Fluorescence intensity in vesicle and cortex of the cell.
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Fluorescence intensity in vesicle and cortex of the cell.
 
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Dear ImageJ community,
I am having trouble analyzing the fluorescence intensity of a FRET biosensor in the cortex of the cell (please, see attached image one as an example). I do not know how to extract only the cortical part of the cell with FIJI, similar to the fig S3 of this paper http://www.nature.com/article-assets/npg/srep/2015/151005/srep14693/extref/srep14693-s1.pdf ( they did this using Matlab, but since I do not know how to use it, I wonder if it is possible to do this with FIJI). There is some process with segmentation using threshold, but I could not do it. Furthermore, I would like to measure the intensity of fluorescence in some vesicles structures ( please, see arrows on image 2) and I am trying to figure it out what is the best method with FIJI to do it. I will appreciate any suggestion or tips with these problems, Thanks in advance, Pablo Munoz -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
image 1.jpg (40K)
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Dear Till,
I tried to install this plugin but my Fiji has no protocol db.xml.gz. Best wishes, Patrizia -----Messaggio originale----- Da: ImageJ Interest Group [mailto:[hidden email]] Per conto di Till Bretschneider Inviato: martedì 17 gennaio 2017 11:22 A: [hidden email] Oggetto: Re: Fluorescence intensity in vesicle and cortex of the cell. Dear Pablo, for quantifying the cortical intensity you might want to try our QuimP software. The latest version is available here: http://www2.warwick.ac.uk/fac/sci/dcs/people/till_bretschneider/quimp/ It is a major revision so please let us know if you encounter any problems. I will announce it more widely on the ImageJ user list once we have enough feedback from users of the new version. The new version includes a random segmentation method which is semi supervised. It might help with segmenting the vesicles. Best wishes, Till -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html La presente comunicazione, che potrebbe contenere informazioni riservate e/o protette da segreto professionale, è indirizzata esclusivamente ai destinatari della medesima qui indicati. Ogni informazione qui contenuta, che non sia relativa alla nostra attività caratteristica, deve essere considerata come non inviata. Nel caso in cui abbiate ricevuto per errore la presente comunicazione, vogliate cortesemente darcene immediata notizia, rispondendo a questo stesso indirizzo di e-mail, e poi procedere alla cancellazione di questo messaggio dal Vostro sistema. E' strettamente proibito e potrebbe essere fonte di violazione di legge qualsiasi uso, comunicazione, copia o diffusione dei contenuti di questa comunicazione da parte di chi la abbia ricevuta per errore o in violazione degli scopi della presente. Ricordiamo che la tecnologia di trasmissione utilizzata non consente di garantire l’autenticità del mittente né l’integrità dei dati This communication, which may contain confidential and/or legally privileged information, is intended solely for the use of the intended addressees. All information or advice contained in this communication is subject to the terms and conditions provided by the agreement governing each particular client engagement. If you have received this communication in error, please notify us immediately by responding to this email; then please delete it from your system. Any use, disclosure, copying or distribution of the contents of this communication by a not-intended recipient or in violation of the purposes of this communication is strictly prohibited and may be unlawful. The transmission technology used to send this mail can grant neither the sender identity nor the data integrity -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Fluorescence intensity in vesicle and cortex of the cell.
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Hi Patrizia,
> I tried to install this plugin but my Fiji has no protocol db.xml.gz. As stated on the QuimP installation page [1], your "Manage update sites" screen should have an entry like this: Regards, Curtis [1] http://www2.warwick.ac.uk/fac/sci/dcs/people/till_bretschneider/quimp/wiki-pages/installation/ P.S. to Till: Cool software. I encourage you to create some content on the ImageJ wiki about it (e.g. https://imagej.net/QuimP) and add your update site to the official list of update sites. It would alleviate problems like this, and make your software accessible. See also http://imagej.net/Distribution -- Curtis Rueden LOCI software architect - http://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Tue, Jan 17, 2017 at 7:35 AM, Casalini Patrizia < [hidden email]> wrote: > Dear Till, > > I tried to install this plugin but my Fiji has no protocol db.xml.gz. > > Best wishes, > > Patrizia > > -----Messaggio originale----- > Da: ImageJ Interest Group [mailto:[hidden email]] Per conto di Till > Bretschneider > Inviato: martedì 17 gennaio 2017 11:22 > A: [hidden email] > Oggetto: Re: Fluorescence intensity in vesicle and cortex of the cell. > > Dear Pablo, > > for quantifying the cortical intensity you might want to try our QuimP > software. > The latest version is available here: > http://www2.warwick.ac.uk/fac/sci/dcs/people/till_bretschneider/quimp/ > > It is a major revision so please let us know if you encounter any problems. > I will announce it more widely on the ImageJ user list once we have enough > feedback from users of the new version. > > The new version includes a random segmentation method which is semi > supervised. It might help with segmenting the vesicles. > > Best wishes, > > Till > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > La presente comunicazione, che potrebbe contenere informazioni riservate > e/o protette da segreto professionale, è indirizzata esclusivamente ai > destinatari della medesima qui indicati. Ogni informazione qui contenuta, > che non sia relativa alla nostra attività caratteristica, deve essere > considerata come non inviata. Nel caso in cui abbiate ricevuto per errore > la presente comunicazione, vogliate cortesemente darcene immediata notizia, > rispondendo a questo stesso indirizzo di e-mail, e poi procedere alla > cancellazione di questo messaggio dal Vostro sistema. E' strettamente > proibito e potrebbe essere fonte di violazione di legge qualsiasi uso, > comunicazione, copia o diffusione dei contenuti di questa comunicazione da > parte di chi la abbia ricevuta per errore o in violazione degli scopi della > presente. Ricordiamo che la tecnologia di trasmissione utilizzata non > consente di garantire l’autenticità del mittente né l’integrità dei dati > > This communication, which may contain confidential and/or legally > privileged information, is intended solely for the use of the intended > addressees. All information or advice contained in this communication is > subject to the terms and conditions provided by the agreement governing > each particular client engagement. If you have received this communication > in error, please notify us immediately by responding to this email; then > please delete it from your system. Any use, disclosure, copying or > distribution of the contents of this communication by a not-intended > recipient or in violation of the purposes of this communication is strictly > prohibited and may be unlawful. The transmission technology used to send > this mail can grant neither the sender identity nor the data integrity > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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