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Lockett, Stephen (NIH/NCI) [C]
To whom it may concern,
I am trying to get “active cells 3D” working, because potentially it might be useful for a segmentation problem. The input requires a “snake”, but there is no documentation about “snakes”. I have tried using a ROI as a snake, but to no avail. When I click on “add a new snake” I get a bug report error message. When I go the the “active cells 3D” webpage under plugins, the documentation gives some general information but does not say how to use the plugin. The online vide comes back with the message “This video is unavailable” when I click on it. Please would someone email me a thorough explanation of how to use this plugin. Thank you.
Likewise, I am having not able to use active cells. This plugin does allow me to add a snake with a given number of control points, but the arrow for moving the snake under snake editing does not work. The whole image and the snake move together. Again, the video in the webpage is unavailable. Please would someone email me a thorough explanation of how to use this plugin. Thank you.
Stephen Lockett, Ph.D.
Principal Scientist,
Director, Optical Microscopy and Analysis Laboratory,
Rm 12-79, Building 560,
https://confocal.cancer.gov/cores/optical-microscopy-and-analysis-laboratory
Frederick National Laboratory and Leidos Biomedical Research, Inc
P.O. Box B
(For Fedex, use Building 1050, Boyles Street)
Fort Detrick,
Frederick,
MD 21702, USA
Office: 301 846 5515
Mobile: 240 731 3551
lock...@mail.nih.gov
Stephane
1) When displaying ROIs, some show up as
solid blobs and some show up as the borders of rectangles. How
do I make them all show up as solid blobs?
All "2D area" ROIS show their content with a
surrounding bounding box (rectangle) used to select / move them.
What you saw is that when a "2D area" ROI becomes tiny (visually)
then we remove the bounding box to preserve the content region
details (as the bounding box would hide it somehow).
2) When changing the size and zoom of an
image with overlays, a mysterious red solid blob shows up over
the image which I can move around and it also produces a green
rectangle over the image when moving the red blob. There is no
intuitive way to remove this useless distraction and searching
for “mysterious red solid blob” finds nothing.
What you see here is the pencil to modify / edit a "2D area" ROI, that mean you have currently a selected "AD area" ROI. To cancel ROI selection (and so cancel ROI edition) just press "ESC" key when the image has the focus.
3) Finding commands is a game of luck. For example, when I wanted to find out how to remove ROIs, I searcher for “remove ROIs” and nothing relevant was returned. Serendipitously, I happened to search for “delete ROIs” and then found the relevant command.
Indeed sometime it's difficult to find or guess command name, even using the search bar (we made it for that basically). But here "removing a ROI" is a very basic operation and pressing "delete" key should do the job but it's why an introduction (even a very basic one) to the software is important : ROIs has a central role in Icy so it's very important to understand how to manipulate and use them efficiently. You can see in page 48 of the Icy Introduction tutorial that you can let the mouse cursor on a ROI tool button to see a tooltip which explain how to manipulate it (see the attached screenshot).
4) Although commands seem to be an important
component of Icy, searching for “commands’, which I did
(unsuccessfully) to get a list of all commands, bizarrely told me
about installed and online plugins and an online protocols, but
nothing about commands !?!
Indeed the internal commands does not reply to "command" key word, they reply to keyword referenced in their name or in their "tooltip" description. That is the way search bar look for matching items (it work the same way for plugins and protocol except it also search inside online documentation).
5) I have tried to “register” to get Icy support and the registration form came back and said it would send me an activation link via email. However, such an email was never received.
I just tested here and i did received the confirmation email but it may arrive in the spam folder so you may check it.
6) Please tell me how to get auto-complete to work in the script editor. I have the auto-complete plugin installed and the auto-complete option set in the script editor, but when I type for example, “add” after a short delay, it shows greys over “add”, but no list of methods appears. This is in contrast to page 10 of the “Scripting in Icy” tutorial.
Auto completion work by showing available fields / methods of your current object, to get it work it needs to know the type of you object.
If you just type "add" without anything before, then it doesn't know what you can to complete
If you type "seq.add" then object "seq" should be a known object at this point... in the script tutorial example you can see we did "seq = getSequence()" first, because of that javascript know the type of the "seq" object, so any subsequent use of "seq" can be auto completed.
So if you write this :
seq = getSequence()
seq.add
Then auto completion will work after writing "add", you can also use the "Ctrl+Space" shortcut to force auto completion to happen (instead of waiting for it to appear). If nothing appear then it means javascript is not able to determine the type of your object at the current line of code.
7) Right clicking in the script window shows a menu that includes “folds”. What is a fold? Searching for “fold” produces nothing.
fold is just to fold a block of code, it's used to
hide some blocks of code (generally blocks inside { }). Not really
useful imo.
8) Page 24 of the protocol tutorial gives a protocol for finding nuclei, measuring them and displaying them, except the display part does not work. The block for doing this apparently, “Add ROI to sequence” is formatted differently to the actual block. Please would someone provide me a working version of this tutorial example.
We just updated the tutorials (there were on old version), you should now see the correct blocks.
9) The Colocalization Studio uses ROIs of type “Area3D” to show locations of colocalization, even when my images are 2D. Since there are restrictions of what can be done with Area3D ROIs, for example I cannot convert them to “shape”, how do I convert an Area3D ROI to some other type of (2D) ROI?
You can do that by using a 2D rectangle ROI
surrounding your original 3D area ROI, put the Z position of the
rectangle ROI to 0 instead of ALL then select both ROIs and compute
their intersection (Boolean operation), you should obtain a new 2D area
ROI. Of course you can do it in a more automatic way using script or
protocol.
10) I am trying to get “active cells 3D” working, because potentially it might be useful for a segmentation problem. The input requires a “snake”, but there is no documentation about “snakes”. I have tried using a ROI as a snake, but to no avail. When I click on “add a new snake” I get a bug report error message. When I go the the “active cells 3D” webpage under plugins, the documentation gives some general information but does not say how to use the plugin. The online vide comes back with the message “This video is unavailable” when I click on it. Please would someone email me a thorough explanation of how to use this plugin. Likewise, I am having not able to use active cells. This plugin does allow me to add a snake with a given number of control points, but the arrow for moving the snake under snake editing does not work. The whole image and the snake move together. Again, the video in the webpage is unavailable. Please would someone email me a thorough explanation of how to use this plugin. Thank you.
Thank you.
Unfortunately these plugins are not maintained (there were developed by the external BIG lab). You can try to look at their official website, they did have documentation back in time. Also i may check in thse plugins to see what they doesn't work anymore but in the meantime you may try other plugin, which kind of segmentation you need ? Active Contour can also work in 3D (but it requires a big enough 3D stack and 3D ROIs for the initialization part).
Hope to have replied all your questions :)
Best,
- Stephane
Lockett, Stephen (NIH/NCI) [C]
Hi Stephane,
Many thanks for these helpful answers. I should be able to now make good progress with Icy. Also, I have contacted the author of the paper about active cells 3D.
Sincerely,
Stephen Lockett
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Lockett, Stephen (NIH/NCI) [C]
Dear Stephane,
I am trying to use Icy to open large, stitched Nikon images. They are 4 color, 2D and about 6GBytes in file size. Icy is able to determine their pixel size, number of colors etc, but I get a Java Heap memory error. I set the Java Heap size in Windows 10 to 10 Gigabytes and in Icy preferences I set the maximum memory 10 GBytes and the memory allocated to data cache to 80%. I am also using virtual mode. I am using 64 bit JRE version 1.7. (Icy would not start with version 1.8 and told me to use version 1.7). I have put the error log below. Please can you help? Thanks.
Sincerely,
Stephen Lockett
Java(TM) SE Runtime Environment 1.7.0_80-b15 (64 bit)
Running on Windows 8.1 6.3 (amd64)
Number of processors : 8
System total memory : 16.7 GB
System available memory : 11.5 GB
Max java memory : 10.3 GB
Image cache initialized (reserved memory = 8012 MB, disk cache location = C:/Users/locketts/AppData/Local/Temp/2)
VTK 6.3.0 library successfully loaded...
Warning: Your version of java does not support HTTPS protocol which will be used soon by the new web site.
You need to upgrade your version of java to 7u111 (Java 7) or 8u101 (Java 8) at least to use online features (as search or plugin update) in future.
Icy Version 2.0.0.0 started !
java.lang.OutOfMemoryError: Java heap space
at icy.type.collection.array.Array1DUtil.createArray(Array1DUtil.java:163)
at plugins.kernel.importer.LociImporterPlugin$LociTileImageReader$TileImageWorkBuffer.<init>(LociImporterPlugin.java:342)
at plugins.kernel.importer.LociImporterPlugin$LociTileImageReader.<init>(LociImporterPlugin.java:495)
at plugins.kernel.importer.LociImporterPlugin.getImageByTile(LociImporterPlugin.java:1396)
at plugins.kernel.importer.LociImporterPlugin.getImage(LociImporterPlugin.java:1347)
at icy.plugin.abstract_.PluginSequenceFileImporter$InternalSequenceIdImporterHelper.getImage(PluginSequenceFileImporter.java:63)
at icy.image.AbstractImageProvider.getImage(AbstractImageProvider.java:192)
at icy.plugin.abstract_.PluginSequenceFileImporter.getImage(PluginSequenceFileImporter.java:124)
at icy.file.Loader.internalLoadSingle(Loader.java:3686)
at icy.file.Loader.loadSequence(Loader.java:2878)
at icy.file.Loader$5.run(Loader.java:2316)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Lockett, Stephen (NIH/NCI) [C]
To whom it may concern,
I would still like to hear an answer to my problem below about opening very large 2D images. Since sending the email below, I have tried again on a large computer with over 100 GBytes of memory. I have had some very limited success by both downsizing the image and selecting only a sub-region during the opening process. However, this involves multiple steps and every step is extremely slow. Several minutes per step. If I try to open an image above a certain size, 2GBytes I think, then the memory usage goes to 100% of physical memory no matter how much physical memory exists and Icy has to be killed via the task manager. Using virtual mode or increasing the JAVA heap size makes no difference. Actually, in virtual mode, I do not see any evidence that the hard disk is being used to any significant extent. Many thanks.
Stephen Lockett
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Robert Smith
Hello Stephen,
I am no expert but if it opens at all on your screen from any software, and you do not necessarily need the pixel size with just the image then try to use “print screen” such as used on Windows.
As I said, I am no expert but I have used this function many times in similar situations.
Good Luck,
Bob
Sent from Mail for Windows 10
To: icy-so...@googlegroups.com; jco...@pasteur.fr
Subject: FW: [icy] Re: more issues
Lockett, Stephen (NIH/NCI) [C]
Hi Bob,
Thanks for responding. Your suggesting of using “print screen” does work when I can get the image to display. However, such as image is opened at a reduced resolution. My images are 2D and generally around 10 GBytes. If, on the other hand, the image is 3D and 10 GBytes and each xy slice is “not too big” (for example there are 100 Z slices), then Icy can handle it. If I use the plugin “montage2D” to covert the 3D image into a 2D image, then Icy hangs up and has to be killed via the task manager.
Sincerely,
Stephen Lockett
To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/DM5PR0101MB298673ABEDA9306BCF7503BEBDF90%40DM5PR0101MB2986.prod.exchangelabs.com.
Robert Smith
Stephane
Lockett, Stephen (NIH/NCI) [C]
Hi Stephane,
Many thanks for your answers. My images are much larger than 2^31, so I will have to use other software.
Stephen Lockett
From: Stephane <stephane.da...@pasteur.fr>
Sent: Tuesday, July 2, 2019 3:26 AM
To: Icy imaging <icy-so...@googlegroups.com>
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