Stephane Dallongeville November 19, 2020 at 12:06 pm
We are migrating forum so now it’s better to ask your question to the community Image.sc forum
Still to quikcly reply you here: incoming Icy 2.1 will fix the launching issue on Catalina but about the 3D VTK view, i think it’s somehow related to this issue. Unfortunately right now it seems that the 3D rendering with OSX Catalina doesn’t work correctly, we are currently investigating the problem (may be related to some incompatiblities with the used openGL library to build up VTK) but it may take sometime to fix it (we will probably need to upgrade to a new VTK version).
– StephaneStephane Dallongeville June 26, 2020 at 12:45 pm
We are now using the image.sc forum so it’s better to post on it now.
I’m replying here as you weren’t aware probably, about your issue, latest versions of Active Contours should manage that better (but not yet perfectly, it can still go outbound sometime). Did you check that you’re actually using the last version of the plugin ? Also i saw you’re using contour inflation parameter with a high value, maybe reducing it will help avoiding that problem.
– StephaneStephane Dallongeville May 12, 2020 at 11:05 am
Unfortunately that is a limitation of the Spot Detector plugin, it’s not really designed to detect spots with important difference in size.
But you can use the protocol to adapt this and make several spot detection and combine the results. You can see an example with the protocol “Spot Detector scale 2 and scale 3” which is available online. Just type its name in the top search bar of Icy, you should be able to access it 🙂
Hope that helps !
– StephaneStephane Dallongeville May 11, 2020 at 5:09 pm
Channel information from ROI are somehow independent from your image. Usually when you use a plugin which generate ROIs, it sets the channel information of the ROI on the channel where the detection /segmentation was made. Sometime it doesn’t, it just set the ROI channel information to -1 (means all channel) in which was you can’t filter on mean intensity descriptor as it requires to know on which channel you compute the mean intensity.
To fix that, you can insert the “set ROI Position C” block (position C means Channel here) before applying filtering so you set it on channel where you want to compute the means intensity (for instance channel 0).
Hope you understand my explanations !
Image cOh yehStephane Dallongeville May 5, 2020 at 12:38 pm
Perimeter and Area are the same information than Contour and Interior but the laters are expressed in pixel while the firsts are given in real units computed from the pixel size information (that you can edit if not properly set) from your image.
It’s possible to observe a small difference between these measures Contour and Interior while really be computed on a binary mask (made from the ROI) while Perimeter and Area will try to use the original ROI geometry if possible.
– StephaneStephane Dallongeville May 4, 2020 at 5:27 pm
I think you can use the sequence file batch block then you can try to build the ROI file name from the image file name (using getFilename and appendFilePath blocks) and if the file doesn’t not exist, the resulting ROIs from Import ROI from ImageJ block will be empty so that is not a problem in your workflow 🙂
– StephaneStephane Dallongeville April 21, 2020 at 6:41 pm
Regarding the download problem you experienced on your laptop, can you copy the content of the received html file here ? It can help in understanding what happened, thanks.
About the plugins installation now, are you using a proxy on your Laptop ? If yes you can go into Icy Preferences and change the network setting so it’s correctly using the proxy. If you’re not using a proxy then i guess there is some kind of limitation to your connection which may also explain why the initial Icy download failed. Maybe you also have an (aggressive) antivirus installed ?
– StephaneStephane Dallongeville April 21, 2020 at 3:43 pm
When you click on the download button you should arrive on the download page looking like this :
Is it your case ? If yes, then just clicking on Download for XXX should give you the zip file (256 MB).
I just tested and it appears to work correctly for the 3 versions (Windows, OSX and Linux). If it doesn’t work for you, please can you give us more information about the browser / system you’re using.
– StephaneStephane Dallongeville April 20, 2020 at 4:51 pm
Glad to hear that 🙂 Thanks for confirming it’s now working as expected !
– StephaneStephane Dallongeville April 20, 2020 at 2:53 pm
As i mentioned above we updated the Plugin has to fix the problem, just use ‘check for updates’ in Icy, you should find an update for this plugin that will fix that 🙂
– StephaneStephane Dallongeville April 20, 2020 at 12:54 pm
it would be better to have the spot position directly from the tracks of the generator.
This is what you have in the tracks export folder, the excel file contains the spot position directly from the tracks generator so you’re sure that is ground true 🙂
– StephaneStephane Dallongeville April 17, 2020 at 12:02 pm
I think that is the way to go: having a folder containing all your images (TIF files) and your spot positions (XLS files). You still need a bit of process to extract spot position from excel files but that is something definitely doable 🙂
– StephaneStephane Dallongeville April 17, 2020 at 11:55 am
Indeed the feature was never implemented. We just updated the plugin so tracks are now properly exported (in Excel format). Also we modified the Sequence export so it just export in a single TIF file.
– StephaneStephane Dallongeville April 17, 2020 at 10:44 am
I’m just discovering that we can use the plugin in that batch form ^^
Indeed the Tracks folder remains empty, which is suspicious for the least…
I will investigate to see if there is something wrong in the code (or if the feature was never really implemented). I will keep you inform of my findings here !
– StephaneStephane Dallongeville April 16, 2020 at 6:46 pm
Which tracks folder are you speaking about ? There is several possible export for tracking, the most direct one is to use the embedded export from Track Manager:
It will save tracks in a XML file containing both tracks and detections information :
You can also use the Export to Excel processor :
To have en export in excel format 🙂
Hope that is what you’re looking for !