FCSalyzer / Blog: Recent posts

I am slowly working on ironining out smaller details and bug fixes. I added two new features to the latest release (0.9.12-alpha) - calculation of the CV and import of compensation matrices from FCS files.

I actually did not want to add new features until 1.0. However, the CV was an easy thing and the compensation matrices seemed very important. I guess many users, including me, do not like the idea of recompensating FCS3 files just because the compensation matrix is not used. So here it is ...... read more

I just uploaded the new version 0.9.9-alpha. There are many new features and bug fixes. The big major change is the support of more FCS data file formats coming from more flow cytometers and acquisition softwares. This was accompanied by some rewrites leading to all FCS data files now treated similarly by FCSalyzer. This means that all data files can now be displayed on linear, log or logicle scale, and all files can be compensated.... read more

I am currently working on expanding FCSalyzer to open FCS3 files from more machines, like the Accuri and the MacsQuant. It turns out that the various files all look slightly different here and there. Most of the files follow the FCS3 standard, but in a way that causes problems for me. This is much more work than I expected.

I want to include a reasonable stable support for more flow cytometers in the next release of FCSalyzer. In other words, it will take some more time for version 0.9.9 to be released.

The first bugfix release was posted right now. I am sure there are many more bugs to be found. The next weeks will be full of excitement while I test, test, and test.

It may be called a holiday miracle. The FCSalyzer project is still alive! I just uploaded a new version (0.9.5-alpha), which has a major new feature: FCS3 support! This includes log-transformation and compensation.

FCS3 implementation took a lot of work and new thinking about the program. That it took me two years, however, was caused by many concurrent things: difficult programming (for me as a non-professional programmer), a demanding job and lots of distractions in my free time. ... read more

A major bug has been corrected - documents can now be saved again. I have no clue how I introduced that bug. To think that the old version was up for three months and nobody was able to save the analysis - horrible. Thanks for the bug report!

Other news: FCS3 support is worked on, but progressing slowly. But the project is not dead ;)

The new version is up. This version has two new features: statistics export and plot alignment.

Statistics can be exported into a tab-delimited text file. The command can be found under the "File" menu.

Panels (Pots, annotations, comments and statistics) can be arranged along the left, right, top, or bottom outermost of the selected panels. This can be done with the keyboard arrow keys (CTRL+arrow key) or under the menu "Arrangement".... read more

The new Version 0.9.2 is ready for download. This version now has density plots and overlays.

Density plots are simply a new plot type in which the areas with more events have a brighter color than low density areas. The color moves from the base color for the lowest density area to white for the highest density area. The algorithm for displaying these densities might change in future releases, I am not sure if I like the plots the way they are now.... read more

The new version is up. It is just a bug fix release, no new features. Unfortunately these bug fixes took forever and don't really change much to bring FCSalyzer closer to beta status. But small steps will also lead to the goal, eventually.

I've always wanted an easy small application for analysing flow cytometry data on Windows. None of the programs available are what I am looking for - either they don't offer "What you see is what you get", or the crash with the large data files I sometimes use, or the analysis plainly doesn't work properly.

So a year ago I decided to write one myself. The start was easy - to load a data file and display a dot plot took me just a day. Since then all the small details of a regular application crushed down on me while I tried to get this application to usable. ... read more