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From Endrov

For simplicity, all platforms are supported in a single package. Source code is included in all releases.

We recommend you to have a look at Configuring available memory right away, as most common problems boil down to have too little/too much memory configured.

On Windows, we recommend you install the OpenJDK (not JRE!). You should always use 64-bit Java if possible to ensure you have enough memory (note: having 64 bit Windows is NOT the same as having 64-bit Java!)

Developer access

We welcome external contributions. The easiest way for a starter is to fork it on GitHub and ask Johan Henriksson to merge when ready.

License

This software is available under the BSD3 license unless a source file tells something else.

In addition to this license we also ask that any work that makes use of our software also cites us. Contact us for details. We cannot enforce this as per license but consider it the terms of fair use. If the use is particularly heavy we might ask for co-authorship but in that case we will also give our support in form of support and all forms of customization.

Port Status

Mac Regularly tested on 10.6, earlier might work. Old PowerPC might still work.

Windows: Sometimes tested on virtualized XP. Probably only limited by Sun Java version support, anything above 2k/NT is likely ok. This port lags behind; we need to know if you run into problems. If you run into memory usage problems, edit javaenv.txt.

Linux: Regularly tested on 64-bit Intel Ubuntu but other CPUs are expected to work.

Example data

C.elegans 2008.2 , map of C.elegans development. Coordinates only. 3.3mb. This is in our OST-format.

The Cell Image Library

The ImageJ example images, mostly 2D

From Broad Institute

For OsirisX

AceTree has some nuclei coordinates of a C.elegans embryo. We provide the data with the small modification that allows it to be loaded. (you need to hit the center button in the model view to see anything; also note current frame)

Deprecated datasets

[1]C.elegans embryo, DIC and fluoresence (non-confocal) over time. 90mb.

[2]Some neuron. Suitable for 3d rendering. 0.5mb.

[3]MRI of brain. Suitable for 3d rendering. 3.5mb. Converted from here.