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Endrov is a multi-purpose image analysis program. Have a look at some screenshots or read more.

Create image processing flows

Create image processing flows (2)

Voxel rendering

Extract and render surfaces

Arbitrary data can be stored with the images and integrated in the analysis

Do overlays, apply filters, all in realtime

2010-02-01

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.

2010-01-18

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

2010-01-13

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.

2010-01-08

• 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!)

2009-10-31

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.

2009-09-04

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.

2009-09-03

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:

• Flows to detect lines on leafs
• C.elegans 2008.2 in the model window
• The new lineage window

Which class of algorithms are you mainly in need of? (45 votes) Segmentation 44% Confocal techniques e.g. FRAP quantification 0% Stereological quantification e.g. cell counting, area 16% Deconvolution 11% Spectral unmixing 7% Stitching 2.2% Clustering 2.2% Classical operations e.g. morphology, moving averages, median 7% Advanced filtering e.g. non-linear diffusion, anisotropic filters 4% Spectral methods, FFT etc 7% Message (ENTER to confirm)

2009-08-20

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.

2009-07-21

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

2009-07-08

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

2009-06-23

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!

2009-06-16

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.

2009-05-17

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!

2009-03-12

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.

2009-03-11

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.

Prioritize improvements or backwards-compatibility? (18 votes) Willing to run 10.6 44% Willing to run 10.5 22% Will stick with older version 0% Willing to switch to Linux 33% Message (ENTER to confirm)

Which operating system would you use for Endrov preferably? (79 votes) Linux 27% Solaris 1.3% BSD 2.5% Mac 29% Windows 41% Message (ENTER to confirm)

What is your main need? (60 votes) New microscope recording software 12% Image browsing & fancy rendering 1.7% Image analysis & data extraction 62% Image restoration 12% Efficient image storage & handling 3% Hypothesis testing/generation & graphing 1.7% General data management 7% Other 1.7% Message (ENTER to confirm)

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