Tjian - Darzacq lab issueshttps://gitlab.com/groups/tjian-darzacq-lab/-/issues2023-06-15T13:41:11Zhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/178Makefile references invalid resources2023-06-15T13:41:11ZAlex HerbertMakefile references invalid resourcesThe following resources are not available for download:
https://spoton.berkeley.edu/static/SPTGUI/resources/170614_fitted_abParams.bz2
https://spoton.berkeley.edu/static/SPTGUI/resources/170616_demoFiles.tar.bz2
This prevents initialis...The following resources are not available for download:
https://spoton.berkeley.edu/static/SPTGUI/resources/170614_fitted_abParams.bz2
https://spoton.berkeley.edu/static/SPTGUI/resources/170616_demoFiles.tar.bz2
This prevents initialisation of a local copy of Spot-Onhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/152Show warnings in the fitting tab2021-03-31T14:53:19ZRoyal KittenShow warnings in the fitting tabDoes not seem to find the JLD file.Does not seem to find the JLD file.https://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/174Issue with the Trackmate Importer2021-03-31T14:24:31ZRoyal KittenIssue with the Trackmate ImporterThanks for sharing "Spot-On". I played with the demo data-set. It looks like a very powerful tool for the kinetic model fitting of SPT files.
I have a problem arises from uploading tracks from Trackmate to Spot-On. I tried the "Spot-On...Thanks for sharing "Spot-On". I played with the demo data-set. It looks like a very powerful tool for the kinetic model fitting of SPT files.
I have a problem arises from uploading tracks from Trackmate to Spot-On. I tried the "Spot-On trackmate connector" plugin and it said the file cannot be processed (please check the image below).
*
I also tried to import the XML file exported from trackmate and it doesn't work as well. Therefore I compare the XML file from my trackmate and the example XML file from the Spot-On website and found there is a
difference in the beginning of the file. It looks like in newer version of Trackmate (5.0.2) they changed the format of the first row of XML file. I wonder if I change the format of the XML file from newer version of
Trackmate and make it resemble to v3.4.2 would make the process-able in Spot-On? ![Capture2](/uploads/7086217b95f40cf0fef2b5dedd43a5f5/Capture2.JPG)
![Capture](/uploads/e43f9a8d86920bc7f87f97c9d0d06e30/Capture.JPG)Royal KittenRoyal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/175Issue with CSV import2021-03-31T13:09:25ZRoyal KittenIssue with CSV importI was playing with your software SpotOn and had some problems importing my csv file directly generated from TrackMate. The status of the uploaded file is always error and the import report says "cannot convert float NaN to integer". Atta...I was playing with your software SpotOn and had some problems importing my csv file directly generated from TrackMate. The status of the uploaded file is always error and the import report says "cannot convert float NaN to integer". Attached is my csv file. I would really appreciate if you could let me know what is causing this problem. Thanks a lot.Royal KittenRoyal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/176Issue with .mat file import2021-03-31T13:02:38ZRoyal KittenIssue with .mat file importcf. datasets received (privately) from Lisa Streitcf. datasets received (privately) from Lisa Streithttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/157Decide what to do with AIC/BIC/F-test2018-07-18T11:46:44ZRoyal KittenDecide what to do with AIC/BIC/F-testhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/168No error message when the number of gaps is too high2018-02-23T14:09:24ZRoyal KittenNo error message when the number of gaps is too highhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/169Spot-On Matlab link not correct on Spot-On website2018-02-23T12:31:40ZAnders Spot-On Matlab link not correct on Spot-On websiteThe link on https://spoton.berkeley.edu/SPTGUI/docs/latest#code to the Matlab version of Spot-On is not correct since we moved the repo. Here's the correct link: https://gitlab.com/tjian-darzacq-lab/spot-on-matlabThe link on https://spoton.berkeley.edu/SPTGUI/docs/latest#code to the Matlab version of Spot-On is not correct since we moved the repo. Here's the correct link: https://gitlab.com/tjian-darzacq-lab/spot-on-matlabRoyal KittenRoyal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/172Update citation2018-02-23T12:31:40ZAnders Update citationHi Maxime,
Another one: Now that Spot-On is online at eLife, we should update the citation info on the website, on GitLab and in the manuals. I'll try and get this done for the Matlab one in the next couple of days. Here's the citati...Hi Maxime,
Another one: Now that Spot-On is online at eLife, we should update the citation info on the website, on GitLab and in the manuals. I'll try and get this done for the Matlab one in the next couple of days. Here's the citation:
Hansen, A.S., Woringer, M., Grimm, J.B., Lavis, L.D., Tjian, R., and Darzacq, X. (2018). Robust model-based analysis of single-particle tracking experiments with Spot-On. Elife 7, e33125. doi: 10.7554/eLife.33125
(I could not add "*" since Gitlab makes Italics then)Royal KittenAnders Royal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/171display frame-rate in online GUI2018-01-04T19:28:01ZAnders display frame-rate in online GUIHi Maxime,
Very small issue, but I was playing around with a collaborators SPT data and noticed that the experimental frame rate is not display by the Spot-On website (the matched dZ,dT are, but this could be slightly different).
It's ...Hi Maxime,
Very small issue, but I was playing around with a collaborators SPT data and noticed that the experimental frame rate is not display by the Spot-On website (the matched dZ,dT are, but this could be slightly different).
It's a really small thing, but I think displaying the frame rate is nice. One possibility would to do this where it says:
"It seems that your dataset contains at most 0 gap(s), so the algorithm has been set accordingly" and change this to e.g.
"It seems that your dataset contains at most 0 gap(s) **and XX ms between frames**, so the algorithm has been set accordingly"
anyway, just a small thought.https://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/170Default fitting option is currently "PDF", but I strongly suggest we make it ...2017-12-23T17:18:57ZAnders Default fitting option is currently "PDF", but I strongly suggest we make it "CDF"Although on simulations it makes a minor difference, on the example Sox2 dataset it makes a big difference. Since CDF generally works better, I think it would be nice to have this as default on the website.
Thanks!Although on simulations it makes a minor difference, on the example Sox2 dataset it makes a big difference. Since CDF generally works better, I think it would be nice to have this as default on the website.
Thanks!Royal KittenRoyal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/142Missing sections in the documentation2017-10-24T15:22:13ZRoyal KittenMissing sections in the documentation* [x] How to measure the localization error?
* [x] How to measure the detection range?
* [x] How to acquire a "good" dataset?
* [x] What tracking software to use?
* [x] Description of the datasets* [x] How to measure the localization error?
* [x] How to measure the detection range?
* [x] How to acquire a "good" dataset?
* [x] What tracking software to use?
* [x] Description of the datasetshttps://gitlab.com/tjian-darzacq-lab/simSPT/-/issues/1Warnings when compiling using MacOS2017-10-23T02:28:33ZRoyal KittenWarnings when compiling using MacOS```{shell}
gcc -o simSPT simSPT.c geometries.c geometries_sphere.c distributions.c z_profiles.c geometries_cube.c heterogeneous.c -lm
simSPT.c:145:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
simSPT.c:375:1: w...```{shell}
gcc -o simSPT simSPT.c geometries.c geometries_sphere.c distributions.c z_profiles.c geometries_cube.c heterogeneous.c -lm
simSPT.c:145:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
simSPT.c:375:1: warning: return type of 'main' is not 'int' [-Wmain-return-type]
void main(int argc, char *argv[]) {
^
simSPT.c:375:1: note: change return type to 'int'
void main(int argc, char *argv[]) {
^~~~
int
simSPT.c:424:5: warning: implicit declaration of function 'make_heterogeneous_nucleus' is invalid in C99 [-Wimplicit-function-declaration]
make_heterogeneous_nucleus(geometry_init); // We actually run it from here
^
simSPT.c:455:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
if (abs(sumpop-1) > FLT_EPSILON) {
^
simSPT.c:455:7: note: use function 'fabsf' instead
if (abs(sumpop-1) > FLT_EPSILON) {
^~~
fabsf
4 warnings generated.
geometries.c:41:1: warning: control may reach end of non-void function [-Wreturn-type]
};
^
1 warning generated.
heterogeneous.c:343:19: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
printf("%d, %d", chksum, 2*3*5*7*11*13*17*19*23);
~~ ^~~~~~
%ld
heterogeneous.c:500:5: warning: implicit declaration of function 'close' is invalid in C99 [-Wimplicit-function-declaration]
close(fout);
^
heterogeneous.c:505:1: warning: control may reach end of non-void function [-Wreturn-type]
}
```https://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/1Implement `alphamethod=1`2017-08-30T03:25:41ZRoyal KittenImplement `alphamethod=1`https://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/2`reconerror` is not properly computed2017-08-30T03:25:41ZRoyal Kitten`reconerror` is not properly computedhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/3Create a demo notebook2017-08-30T03:25:41ZRoyal KittenCreate a demo notebookhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/4`demo==2` and `demo==3` are not implemented2017-08-30T03:25:41ZRoyal Kitten`demo==2` and `demo==3` are not implementedhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/5*TV* (total variation)-based objective function is not available2017-08-30T03:25:41ZRoyal Kitten*TV* (total variation)-based objective function is not available- The function `tlv` is not implemented
- The function `denoise_bound` is not implemented
- Input is not properly checked when selecting the 'tv' penalty- The function `tlv` is not implemented
- The function `denoise_bound` is not implemented
- Input is not properly checked when selecting the 'tv' penaltyhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/6The code should run on Python32017-08-30T03:25:41ZRoyal KittenThe code should run on Python3I suggest starting a Travis continuous integration systemI suggest starting a Travis continuous integration systemhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/7`finit` do not work2017-08-30T03:25:41ZRoyal Kitten`finit` do not workSetting up a `finit` does not work, at least in my tests.Setting up a `finit` does not work, at least in my tests.