Here you can find the releases and change notes of Cytosplore. If you need an older build for reproducing previous results please download them below.
- Up to 100x speedup (macOS: 10x) for a-tSNE and HSNE gradient descent by adding latest HDI, providing gradient descent using the GPU.
- Up to 10x speedup for a-tSNE and HSNE knn computation using the annoy aknn library.
- Now provides selection of three different approximated knn algorithms in A-tSNE and HSNE (annoy, Flann, and HNSW (macOS only)). With annoy being the new default.
- Provides selection of different distance metrics for the knn computation, depending on the selected library.
- Now allows caching the HSNE hierarchy to disk to remove pre-computation time on re-computation HSNE with the same data and parameters.
- Several architecture changes to improve stability.
- On startup, now opens the main application window larger, depending on the screen size.
- Now hides the color-map legend in the A-tSNE and HSNE views when sample is selected.
- Changes the labels of the color-map legend in the A-tSNE and HSNE views to indicate that the color-scale corresponds to min/max values of the data, not low/high expression values.
- Fixes an issue if fcs files contain infinite values.
- Several minor bugfixes affecting the drawing of the A-tSNE and HSNE plots.
- Now suggests the number of scales for HSNE based on the input size.
- Fixes a bug, where the HSNE embedding would not initialize properly on re-embedding.
Initial Release for MacOS
- Now uses A-tSNE implementation from HDI Library.
- Increases the range for arcsin co-factors.
- Application now closes without confirmation dialog when updating.
Version 2.1.5 Windows 7 and higher
- Fixes an issue with some out of spec fcs files.
Version 2.1.4 Windows 7 and higher
- It is now possible to set the co-factor for the arcsinh transformation.
- Several minor bugfixes.
- Fixes a bug that would incrroectly represent the default value for ‘Random Walks Threshold’ in HSNE advanced parameters as 1.0 and limit its range to 0.0 .. 1.0 even though 1.5 is used as the default setting.
- If one of the name fields in fcs is not set but the other is the name will be copied to the empty one.
- Sets NaN values to zero on load (a warning will be printed in the console window).
- Data Level HSNE Coordinates are now added to exported fcs files if available.
If not zoomed into the data level coordinates will be (0, 0) for the corresponding points.
There is no indication of the map the coordinates belong to within the files, make sure to aptly name your HSNE analyses and exported files to keep this information.
- It is now possible to save clusters while maintaining the original sample structure.
I.e. assume you have two samples as separate fcs files and 3 resulting clusters
- Using Save Clusters … saves them as cluster1.fcs, cluster2.fcs and cluster3.fcs as before
- Using Save Clusters (per sample)… saves them as cluster1-Sample1.fcs, cluster1-Sample2.fcs, cluster2-Sample1.fcs and and so on.
- Added a confirmation dialog on exit.
Public Release of Cytosplore+HSNE
- This version of Cytosplore makes HSNE publicly available for the first time.
Please see the Nature Communications paper Interactive Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types for full detail.
- FCS writer now saves to FCS 3.1 to fix a problem with large files introduced in 1.0.1.
If you have saved fcs files with more than 500.000 cells in version 1.0.1 these might be broken.
Test them in another tool to make sure they are OK.
Version 1.0.1 New Features
- FCS Reader: Supports loading of some FCS 3.1 files.
- Fixes t-SNE/HSNE rendering on some low-end integrated graphics cards.
- Initial Release of Cytosplore for research use.