region of interest and make a mask. Then use that mask to extract the intensity information from the R, G & B channels (if you 'split'' the image).
@@CraigDaly Yeah. After doing some research i figured that after masking, from set measurement i need to select area fraction and this will give me painted area to region of interest ratio. Then i need to compare slides based on this value. i think the hard part will be calibrating slides' brightness. Cause mostly dyed pixel's brightness will differ from slide to slide. I need to work one by one on those RGB values. Thank you for your answer. Your videos are so educative and inspiring.