import tracking files

[ieca...@gmail.com]

Hi,

I have recently downloaded Icy and I am currently learning to use it.  I particularly like the spot detection and tracking plugins, but I am also using TrackMate from ImageJ.  Is it possible to import tracking files generated by TrackMate in the Icy Track Manager?  This may seem redundant but at this time TrackMate gives me more options to filter out undesired spots and/or tracks (or I am not used to Icy, yet) but, it doesn't calculate MSDs or determine the flow.

Thank you!

Irina

[Fabrice de Chaumont]

Hi Irina !

The maintainer of TrackMate is Jean Yves Tenevez at 300 meters from me at Pasteur Institute, so I think we can arrange something !

:)

I will tell him there is a question about his plugin here. Maybe he has some add on to also export the same things as we do.

Best,

Fabrice

[Irina Catrina]

Hi Fabrice,

Sounds great! Thank you very much and I am looking forward to hearing
more about this!

Best wishes,
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/icy-software/45455bac-1506-4840-a2f4-bb0e06369a1c%40googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.

[Jean-Yves Tinevez]

Hi Irina

 My name is Jean-Yves Tinevez and I am one of the authors of TrackMate. Fabrice kindly pointed me to your post and I will try to answer the best I can. 

Since you want to do MSD analysis, I supped you have non-merging and and non-branching tracks. So for this we can conveniently use the simplified XML export of TrackMate. Go to the last panel of the GUI, called 'Select a action' (yes I know, grammar). 

One of the action proposed is called 'Export tracks to XML file'. This will generate a XML file the ICY guys know how to import. 

Fabrice also authorized me to point you to another MSD solution in MATLAB, here:

http://www.mathworks.com/matlabcentral/fileexchange/40692-mean-square-displacement-analysis-of-particles-trajectories

documented here:

http://www.mathworks.com/matlabcentral/fileexchange/40692-mean-square-displacement-analysis-of-particles-trajectories/content/msdanalyzer/MSDTuto.html

And there is a script in Fiji to import this TrackMate XML file in MATLAB:

https://github.com/fiji/TrackMate/blob/master/scripts/importTrackMateTracks.m

Hope it helps

Good luck!

jy

[Irina Catrina]

Hi Jean-Yves,

Thank you very much for your quick reply and help.

I have already tried to load the xml file generated by TrackMate as you
described and I received the error "Invalid Track File".

Unfortunately, I do not have Matlab and I was looking for an open access
software that will allow me to do the MSD and flow analysis. Moreover,
the PI of the lab where I work has collaborated with Dr. Olivo-Marin
before Icy become freely available, so I should be able to successfully
use Icy for our data (http://www.ncbi.nlm.nih.gov/pubmed/19597554).

But, if needed I can probably find a computer with Matlab in our
College, and will use ParticleStats from Ilan Davis's group for
Directionality.

Thank you for your help!
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com.

[Jean-Yves Tinevez]

On Monday, January 20, 2014 3:44:36 PM UTC+1, Irina Catrina wrote:

Hi Jean-Yves,

Thank you very much for your quick reply and help.

I have already tried to load the xml file generated by TrackMate as you
described and I received the error "Invalid Track File".

I think the Icy guys need to build an importer for this first...

Best

jy 

[Irina Catrina]

Sorry, I misunderstood, I thought it should work with Icy in the
simplified form. Hopefully they can easily build the importer because I
really like both, Icy TrackManager and TrackMate, and find that they
work well for our data.

Thank you again,
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/19157a6f-833f-40a5-8ced-44dab3027593%40googlegroups.com.

[Fabrice de Chaumont]

Hi,

Jean Yves is recording the XML track in the ISBI Challenge format. So you should use the ISBI track Importer processor in the track manager to load them. If you don't have it, simply type ISBI in the search bar and select ISBI track importer. This will download and install it.

Then run the trackprocessor, click "add processor" and select ISBI file importer. You should then be able to lad the XML file !

Best,

Fabrice

[Irina Catrina]

Hello,

I just tried what you suggested and I get the message "Unable to load
track file". I will play with it more maybe I am doing something wrong.

Thank you!
Irina

> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.

>
> > To unsubscribe from this group and all its topics, send an email to

> > icy-software...@googlegroups.com <javascript:>.

> > To post to this group, send email to icy-so...@googlegroups.com

> <javascript:>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/icy-software/19157a6f-833f-40a5-8ced-44dab3027593%40googlegroups.com

> <https://groups.google.com/d/msgid/icy-software/19157a6f-833f-40a5-8ced-44dab3027593%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out

> <https://groups.google.com/groups/opt_out>.

>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/a3eb350f-9d4d-4a3d-a418-4e6def9c7e63%40googlegroups.com.

[Irina Catrina]

Hi Fabrice,

I tried loading xml files generated by TrackMate for various data. I
tried both XYT and XYZT and every time I get the same message "Unable to
load the track file"

I attached the output file maybe that will give you some idea why this
is not working for me.

Thank you!
Irina

> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.

>
> > To unsubscribe from this group and all its topics, send an email to

> > icy-software...@googlegroups.com <javascript:>.

> > To post to this group, send email to icy-so...@googlegroups.com

> <javascript:>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/icy-software/19157a6f-833f-40a5-8ced-44dab3027593%40googlegroups.com

> <https://groups.google.com/d/msgid/icy-software/19157a6f-833f-40a5-8ced-44dab3027593%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out

> <https://groups.google.com/groups/opt_out>.

>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/a3eb350f-9d4d-4a3d-a418-4e6def9c7e63%40googlegroups.com.

[Fabrice de Chaumont]

Hi Irina,

I thought that the export from TackMate was compliant with the format we proposed for the ISBI challenge...
Can you post the xml file containing track that you output from trackmate ? Then I will see why it does not import.

Best,

Fabrice

[Irina Catrina]

Hi Fabrice,

Thank you very much for your time and for looking into this.

Please find attached the simple xml file exported from TrackMate
(TM_Track_export.xml).

Please let me know if you need additional information.
Irina

> https://groups.google.com/d/msgid/icy-software/a3eb350f-9d4d-4a3d-a418-4e6def9c7e63%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/a3eb350f-9d4d-4a3d-a418-4e6def9c7e63%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com.

[Fabrice de Chaumont]

Hi,

I just published a new version where you will see 'import from TrackMate' in the File menu of the trackmanager.

Best,

Fabrice

[Irina Catrina]

I just tried the new importing feature. The tracks are loaded in the
tracking manager, but there is an error in the output section:

TrackSegment : The detection must be added with consecutive T value.
Detection was not added

And, the tracks are not properly displayed on the corresponding image. I
attached a screenshot as png.

Thank you and sorry for taking so much of your time,
irina

On 1/24/2014 11:53 AM, Fabrice de Chaumont wrote:
> Hi,
>

> I just published a new version where you will see 'import from

> TrackMate' in the File menu.
>
> Best,
>
> Fabrice

> https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com.

[Fabrice de Chaumont]

Hi Irina,

On Friday, January 24, 2014 6:36:36 PM UTC+1, Irina Catrina wrote:

I just tried the new importing feature.  The tracks are loaded in the
tracking manager, but there is an error in the output section:

TrackSegment : The detection must be added with consecutive T value.
Detection was not added
 

In Icy, the tracks cannot have 'holes'. In the following piece of the XML you provide me you can see that the track is not defined for t position 14 and 15 for instance.

 <particle nSpots="83">
    <detection t="0" x="74.02161554067762" y="37.371732476822686" z="0.0" />
    <detection t="1" x="74.46586133955329" y="37.33492449372799" z="0.0" />
    <detection t="2" x="74.22205749538065" y="37.31304955855918" z="0.0" />
    <detection t="3" x="74.42227314840251" y="37.414660756831886" z="0.0" />
    <detection t="4" x="74.51895908455373" y="37.38879995791907" z="0.0" />
    <detection t="5" x="74.42647443896462" y="37.432505351780364" z="0.0" />
    <detection t="6" x="74.16022466586382" y="37.454737830476475" z="0.0" />
    <detection t="7" x="73.95540507869818" y="37.23268034198248" z="0.0" />
    <detection t="8" x="74.0074969188451" y="37.48086821860951" z="0.0" />
    <detection t="9" x="73.80548745021834" y="37.43629170367967" z="0.0" />
    <detection t="10" x="74.02611572057242" y="37.14134524110345" z="0.0" />
    <detection t="11" x="74.24271513018012" y="36.81589462837397" z="0.0" />
    <detection t="12" x="74.12304621031183" y="36.78808337228767" z="0.0" />
    <detection t="13" x="74.06381986540923" y="36.62077660961168" z="0.0" />
14 and 15 are not defined here
    <detection t="16" x="74.14913967725488" y="36.38871011977299" z="0.0" />
    <detection t="17" x="74.25070236232072" y="36.50515928378066" z="0.0" />
    <detection t="18" x="74.42886140804075" y="36.362808292642704" z="0.0" />
    <detection t="19" x="74.41791114011986" y="35.891361091343974" z="0.0" />
    <detection t="20" x="74.47393765196617" y="35.81516894373525" z="0.0" />
    <detection t="23" x="74.7778508391319" y="35.90606246687385" z="0.0" />
    <detection t="24" x="74.8931714595233" y="35.95075195490354" z="0.0" />
    <detection t="25" x="74.80097544507083" y="35.88136657387194" z="0.0" />
    <detection t="26" x="75.10398761347393" y="35.78730163811862" z="0.0" />
    <detection t="29" x="75.86861337160975" y="35.5902032962494" z="0.0" />
    <detection t="32" x="75.69082124032852" y="35.71756428495733" z="0.0" />
    <detection t="33" x="75.77289825302569" y="35.83652477814102" z="0.0" />
    <detection t="34" x="76.07298991197776" y="35.86637436397504" z="0.0" />
    <detection t="35" x="76.1234865544384" y="35.681039279961595" z="0.0" />
    <detection t="36" x="76.29098273087428" y="35.74597146646813" z="0.0" />
    <detection t="37" x="76.44433231470283" y="35.812710429008106" z="0.0" />
    <detection t="38" x="76.35697031478053" y="35.81944614938764" z="0.0" />
    <detection t="39" x="76.30143785959281" y="36.149669829735195" z="0.0" />
    <detection t="41" x="76.46231826456727" y="36.6445367231018" z="0.0" />
    <detection t="43" x="76.1478991804162" y="36.629220378338786" z="0.0" />
    <detection t="44" x="76.19988726794739" y="36.889924411555945" z="0.0" />
    <detection t="45" x="76.27257407521563" y="36.75240745816413" z="0.0" />
    <detection t="46" x="76.393278051052" y="36.63544404861182" z="0.0" />
    <detection t="47" x="76.27935830067936" y="36.57309309833818" z="0.0" />
    <detection t="48" x="76.31751998995456" y="36.632243102176794" z="0.0" />
    <detection t="49" x="76.04454394515803" y="36.57500378273325" z="0.0" />
    <detection t="50" x="75.96645623815321" y="36.87970297965062" z="0.0" />
    <detection t="51" x="75.92217190666352" y="37.05629919024058" z="0.0" />
    <detection t="52" x="75.84750296592769" y="37.19352867389141" z="0.0" />
    <detection t="53" x="75.8935416976792" y="37.491297469954304" z="0.0" />
    <detection t="54" x="75.89859727071722" y="37.87263287142531" z="0.0" />
    <detection t="55" x="75.97869835189492" y="37.858711085474425" z="0.0" />
    <detection t="56" x="76.40134045571462" y="37.84195519889721" z="0.0" />
    <detection t="57" x="76.51354144840788" y="37.651666951185675" z="0.0" />
    <detection t="58" x="76.75379820956984" y="37.63898784152623" z="0.0" />
    <detection t="59" x="76.69982190987143" y="37.64693537911494" z="0.0" />
    <detection t="60" x="76.708864421948" y="37.60290620698747" z="0.0" />
    <detection t="61" x="76.81417354082613" y="37.72196613300744" z="0.0" />
    <detection t="62" x="76.87172609552736" y="37.690711477204445" z="0.0" />
    <detection t="63" x="76.68230989048362" y="37.7542104006174" z="0.0" />
    <detection t="64" x="76.66355484392044" y="37.99262031162115" z="0.0" />
    <detection t="65" x="76.99460297948131" y="37.97875640072205" z="0.0" />
    <detection t="66" x="77.12442510510499" y="38.16138861195177" z="0.0" />
    <detection t="67" x="77.00429915834488" y="38.22894642136456" z="0.0" />
    <detection t="68" x="77.05932534817866" y="37.977566367341154" z="0.0" />
    <detection t="69" x="76.84537847044338" y="38.068652992845145" z="0.0" />
    <detection t="70" x="76.54981530884638" y="37.49732846058662" z="0.0" />
    <detection t="71" x="76.67199946766188" y="37.630668430282746" z="0.0" />
    <detection t="72" x="76.81939876105338" y="37.624698576099085" z="0.0" />
    <detection t="73" x="77.28045457206217" y="37.763804085565155" z="0.0" />
    <detection t="74" x="77.47965176262292" y="37.69699481410396" z="0.0" />
    <detection t="75" x="77.65076135160888" y="37.825857229017075" z="0.0" />
    <detection t="76" x="77.35046102909786" y="37.55080522754493" z="0.0" />
    <detection t="77" x="77.44768889198188" y="37.767236765879275" z="0.0" />
    <detection t="78" x="77.76237657403571" y="37.651536360059346" z="0.0" />
    <detection t="79" x="77.65036091340973" y="37.65657088545169" z="0.0" />
    <detection t="80" x="77.65131761405694" y="37.422818689062176" z="0.0" />
    <detection t="81" x="77.36912552226673" y="37.48473509636058" z="0.0" />
    <detection t="82" x="77.09431318883998" y="37.37012526843107" z="0.0" />
    <detection t="83" x="77.4179288924662" y="37.32355670355866" z="0.0" />
    <detection t="84" x="77.2028311216366" y="37.178313984508904" z="0.0" />
    <detection t="85" x="77.28694325003437" y="36.752625215887036" z="0.0" />
    <detection t="86" x="77.30689506408834" y="36.98613010661815" z="0.0" />
    <detection t="87" x="77.43956194547211" y="36.83547668271824" z="0.0" />
    <detection t="88" x="77.8471040903598" y="36.69025063463128" z="0.0" />
    <detection t="89" x="77.99340627123206" y="36.53475486729205" z="0.0" />
    <detection t="90" x="77.69520885829859" y="36.445683320837894" z="0.0" />
    <detection t="91" x="77.9274607505335" y="36.67036855009522" z="0.0" />
    <detection t="92" x="77.90953297476996" y="36.67875283814188" z="0.0" />
  </particle>
 
So I could create new sub-tracks, but before this, I would like to know if it's a normal behaviour ?

And, the tracks are not properly displayed on the corresponding image. I
attached a screenshot as png.

I guess there is a scale factor ( pixel Size ? )

I will ask Jean-Yves about this !

Fabrice
 

[Irina Catrina]

Hi Fabrice,

Yes indeed, the errors disappear after disabling "allow gap closing" in
TrackMate.

Regarding the scale, is it possible that TrackMate uses micrometers
while Icy uses pixels?

Thank you!
Irina

> https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com>

>
> >
> <https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/5a239443-e23e-42c1-b10a-b90fb648e2a8%40googlegroups.com>>.
>
> >
> > > For more options, visit
> https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>
> > <https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>>.
> >
> > --
> > You received this message because you are subscribed to a topic
> in the
> > Google Groups "Icy imaging" group.
> > To unsubscribe from this topic, visit
> >
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe
> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.
>
> > To unsubscribe from this group and all its topics, send an email to
> > icy-software...@googlegroups.com <javascript:>.
> > To post to this group, send email to icy-so...@googlegroups.com
> <javascript:>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/5707a5d4-a596-4b46-bd45-c628696b68e8%40googlegroups.com.

[Fabrice de Chaumont]

Hi Irina

On Tuesday, January 28, 2014 3:03:20 PM UTC+1, Irina Catrina wrote:

Hi Fabrice,

Yes indeed, the errors disappear after disabling "allow gap closing" in
TrackMate.

Regarding the scale, is it possible that TrackMate uses micrometers
while Icy uses pixels?

Exactly, Jean-Yves just explained me that he use a field in the XML file where in stores the pixelSize of the tracking information. Yours is micron but he told me that it could be anything and at the moment I don't have a list of unit that he can generate to finish the plugin. Anyway I will release it with micron, still I need your image that you post in your example to perform a test, because I need to test the way I convert my units to see if everything is fine.

This simple problem takes some times... sorry about that !

 

[Irina Catrina]

Fabrice,

No problem, please take your time, I am very happy you can do something
about it, and I am looking forward to using it whenever is ready.

I chose the XYT and also shortened the time series (I assume the same
importer will also work with xml files generated by Track Mate for XYZT
data).

Please find attached the image in zip format and the corresponding xml
file generated by TrackMate (no gaps allowed). If it is not too much
trouble could you please confirm that you have received the files?

Thank you!
Irina

> https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com>

>
> >
> <https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/6f88ea44-5b98-49d2-bdea-679cabed517e%40googlegroups.com>>.
>
> >
> > > For more options, visit
> https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>
> > <https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>>.
> >
> > --
> > You received this message because you are subscribed to a topic
> in the
> > Google Groups "Icy imaging" group.
> > To unsubscribe from this topic, visit
> >
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe
> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.
>
> > To unsubscribe from this group and all its topics, send an email to
> > icy-software...@googlegroups.com <javascript:>.
> > To post to this group, send email to icy-so...@googlegroups.com
> <javascript:>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/icy-software/5707a5d4-a596-4b46-bd45-c628696b68e8%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/5707a5d4-a596-4b46-bd45-c628696b68e8%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out
> <https://groups.google.com/groups/opt_out>.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/ddf80ade-a3ef-4280-8858-5a9b1014a81a%40googlegroups.com.

[Irina Catrina]

Hi Fabrice,

I hope you are well.

I couldn't help but to play with the data more while waiting to hear
from you. I found that if I change the image properties to pixels in
ImageJ, TrackMate will yield the tracking data in pixels. Importing in
Icy the simple xml file generated by TrackMate, will display the tracks
properly in 2D (but not in the 3D VTK, which probably uses microns). I
then edit the sequence properties directly in Icy. Anyway, I can switch
between the image properties if I want the 2D or 3D display, although
not having to perform tracking with both units will save me a lot of time.

I have two more of questions:

1. is there a way to display only the current timepoint in each track
(to show just the active spot, this in TrackMate is "show local track"
OR keep the backbone track and show just the current timepoint spot),
and/or to built the whole or partial track as you play the time series?
This will look great in the 3D display but it is not of high priority.
Thanks to you and Jean-Yves I now feel more confident about analyzing
tracks using both TrackMate and Icy's Track Manager.

2. is the track flow processor designed for 2D display only? I don't
necessarily need it for the 3D display, I am just wondering, because I
get an error if I try it. I only used TrackMate generated tracks
because I am having issues when trying to do 3D spot tracking with Icy
(similar issue as you addressed previously for a different user).

Thank you for all your help,
Irina

[Fabrice de Chaumont]

Hi Irina,

Jean-Yves explained me that there is a value by which all the track coordinates are multiplied in track mate, but it's not in the file so I can't recover it. So the only way will be to prompt the user to enter this scaling value, for x/y and z.
I am happy you found a way to export it correctly for now.

If you wish to display only the current t, you can click "add track processor" and then add the Track Clipper, and set the value to 1. This will define a time windows around the current time point. All others detections will be filtered.

The track flow is only in 2D for now.

Best,

[Irina Catrina]

Hi Fabrice,

Sounds like a great solution to me, looking forward for you to implement it.

Thank you for the info on the track clipper.

Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/801b5d7c-ac81-41cb-b9e3-990e87c713c4%40googlegroups.com.

[Fabrice de Chaumont]

Hi Irina !

The very good news is that Jean-Yves is also currently creating an exporter in trackmate for the track manager !

At some point this is going to be uniformed !

Best,

Fabrice

[Irina Catrina]

That is indeed very good news!!!

Thank you very much,
Irina

> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.

>
> > To unsubscribe from this group and all its topics, send an email to

> > icy-software...@googlegroups.com <javascript:>.

> > To post to this group, send email to icy-so...@googlegroups.com

> <javascript:>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/icy-software/801b5d7c-ac81-41cb-b9e3-990e87c713c4%40googlegroups.com

> <https://groups.google.com/d/msgid/icy-software/801b5d7c-ac81-41cb-b9e3-990e87c713c4%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out

> <https://groups.google.com/groups/opt_out>.

>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/091d6757-a430-446b-a806-bda6c59cae70%40googlegroups.com.

[Irina Catrina]

Hi Jean-Yves,

I have updated the Fiji today and when I use TrackMate no objects are
detected, even when using files that I have analyzed before. Even
before this last update I noticed that the tracks will stop too early
even though the image clearly had particles within the detection limits.
For example the XYZT would have 120 time points but tracks will extend
for only the first 56 or so frames.

Do you have any idea what could be the problem(s)?
Thank you,

Irina

On 1/20/2014 4:31 AM, Jean-Yves Tinevez wrote:

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com.
> To post to this group, send email to icy-so...@googlegroups.com.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com.

[Fabrice de Chaumont]

Hi Irina,

Could you post the exported file please ?

Best,

Fabrice

> icy-software+unsubscribe@googlegroups.com.

[Irina Catrina]

Hi Fabrice,

Do you mean for the ones that end prematurely?  I may have saved some, which I can send them to you later today, but I do not have that version of Fiji anymore to generate new files.

For the newest version since no spots are detected the protocol doesn't proceed to tracking.

This is a TrackMate question, I apologize if I was not supposed to post it here.

Thank you,

Irina

Sent from my iPad

To unsubscribe from this group and all its topics, send an email to icy-software...@googlegroups.com.

To post to this group, send email to icy-so...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/e647d1bb-249d-45c2-ac00-8a31a6a4a4b3%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Irina Catrina]

Hi Fabrice,

This is the exported file from TrackMate, but I think the problem starts
in Fiji/TrackMate. Again, I apologize if this is not where I should
post it, but you and Jean-Yves did help me before with TrackMate.

Thank you!
Irina

> <https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe>.

>
> > To unsubscribe from this group and all its topics, send an email to

> > icy-software...@googlegroups.com
> <mailto:icy-software%2Bunsu...@googlegroups.com>.

> > To post to this group, send email to

> icy-so...@googlegroups.com <mailto:icy-so...@googlegroups.com>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com

> <https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com>.

>
> > For more options, visit https://groups.google.com/groups/opt_out

> <https://groups.google.com/groups/opt_out>.

>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to

> icy-software...@googlegroups.com
> <mailto:icy-software...@googlegroups.com>.

> To post to this group, send email to icy-so...@googlegroups.com

> <mailto:icy-so...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/e647d1bb-249d-45c2-ac00-8a31a6a4a4b3%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/e647d1bb-249d-45c2-ac00-8a31a6a4a4b3%40googlegroups.com?utm_medium=email&utm_source=footer>.
> For more options, visit https://groups.google.com/d/optout.

[Fabrice de Chaumont]

Hi Irina,

Jean-Yves will answer you I guess, but at the moment he is out of office.

Best,

Fabrice

>      > icy-software+unsubscribe@googlegroups.com

>     <mailto:icy-software%2Bunsu...@googlegroups.com>.
>      > To post to this group, send email to

>     icy-so...@googlegroups.com <mailto:icy-software@googlegroups.com>.

>      > To view this discussion on the web visit
>      >
>     https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com
>     <https://groups.google.com/d/msgid/icy-software/7c30b686-c95b-4209-9fff-aae9b2ae84ea%40googlegroups.com>.
>
>      > For more options, visit https://groups.google.com/groups/opt_out
>     <https://groups.google.com/groups/opt_out>.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to

> icy-software+unsubscribe@googlegroups.com
> <mailto:icy-software+unsub...@googlegroups.com>.

> To post to this group, send email to icy-so...@googlegroups.com

> <mailto:icy-software@googlegroups.com>.

[Jean-Yves Tinevez]

Hi all

Irina I see you have problems with TrackMate directly. Since I am just catching up I am a bit confused at what and where the problem is. 

Could you just describe it again here? And ship the faulty files for me to reproduce the problem?

Thanks

Best

jy

[Irina Catrina]

Hi Jean-Yves,
Yes, I started having issues after the last two updates of Fiji.

After the second to last update the tracking procedure did proceed to
completion but the tracks stopped prematurely, e.g. at time point 37
although spots were present through all 90 time points and have been
detected with previous versions. I still have an older version of Fiji
and I was able to perform tracking on the same file without problems.

After the last update, when using the same file and parameters no spots
are detected so no tracking can be performed.

The original data for which I performed tracking and the TrackMate
tracking xml files are rather large but I can send you the simplified
xml files that I import in Icy. I do not have the Fiji version before
the latest update but I do have a couple of files, please see attached.

In addition for the newest version I get errors when trying to open
TrackMate xml files saved with previous versions, please see below:

Problem reading the model:
Could not read the isInt attribute for feature QUALITY.
Could not read the isInt attribute for feature POSITION_X.
Could not read the isInt attribute for feature POSITION_Y.
Could not read the isInt attribute for feature POSITION_Z.
Could not read the isInt attribute for feature POSITION_T.
Could not read the isInt attribute for feature FRAME.
Could not read the isInt attribute for feature RADIUS.
Could not read the isInt attribute for feature ESTIMATED_DIAMETER.
Could not read the isInt attribute for feature MEAN_INTENSITY.
Could not read the isInt attribute for feature MEDIAN_INTENSITY.
Could not read the isInt attribute for feature MIN_INTENSITY.
Could not read the isInt attribute for feature MAX_INTENSITY.
Could not read the isInt attribute for feature TOTAL_INTENSITY.
Could not read the isInt attribute for feature STANDARD_DEVIATION.
Could not read the isInt attribute for feature CONTRAST.
Could not read the isInt attribute for feature SNR.
Could not read the isInt attribute for feature EDGE_TIME.
Could not read the isInt attribute for feature EDGE_X_LOCATION.
Could not read the isInt attribute for feature EDGE_Y_LOCATION.
Could not read the isInt attribute for feature EDGE_Z_LOCATION.
Could not read the isInt attribute for feature SPOT_SOURCE_ID.
Could not read the isInt attribute for feature SPOT_TARGET_ID.
Could not read the isInt attribute for feature LINK_COST.
Could not read the isInt attribute for feature VELOCITY.
Could not read the isInt attribute for feature DISPLACEMENT.
Could not read the isInt attribute for feature TRACK_X_LOCATION.
Could not read the isInt attribute for feature TRACK_Y_LOCATION.
Could not read the isInt attribute for feature TRACK_Z_LOCATION.
Could not read the isInt attribute for feature TRACK_MEAN_SPEED.
Could not read the isInt attribute for feature TRACK_MAX_SPEED.
Could not read the isInt attribute for feature TRACK_MIN_SPEED.
Could not read the isInt attribute for feature TRACK_MEDIAN_SPEED.
Could not read the isInt attribute for feature TRACK_STD_SPEED.
Could not read the isInt attribute for feature NUMBER_SPOTS.
Could not read the isInt attribute for feature NUMBER_GAPS.
Could not read the isInt attribute for feature NUMBER_SPLITS.
Could not read the isInt attribute for feature NUMBER_MERGES.
Could not read the isInt attribute for feature NUMBER_COMPLEX.
Could not read the isInt attribute for feature TRACK_INDEX.
Could not read the isInt attribute for feature TRACK_ID.
Could not read the isInt attribute for feature TRACK_DURATION.
Could not read the isInt attribute for feature TRACK_START.
Could not read the isInt attribute for feature TRACK_STOP.
Could not read the isInt attribute for feature TRACK_DISPLACEMENT.
Problem reading the settings:
Could not read the isInt attribute for feature QUALITY.
Could not read the isInt attribute for feature POSITION_X.
Could not read the isInt attribute for feature POSITION_Y.
Could not read the isInt attribute for feature POSITION_Z.
Could not read the isInt attribute for feature POSITION_T.
Could not read the isInt attribute for feature FRAME.
Could not read the isInt attribute for feature RADIUS.
Could not read the isInt attribute for feature ESTIMATED_DIAMETER.
Could not read the isInt attribute for feature MEAN_INTENSITY.
Could not read the isInt attribute for feature MEDIAN_INTENSITY.
Could not read the isInt attribute for feature MIN_INTENSITY.
Could not read the isInt attribute for feature MAX_INTENSITY.
Could not read the isInt attribute for feature TOTAL_INTENSITY.
Could not read the isInt attribute for feature STANDARD_DEVIATION.
Could not read the isInt attribute for feature CONTRAST.
Could not read the isInt attribute for feature SNR.
Could not read the isInt attribute for feature EDGE_TIME.
Could not read the isInt attribute for feature EDGE_X_LOCATION.
Could not read the isInt attribute for feature EDGE_Y_LOCATION.
Could not read the isInt attribute for feature EDGE_Z_LOCATION.
Could not read the isInt attribute for feature SPOT_SOURCE_ID.
Could not read the isInt attribute for feature SPOT_TARGET_ID.
Could not read the isInt attribute for feature LINK_COST.
Could not read the isInt attribute for feature VELOCITY.
Could not read the isInt attribute for feature DISPLACEMENT.
Could not read the isInt attribute for feature TRACK_X_LOCATION.
Could not read the isInt attribute for feature TRACK_Y_LOCATION.
Could not read the isInt attribute for feature TRACK_Z_LOCATION.
Could not read the isInt attribute for feature TRACK_MEAN_SPEED.
Could not read the isInt attribute for feature TRACK_MAX_SPEED.
Could not read the isInt attribute for feature TRACK_MIN_SPEED.
Could not read the isInt attribute for feature TRACK_MEDIAN_SPEED.
Could not read the isInt attribute for feature TRACK_STD_SPEED.
Could not read the isInt attribute for feature NUMBER_SPOTS.
Could not read the isInt attribute for feature NUMBER_GAPS.
Could not read the isInt attribute for feature NUMBER_SPLITS.
Could not read the isInt attribute for feature NUMBER_MERGES.
Could not read the isInt attribute for feature NUMBER_COMPLEX.
Could not read the isInt attribute for feature TRACK_INDEX.
Could not read the isInt attribute for feature TRACK_ID.
Could not read the isInt attribute for feature TRACK_DURATION.
Could not read the isInt attribute for feature TRACK_START.
Could not read the isInt attribute for feature TRACK_STOP.
Could not read the isInt attribute for feature TRACK_DISPLACEMENT.
Could not find the tracker key element in file.


Thank you,
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to

> icy-software...@googlegroups.com
> <mailto:icy-software...@googlegroups.com>.

> To post to this group, send email to icy-so...@googlegroups.com

> <mailto:icy-so...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/33591006-7d07-4ed5-8615-b27753befacb%40googlegroups.com
> <https://groups.google.com/d/msgid/icy-software/33591006-7d07-4ed5-8615-b27753befacb%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Jean-Yves Tinevez]

On Wed, Apr 30, 2014 at 2:27 PM, Irina Catrina <ieca...@gmail.com> wrote:

Hi Jean-Yves,
Yes, I started having issues after the last two updates of Fiji.

After the second to last update the tracking procedure did proceed to completion but the tracks stopped prematurely, e.g. at time point 37 although spots were present through all 90 time points and have been detected with previous versions.  I still have an older version of Fiji and I was able to perform tracking on the same file without problems.

After the last update, when using the same file and parameters no spots are detected so no tracking can be performed.

What version do you have?

Because from the error message below it seems like you are running TrackMate downloaded from the unstable update-site. 

To make sure, just download a "fresh" Fiji, and re-run the tracking making sure that the version displayed by TrackMate is v2.2.0

best

jy

[Irina Catrina]

I will try that and get back to you later today.

Thank you,

Irina

Sent from my iPad

--
You received this message because you are subscribed to a topic in the Google Groups "Icy imaging" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.

To unsubscribe from this group and all its topics, send an email to icy-software...@googlegroups.com.
To post to this group, send email to icy-so...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/CAAgB9O46Eo9BVuJW3gBtqeJLagTYdphRVrTs94UY74ojeRcWfw%40mail.gmail.com.

[Irina Catrina]

Hi Jean-Yves,

I reinstalled Fiji, the continuous release and indeed the TrackMate
version is 2.2.0, as you mentioned.

I ran TrackMate for a XYZT tiff file and again, the tracks stopped
prematurely. After performing a Z-projection and running TrackMate for
the XYT file, the tracking proceeded to the end of the time series. I
am not sure that I am doing anything different, as I do not run into
this problem with an older version of Fiji, with TrackMate v.2.0.4. Do
you have any suggestions? The Z-step is 0.5um, the particle size, ~1um
and the maximum distance 2um.

Thank you,
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com
> <mailto:icy-software...@googlegroups.com>.
> To post to this group, send email to icy-so...@googlegroups.com
> <mailto:icy-so...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/CAAgB9O46Eo9BVuJW3gBtqeJLagTYdphRVrTs94UY74ojeRcWfw%40mail.gmail.com
> <https://groups.google.com/d/msgid/icy-software/CAAgB9O46Eo9BVuJW3gBtqeJLagTYdphRVrTs94UY74ojeRcWfw%40mail.gmail.com?utm_medium=email&utm_source=footer>.

[Jean-Yves Tinevez]

On Thu, May 1, 2014 at 2:57 AM, Irina Catrina <ieca...@gmail.com> wrote:

Hi Jean-Yves,

I reinstalled Fiji, the continuous release and indeed the TrackMate version is 2.2.0, as you mentioned.

I ran TrackMate for a XYZT tiff file and again, the tracks stopped prematurely.  After performing a Z-projection and running TrackMate for the XYT file, the tracking proceeded to the end of the time series.  I am not sure that I am doing anything different, as I do not run into this problem with an older version of Fiji, with TrackMate v.2.0.4.  Do you have any suggestions?  The Z-step is 0.5um, the particle size, ~1um and the maximum distance 2um.

Hi Irina

This is very weird and of course I cannot reproduce.

Could you ship the raw image? 

If it's too big I suspect a memory problem. If you cannot ship the image, could you tell us its size, dimensions and the computer you run TrackMate on?

best

jy 

[Irina Catrina]

Hi Jean-Yves,
Thank you for your suggestion.
Here is the information you requested:

file size: 1.011GB

image Dimensions: XYZT; 512x512 pixels; X and Y 0.241um/pixel,
21Zs/0.5um, 94 time points/20seconds

Computer:
Manufacturer: Dell
Model: INSPIRON N411Z
Processor: Intel(R) Core(TM) i5-2430M CPU @ 2.40 GHz 2.40 GHz
Installed Memory (RAM): 8.00 GB (7.89 GB usable)
System Type: 64-bit Operating System
Windows 7 Home Premium

I will try to reduce the stack and/or increase the memory in Fiji and
run TrackMate again.

Thank you,
Irina

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com
> <mailto:icy-software...@googlegroups.com>.
> To post to this group, send email to icy-so...@googlegroups.com
> <mailto:icy-so...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/CAAgB9O6MSmJpczWJ2_S8Erev9yNpayGumu7qoFpXJzsOMpOzHQ%40mail.gmail.com
> <https://groups.google.com/d/msgid/icy-software/CAAgB9O6MSmJpczWJ2_S8Erev9yNpayGumu7qoFpXJzsOMpOzHQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.

[Jean-Yves Tinevez]

On Thu, May 1, 2014 at 1:22 PM, Irina Catrina <ieca...@gmail.com> wrote:

Hi Jean-Yves,
Thank you for your suggestion.
Here is the information you requested:

file size: 1.011GB

image Dimensions: XYZT; 512x512 pixels; X and Y 0.241um/pixel, 21Zs/0.5um, 94 time points/20seconds

Computer:
Manufacturer: Dell
Model: INSPIRON N411Z
Processor:  Intel(R) Core(TM) i5-2430M CPU @ 2.40 GHz 2.40 GHz
Installed Memory (RAM): 8.00 GB (7.89 GB usable)
System Type: 64-bit Operating System
Windows 7 Home Premium

It's not even big. So I do not understand.

any chance I could get the data? 

[Jean-Yves Tinevez]

Hi Irina, all

Thank you very much for the data. I could download it, reproduce and diagnose the problem. 

We are facing here a memory problem due to the creation of a massive number of spurious spots in the detection step. Even on my beefy computer, the number of spots created during the detection process is so huge that it completely saturates the memory, and after a while, TrackMate just gives up and stops prematurely. 

Of course, you can normally filter out these spots in the following step. But the problem is that they are created nonetheless and saturate the memory before you get a chance to filter them out. 

The solution is to forbid the creation of spurious spots (d'oh!). The way to do that is to use the Threshold parameter in the detector settings, and to pick a value high enough so that roughly only interesting spots are created. The Preview button can help you setting this parameter by running the detection process on a single frame and displaying the results. In the case of your data I have found thresholds in the order of 10000 to be a good starting point. 

In my humble opinion, you will still get a massive chunk of undesired detections, mainly coming from the cell edges. I recommend using a ROI to a analyze the inside of each cell separately. 

Tell me if it works

best

jy

[Irina Catrina]

Hi Jean-Yves,

Thank you very much for taking the time to figure this out for me.
Indeed, I have only performed the filtering after the detection step.
Thank you for the solution, setting the threshold will save me a lot of
time in the future, but at the same time I feel that I wasted your time!
I am sorry for any inconvenience.

I just tried the detection with the threshold value you suggested and it
worked great, and as expected the detection step is so much faster. I
will also follow your advice to use ROIs, but since the detection is
taking less time I can filter the tracks to eliminate undesired regions.
For our type of data the TrackMate filters and the ease of using them
are two of the reasons I chose TrackMate. I have tried, unsuccessfully,
to use Volocity for tracking, and I have also used Imaris, before I was
aware of TrackMate and Icy. I am so grateful these resources are freely
available, and the support is amazing. Thank you again!

Best wishes,
Irina

On 5/2/2014 3:53 AM, Jean-Yves Tinevez wrote:
> Hi Irina, all
>
> Thank you very much for the data. I could download it, reproduce and
> diagnose the problem.
>
> We are facing here a memory problem due to the creation of a massive
> number of spurious spots in the detection step. Even on my beefy
> computer, the number of spots created during the detection process is so
> huge that it completely saturates the memory, and after a while,
> TrackMate just gives up and stops prematurely.
>
> Of course, you can normally filter out these spots in the following
> step. But the problem is that they are created nonetheless and saturate
> the memory before you get a chance to filter them out.
>
> The solution is to forbid the creation of spurious spots (d'oh!). The

> way to do that is to use the *Threshold* parameter in the detector

> settings, and to pick a value high enough so that roughly only

> interesting spots are created. The *Preview* button can help you setting

> this parameter by running the detection process on a single frame and
> displaying the results. In the case of your data I have found thresholds
> in the order of 10000 to be a good starting point.
>
> In my humble opinion, you will still get a massive chunk of undesired
> detections, mainly coming from the cell edges. I recommend using a ROI
> to a analyze the inside of each cell separately.
>
> Tell me if it works
> best
> jy
>

> --
> You received this message because you are subscribed to a topic in the
> Google Groups "Icy imaging" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/icy-software/EFunAOiWeCc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> icy-software...@googlegroups.com
> <mailto:icy-software...@googlegroups.com>.
> To post to this group, send email to icy-so...@googlegroups.com
> <mailto:icy-so...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/icy-software/CAAgB9O5dr0aFe-SPZ_TgRFrYxjjSM%2BjquiTwPGLErZwbbwLpTw%40mail.gmail.com
> <https://groups.google.com/d/msgid/icy-software/CAAgB9O5dr0aFe-SPZ_TgRFrYxjjSM%2BjquiTwPGLErZwbbwLpTw%40mail.gmail.com?utm_medium=email&utm_source=footer>.

[Jean-Yves Tinevez]

On Fri, May 2, 2014 at 2:09 PM, Irina Catrina <ieca...@gmail.com> wrote:

Hi Jean-Yves,

Thank you very much for taking the time to figure this out for me. Indeed, I have only performed the filtering after the detection step. Thank you for the solution, setting the threshold will save me a lot of time in the future, but at the same time I feel that I wasted your time!  I am sorry for any inconvenience.

I just tried the detection with the threshold value you suggested and it worked great, and as expected the detection step is so much faster. I will also follow your advice to use ROIs, but since the detection is taking less time I can filter the tracks to eliminate undesired regions.  For our type of data the TrackMate filters and the ease of using them are two of the reasons I chose TrackMate.  I have tried, unsuccessfully, to use Volocity for tracking, and I have also used Imaris, before I was aware of TrackMate and Icy. I am so grateful these resources are freely available, and the support is amazing. Thank you again!

Thank you for these kind words.

Good luck!

jy 

[Krishna Mudumbi]

Is there any way around this? When I disable the gap closing option I have 2,000 + tracks to deal with and Icy will not import them. TrackMate has been working fine, but I really need to determine the MSD (which I can't seem to do directly from TrackMate). Any help with this would be much appreciated.

Cheers,

Krishna

[Irina Catrina]

Not that I know of, and we are now using Icy tracking, which for our data works well. I also tried to perform MSD analysis using Icy, but at the time only pixel measurements were available, and I ended up using the Icy tracking results with an R script to do the analysis.

Irina

You received this message because you are subscribed to the Google Groups "Icy imaging" group.
To unsubscribe from this group and stop receiving emails from it, send an email to icy-software...@googlegroups.com.

To post to this group, send email to icy-so...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/icy-software/61448bcb-ba13-4cc6-ba76-659388609af9%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.