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MontpellierRessourcesImagerie / imagej_macros_and_scripts

ImageJ macros and scripts written at the imaging facility MRI
MIT License
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Inquiring about Intensity Ratio Nuclei Cytoplasm Tool - selection error #4

Closed hschoi-up closed 3 years ago

hschoi-up commented 3 years ago

Hi. thank you for developing this tool. I'm trying to use this tool in ImageJ. But I got a message - selection area required. and the nucleus area wasn't selected. Could you please help me out to solve this problem? Thank you in advance.

volker-baecker commented 3 years ago

Hi @hschoi-up, can you make a pair of images (nuclei and cytoplasm) available, so that I can try to reproduce the problem? Thank you.

hschoi-up commented 3 years ago

Hi Volker,

Test images that I've tried are attached. ch00 is DAPI. ch02 is Alexa488 signals. Thank you in advance.

volker-baecker commented 3 years ago

Hi @hschoi-up, technically it seems to work if you put in ch00 and ch02 for the channels (right click on the s-button), select the remove scale checkbox (there is a spatial calibration in inch on the images) and enter a small min. size in pixel (for example 5). However I don't think you can use the tool for these images. ch00 should be the nuclei, right? The tool expects to that wherever there is a signal for the nuclei there is a signal for the cytoplasm. This is not the case in these images.

hschoi-up commented 3 years ago

Ah! Thank you!!!