Old news

From Endrov



Version 2.19.0 has been released. Micro-manager has been updated to 1.4.7 (there is still one crash-bug after configuration but it can be worked around). Many plugins have been generalized, the OMERO connection rewritten, bio-formats integrates better and too many other things to be mentioned. This release is still primarily of use for developers but regular users will find, at minimum, the annotation and visualization features to be very handy. We want your feedback on bugs! We want the next release to be ready for the masses, which means, plenty of work on the small details, and wrapping up some half-done components.

The wiki has also been overhauled. If you spot a problem and want to fix it, don't hesitate to ask for an account.


The source code has been moved to GitHub, and while at it, we have rewritten the history to make up for some past mistakes. Nightly builds should be functional again. There are many features in the nightly version not yet made public; expect a new release soon!

For those who have checked out the source code already: it is easiest to checkout anew and copy over your changes. Otherwise, do a rebase.


www.endrov.net has been moved to a new host. Hopefully this will eliminate all the downtime we've had the past half a year.


Finally there is a new release, 2.18.0! Many small improvements and bug fixes. To speed up future releases there are now nightly builds. These are recommended also for normal users.


Endrov version 2.17.0 is out! Many bugs have been fixed and small things have been tweaked. The OSX version works better now, we had to work around a bug introduced in OSX 10.5 and still not fixed. Most effort has been spent on the acquisition part of Endrov; both Micro-manager and the new virtual microscope Frivolous (the result of a master thesis project by David & Arvid Johansson).


Website moved - if we accidentally broke some link, please let us know. A new version of Endrov will soon be released.


Version 2.16.0 is released! In particular, it has the first version of Particle Measure which finally allows non-programmers to extract analyzed data. Data can be stored in both CSV and SQL.


Version 2.15.5 is released! Some small features and improvements, updated libraries, but in particular many bug fixes.


We're working on improving the documentation. To make sure all details are covered, we're trying screencasts instead of written text. Find them to the left.


  • There are new instructions on how to pull Endrov from GIT and compile from source
  • The source can be browsed online with gitweb
  • Linux - there is now a repository, much easier to install
  • Linux - AMD64 and i386 are now both supported (and tested!)


We have fully opened up the project, including direct access to the source code through GIT. See the download section. We are hanging out in Freenode #endrov on IRC.


How do we proceed with support for OSX? I'm very interested to hear from anyone who has experience of OpenJDK on OSX. Apple Java6 only exists on Intel Macs, OSX10.5+, meaning PowerPC-users have to look for another way. It seems that means installing Linux or figuring out how to use OpenJDK.


new version: 2.15.4

  • Old formats of OST have been dropped (use 2.15.3 to update old files)
  • Several bugfixes
  • Added links to more test datasets on the download page

Some screencasts:

<poll> Which class of algorithms are you mainly in need of? Segmentation Confocal techniques e.g. FRAP quantification Stereological quantification e.g. cell counting, area Deconvolution Spectral unmixing Stitching Clustering Classical operations e.g. morphology, moving averages, median Advanced filtering e.g. non-linear diffusion, anisotropic filters Spectral methods, FFT etc </poll>


new version: 2.15.3

  • Lineage window totally rewritten, now with support for any number of expression patterns
  • New version of OST (3.3). This is the last Endrov with support for older versions, use it to upgrade
  • Due to OST, flows behaves better. Generated channels (or other objects) are not stored to disk
  • Semi-automatic DIC-lineaging included, but don't bother with it yet
  • Morphological operations rewritten. Now easy to use and more complete
  • Levelsets are buggy, fixes postponed to next release
  • Many other fixes

Do not use ImServ, it is pending an overhaul.


2.15.2 is out:

  • Fixes in bio-formats, upstream and in binding. Can now load images without a resolution. Micro-manager recordings can be opened
  • New Acetree plugin, can load Acetree/Starrynight lineages and associated images (beta)
  • Semi-automatic lineaging plugin for His::RFP included. Needs more tweaking and documentation (beta)
  • Clean-up among files, better instructions for compilation, should be easier to start developing plugins
  • Other internal improvements


Endrov 2.15.1 is out. Focus is on maturity:

  • Tons of bugs fixed regarding to flows - they should now be in a useful state
  • New flow units available
  • Flow window easier to use with various right-click short-cuts
  • Movie output on Linux through FFMPEG
  • Bug fixes a bit everywhere
  • The old filter system is being deprecated

Some new documentation has been written, more is on the way.

The overall plan is now 1. remove the old filter system 2. finalize ROIs 3. look into segmentation. In parallel, the microscope control GUI will be made ready for normal users.

Some statistics:

  • 100882 lines of code! we just broke the 100k-barrier
  • 805 top-level classes
  • 1396 classes in total


We're going to the international C. elegans meeting and will be unresponsive for a few days. You're welcome to the talk in the Gene expression-session, and to the Endrov poster!


Endrov 2.15 is out and a great leap forward. The image processing algorithms are now accessible from the GUI and flows are functional. Not all algorithms are tied and more flow units are needed to make everything useful, but the basics are there.

Several very important bug fixes are in. It is also easier to restore images stored without metadata. A lot of documentation has been written, especially for developers - have a look at it.


Endrov 2.14 is here. It contains bug fixes and many new features. It includes very rudimentary support for snapping images from a microscope and controlling it with a gamepad. Windows 64-bit support hopefully added but we cannot test it ourselves.

Most features are for programmers only, it has not yet been included in the GUI:

  • The image classes are almost complete, and handles all pixel formats, stacks and most importantly, lazy evaluation
  • Linear kernel with very fast special cases e.g. moving average is O(number of pixels)
  • Non-linear kernels such as local percentile
  • Fast calculation of optimal thresholds given several algorithms
  • Flood fills
  • Binary and grayscale morphology
  • Spectral mixing
  • Geometric momentum
  • Finding local extremes, including those which are flat
  • Histograms
  • Image math and logical operations
  • Watershed
  • Convex hulls
  • Deconvolution
  • Fourier transform and related operations
  • Finding pixel groups, fixing scanning confocal image shifts, etc

Many things have changed, new bugs are likely. Use the last version if this doesn't work, and report back so we can fix it!


Support Open hardware! There are plenty of new specialized applications that you will never be able to buy from a traditional microscope company but is perfectly feasible as open source. But to support your hardware you have to help us by putting pressure on you microscope vendor. Demand at least ABC-compliant Open hardware.


An issue: Apple is extremely slow at introducing new technology. In particular, they are 2 years behind on Java. Version 1.6 exists finally as beta while Sun will release the next major version this summer. OSX 10.4 will not support 1.6 and OpenCL which would greatly speed up calculations will only exist on OSX 10.6. So the question is, would you be willing to upgrade to OSX 10.6 or would you prefer to sacrifice functionality? Those who cannot upgrade (PowerPC users) can always install Linux on their Mac, where even Java 1.7 can be previewed now.

<poll> Prioritize improvements or backwards-compatibility? Willing to run 10.6 Willing to run 10.5 Will stick with older version Willing to switch to Linux </poll>

<poll> Which operating system would you use for Endrov preferably? Linux Solaris BSD Mac Windows </poll>

<poll> What is your main need? New microscope recording software Image browsing & fancy rendering Image analysis & data extraction Image restoration Efficient image storage & handling Hypothesis testing/generation & graphing General data management Other </poll>


More minor bug fixes available as 2.13.4. Among other things, making movies work on Mac again.


Minor bug fixes available as 2.13.3. Full support for lineages without coordinates.


More bugs fixed as version 2.13.2, in particular visualization and mac support. Keep the bug reports coming!


Some nasty bugs have been pointed out, thanks. 2.13.1 contains fixes, upgrade immediately.


Finally! Version 2.13.0 is out. This release does not offer much new for the user but is a huge internal reworking (every single file has been affected). This has been in the way of further progress but is now taken care of. To this comes a file format upgrade that moves OST from a simple image container closer to an object oriented database. The better internals will show through as a better GUI structure. To improve speed of your recordings you can convert them to OST by using "Save As" but we recommend keeping the originals until file format freeze at version 3.0.


Example imagesets have been updated. The next release will be delayed a bit, had to reinvent the wheel (two-way socket communication is apparently old-school these days).


Version 2.12.0 is out. This is a bug fix release, I'm actually working on 3.x.x. Nevertheless, the old script language is dropped in this release. Java beanshell is used instead. Earlier versions have not worked at all on Windows ever since I cranked up the maximum memory usage limit. This release fixes this. The documentation will be a be off until the next release; sorry about this.


Version 2.11.0 is out. It implements OST3 better and fixes some small things. Experimental features are included; expect an adventure

  • The new ImServ image server is included
  • The model window can be navigated with a Play station style gamepad (or any standard joystick/gamepad)

webstart is still 2.10.0.


Version 2.10.0 is out with a big overhaul of 3D rendering. It supports multiple transparent objects better, and has many internal improvements to simplify writing new plugins. Other than reacting faster to user input and making use of all your CPUs/cores it comes with

  • New voxel renderer, render modes and improvements to the old one
  • Clipping planes
  • Scale bar
  • Partial OST3-support
  • Reworked Matlab bindings
  • New nuclei rendering options

and plenty of small fixes. Webstart is up to date.

Wishlist section now points to the tracker at SF. Make use of it!


Version 2.9.0 is ready. Main visible improvement is in usability; drag and drop is supported and there is no need to convert everything to OST. Metadata works for all file formats. We still recommend OST for larger recordings but if you want to edit single JPEG's then it is much more convenient now. File loading has been unified so for simple formats you no longer have to care how they are handled internally. The other big thing is Matlab integration and we have found the EV+Matlab combination to be a killer for quantitative phenotyping. There is a new tool to annotate lines and I have added a port to Linux on PowerPC.

Webstart has not been updated yet.


Version 2.8.0 is out. Importing has been improved (some nasty bugs addressed). A new tool, the OST Maker, can batch import common proprietary formats with simple drag-n-drop. Webstart has been updated.


Version 2.7.1 is out. Main update is a library update of JOGL which makes the model window a lot faster. Then follows GUI improvements. Webstart is up to date.


Version 2.7.0 is out. It contains some bleeding edge code so bugs are expected. This version adds a dozen of filters and some improvements to lineaging. The webstart is still the old stable 2.6.x.


Due to grant and publishing technicalities, files are for now no longer publicly available. We can still grant preliminary access but you have to contact us.


Version 2.6.2 is out, with some minor improvements for Mac.


Version 2.6.1 has been released, and fixes some portability problems on Linux with the new starter system. Documentation on Wiki has been expanded with a tutorial on the OST daemon and some other things.


Version 2.6.0 has been released. Compared to 2.5.0, there are bug fixes and much improved ROIs. The Windows port has been emphasized and the startup system has been redone from scratch. startEndrov.jar replaces the old run.bat. Linux support should also be slightly improved. Quicktime7-support is included for Windows, you just need to download and install Quicktime and you can make movies from your recordings. They will go into the OST data-folder.

JavaDoc has been made available online.


Webstart updated. Import-by-name has been fixed. Compound ROIs added. Various other fixes.


We're switching to a new domain, www.endrov.net. Old address will point to here for quite a while though.


Updated webstart with single 3d slices. namebased import working again, will recheck all code for importing for next release.


Late christmas gift: 2.5.0 now available for download and webstart. Focus is on visualization and internal improvements. Once again, Windows port might be lagging behind and will be the priority of next release.


Webstart update: bugfixes. making QT movies much improved (not tested on windows yet; you need qt6 dll's most likely). More filters. The first item off the wish list is included by the way.


Webstart updated; JOGL linker error fixed. Apparently the version we linked earlier was out of date. But if you run into more problems with GL, get in contact.


The webstart version has been updated to CVS. We've tried it on Windows XP and added instructions on how to get it running. No major bugs. If you experience additional problems, please contact Johan, as we want to get this port up to quality.


Endrov version 2.4.0 beta has been released. It adds support for filters and ROI's, image caching etc. imagesets have become editable. I expect quite a few bugs to have been introduced, and the windows port is still lagging behind.


Changed to a new wiki; documentation greatly improved. Guests should be able to edit pages but not create new ones (some pages protected). Developers who want to add documentation should request an account.


Endrov version 2.3.0 beta has been released. This is a maturity release; bugs and quirks has been addressed. Nothing depends on the database part any longer so it has been removed. Additional testing on Linux and Windows might be needed; revert to 2.2.0 if this version fails.


Endrov version 2.2.0 beta has been released. I have also made the coordinates from AceTree available (they are nice and good for testing the lineage and model window). Several windows/linux-specific bugs has been pointed out and these have been fixed; portability should no longer be a problem. Lineaging is rather mature and complete in this version but we keep working on it.


Endrov version 2.1.0 beta has been released. This is rather close to a fully working version but still beta. It has not been tested extensively on Windows and Linux yet but has been confirmed to work on our test machine. Some glitches are known. I have made an OST imageset available for reference. The OST imageset whitepaper has also been updated.


Thanks everyone who came by at the International C.elegans meeting! We got many valuable comments and the interest in new software for spatio-temporal recordings made us decide to put much higher priority on the EViewer. There is a mailing list now and anyone who wants updates on the progress are urged to join. The website has not yet been updated to reflect the radical changes in the software so don't read too much of the details.

The OST imageset whitepaper will be updated shortly according to the feedback we got, and also to allow further extensibility based on the EViewer framework. If you haven't given us feedback yet, then now is the time.


Screenshots and other things


Set up the website