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SynPuCo / SynapseCounter

Synapse Counter plug-in for ImageJ, developed by Egor Dzyubenko and Andrey Rozenberg, is a helpful scientific tool designed for synapse formation studies. It is developed for rapid, automatic, unbiased quantification of synaptic puncta revealed by synaptic marker proteins fluorescence.
GNU General Public License v3.0
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ParticleAnalyzer warning in the Log #5

Open srussek-7 opened 1 year ago

srussek-7 commented 1 year ago

Hi, We are trying to use the counter with hippocampal confocal images in Max Z projections that are rectangular but not square. We keep getting what appears to be an error message in the log "threshold not set; assumed to be 255-255 ("Black background" not set). We assumed that the SynPuCo is doing auto thresholding so do not know why this error appear. Also tried to resize to 1024. Thank you for your time!

Best,

Shelley

Neurogorka commented 1 year ago

Hello Shelley! Sorry for the late reply and to hear you have problems with the counter. Since a few months after several ImageJ updates the 3D counting became problematic. However, there should be problem using the 2D mode on Z projections. Rectangular ROIs shouldn't be a problem. Simpply make sure that you have Process->Binary->Options->Black background tick activated. If you continue having the problems, send me a few files and a request at egor.dzyubenko@rub.de Best regards, Egor

Neurogorka commented 1 year ago

Hello Shelley!Sorry for the late reply and to hear you have problems with the counter. Since a few months after several ImageJ updates the 3D counting became problematic. However, there should be problem using the 2D mode on Z projections. Rectangular ROIs shouldn't be a problem. Simpply make sure that you have Process->Binary->Options->Black background tick activated. If you continue having the problems, send me a few files and a request @. regards,Egor    06.03.2023, 21:59, "srussek-7" @.>: Hi,We are trying to use the counter with hippocampal confocal images in Max Z projections that are rectangular but not square. We keep getting what appears to be an error message in the log "threshold not set; assumed to be 255-255 ("Black background" not set). We assumed that the SynPuCo is doing auto thresholding so do not know why this error appear. Also tried to resize to 1024. Thank you for your time!Best,Shelley—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>