Dependency retistructgui can't be installed

[EPMalkemper]

I always get the following error. Could it be that the retistructgui does not exist anymore but is included in retistruct?

ERROR: dependency 'retistructgui' is not available for package 'retina'

removing 'C:/Users/Pascal/Documents/R/win-library/3.3/retina'

[briancohn]

Thanks for posting the issue! give this a try and let me know if you still get the same complaint from R:

install.packages(c("retistructgui"), type='source')

[EPMalkemper]

Thanks for your response. I tried and got the following error:

Warning in install.packages : package ‘retistructgui’ is not available (for R version 3.3.1)

[EPMalkemper]

Are you working on the issue? I would really like to use the retina package soon. Thanks a lot!

[lschmitz]

Looking into it --- hope to have a solution soon!!

On Mon, Jul 25, 2016 at 11:15 PM, EPMalkemper notifications@github.com wrote:

Are you working on the issue? I would really like to use the retina package soon. Thanks a lot!

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Lars Schmitz, PhD Assistant Professor of Biology W.M. Keck Science Department Claremont McKenna, Pitzer, and Scripps Colleges schmitzlab.info

[briancohn]

Just ping'ed David Sterratt (author of retistruct) https://github.com/davidcsterratt/retistruct/issues/9

You can also try installing his newest version

install.packages('devtools')
devtools:install_github('davidcsterratt/retistruct')

[EPMalkemper]

Dear Brian,

thanks a lot – I am pretty sure the package is running now. However, could you elaborate a bit more on how the files need to look like when having samples with non-regular counts? Is it just a file with x,y,z with x,y being the coordinates and z being the counts in cells per mm²?

Best, Pascal

---

Dr. E. Pascal Malkemper

Keays Group Institute of Molecular Pathology (IMP) Dr Bohr-Gasse 7

Vienna, 1030, Austria

University of Duisburg-Essen Department of General Zoology Universitätsstr. 5 45141 Essen Germany

Room S05 R04 H88 Phone: 0201 183-4310 Fax: - 3768 Web: https://www.uni-due.de/zoologie/malkemper.php

Von: Brian Cohn [mailto:notifications@github.com] Gesendet: 01 August 2016 15:40 An: lschmitz/retina Cc: Malkemper, Pascal, Dr.; Author Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

Just ping'ed David Sterratt (author of retistruct) davidcsterratt/retistruct#9https://github.com/davidcsterratt/retistruct/issues/9

You can also try installing his newest version

install.packages('devtools')

devtools:install_github('davidcsterratt/retistruct')

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[briancohn]

When you say non-regular, do you mean, sampled in another way than a non-uniform grid?

[EPMalkemper]

Yes - that's exactly what I meant.

Von unterwegs gesendet, daher sicherlich nicht frei von Fehlern.

-------- Ursprüngliche Nachricht -------- Von: Brian Cohn notifications@github.com Datum: 08.08.2016 22:24 (GMT+01:00) An: lschmitz/retina retina@noreply.github.com Cc: "Malkemper, Pascal, Dr." pascal.malkemper@uni-due.de, Author author@noreply.github.com Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

When you say non-regular, do you mean, sampled in another way than a non-uniform grid?

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[briancohn]

Ohh, the model we used in the paper to smooth the data is specifically tailored for stereologic sampling with a uniform grid; this is typically done because this method supports estimation of the cell population. @lschmitz what do you recommend for EPMalkemper?

[EPMalkemper]

In the tutorial you write: Note: If cell counts were collected on the basis of a non-uniform sampling grid, it is still possible to use retina, even though it takes some more effort from the user. Instead of supplying the min and max values of the sampled location, it is necessary to determine the (x, y) pixel location of every single sampling site manually. You can retrieve these location in ImageJ and save the coordinates in *.csv format."

I am just not sure how exactly this file needs to look like.

Thanks

---

Dr. E. Pascal Malkemper

Keays Group Institute of Molecular Pathology (IMP) Dr Bohr-Gasse 7

Vienna, 1030, Austria

University of Duisburg-Essen Department of General Zoology Universitätsstr. 5 45141 Essen Germany

Room S05 R04 H88 Phone: 0201 183-4310 Fax: - 3768 Web: https://www.uni-due.de/zoologie/malkemper.php

Von: Brian Cohn [mailto:notifications@github.com] Gesendet: 09 August 2016 17:26 An: lschmitz/retina Cc: Malkemper, Pascal, Dr.; Author Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

Ohh, the model we used in the paper to smooth the data is specifically tailored for stereologic sampling with a uniform grid; this is typically done because this method supports estimation of the cell population. @lschmitzhttps://github.com/lschmitz what do you recommend for EPMalkemper?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/lschmitz/retina/issues/1#issuecomment-238589669, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ATlJQly-xx2uGmSbOKHGpgqcZDc1h8Y7ks5qeJwagaJpZM4JR93L.

[lschmitz]

Hi Pascal, You will end up with a 3-column spreadsheet (x, y, z), where (x, y) are the coordinates of your sampling locations that you need to extract from ImageJ. Z contains the counts for each sampling location. We will also need to modify the retina_object() function as it currently expects a uniform grid. As for the potential smoothing issue that Brain mentioned, how dispersed are your sampling locations? Do they cover most of the retina and are fairly well-dispesed? Thanks! Lars

On Tue, Aug 9, 2016 at 11:26 AM, EPMalkemper notifications@github.com wrote:

In the tutorial you write: Note: If cell counts were collected on the basis of a non-uniform sampling grid, it is still possible to use retina, even though it takes some more effort from the user. Instead of supplying the min and max values of the sampled location, it is necessary to determine the (x, y) pixel location of every single sampling site manually. You can retrieve these location in ImageJ and save the coordinates in *.csv format."

I am just not sure how exactly this file needs to look like.

Thanks

---

Dr. E. Pascal Malkemper

Keays Group Institute of Molecular Pathology (IMP) Dr Bohr-Gasse 7

Vienna, 1030, Austria

University of Duisburg-Essen Department of General Zoology Universitätsstr. 5 45141 Essen Germany

Room S05 R04 H88 Phone: 0201 183-4310 Fax: - 3768 Web: https://www.uni-due.de/zoologie/malkemper.php

Von: Brian Cohn [mailto:notifications@github.com] Gesendet: 09 August 2016 17:26 An: lschmitz/retina Cc: Malkemper, Pascal, Dr.; Author Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

Ohh, the model we used in the paper to smooth the data is specifically tailored for stereologic sampling with a uniform grid; this is typically done because this method supports estimation of the cell population. @lschmitzhttps://github.com/lschmitz what do you recommend for EPMalkemper?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ lschmitz/retina/issues/1#issuecomment-238589669, or mute the thread< https://github.com/notifications/unsubscribe-auth/ATlJQly- xx2uGmSbOKHGpgqcZDc1h8Y7ks5qeJwagaJpZM4JR93L>.

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Lars Schmitz, PhD Assistant Professor of Biology W.M. Keck Science Department Claremont McKenna, Pitzer, and Scripps Colleges schmitzlab.info

[EPMalkemper]

Hi Lars,

the sampling is fairly regular and dispersed but regions of higher ganglion cell density are sampled with a finer and more irregular grid. I’ve attached an example map to give you a better impression.

It would be so great if that would work.

Best, Pascal

Von: Lars Schmitz [mailto:notifications@github.com] Gesendet: 09 August 2016 21:41 An: lschmitz/retina Cc: Malkemper, Pascal, Dr.; Author Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

Hi Pascal, You will end up with a 3-column spreadsheet (x, y, z), where (x, y) are the coordinates of your sampling locations that you need to extract from ImageJ. Z contains the counts for each sampling location. We will also need to modify the retina_object() function as it currently expects a uniform grid. As for the potential smoothing issue that Brain mentioned, how dispersed are your sampling locations? Do they cover most of the retina and are fairly well-dispesed? Thanks! Lars

On Tue, Aug 9, 2016 at 11:26 AM, EPMalkemper notifications@github.com<mailto:notifications@github.com> wrote:

In the tutorial you write: Note: If cell counts were collected on the basis of a non-uniform sampling grid, it is still possible to use retina, even though it takes some more effort from the user. Instead of supplying the min and max values of the sampled location, it is necessary to determine the (x, y) pixel location of every single sampling site manually. You can retrieve these location in ImageJ and save the coordinates in *.csv format."

I am just not sure how exactly this file needs to look like.

Thanks

---

Dr. E. Pascal Malkemper

Keays Group Institute of Molecular Pathology (IMP) Dr Bohr-Gasse 7

Vienna, 1030, Austria

University of Duisburg-Essen Department of General Zoology Universitätsstr. 5 45141 Essen Germany

Room S05 R04 H88 Phone: 0201 183-4310 Fax: - 3768 Web: https://www.uni-due.de/zoologie/malkemper.php

Von: Brian Cohn [mailto:notifications@github.com] Gesendet: 09 August 2016 17:26 An: lschmitz/retina Cc: Malkemper, Pascal, Dr.; Author Betreff: Re: [lschmitz/retina] Dependency retistructgui can't be installed (#1)

Ohh, the model we used in the paper to smooth the data is specifically tailored for stereologic sampling with a uniform grid; this is typically done because this method supports estimation of the cell population. @lschmitzhttps://github.com/lschmitz what do you recommend for EPMalkemper?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ <https://github.com/%0b> lschmitz/retina/issues/1#issuecomment-238589669>, or mute the thread< https://github.com/notifications/unsubscribe-auth/ATlJQly- xx2uGmSbOKHGpgqcZDc1h8Y7ks5qeJwagaJpZM4JR93L>.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lschmitz/retina/issues/1#issuecomment-238645537, or mute the thread https://github.com/notifications/unsubscribe-auth/AEbZu5qv-s6E0yGcFB-iXTb6yx1cGri5ks5qeMZxgaJpZM4JR93L .

Lars Schmitz, PhD Assistant Professor of Biology W.M. Keck Science Department Claremont McKenna, Pitzer, and Scripps Colleges schmitzlab.info

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