gunpowder
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funkelab
A library to facilitate machine learning on multi-dimensional images.
Many of the specifics of reading Zarr files are already handled in `fun lib.persistence`. It also already generalizes to other sources of array data. Goal is to generalize the `ZarrSource`...
Hi, I want to write my own augmentation nodes because my data shows artefacts that are not mimicked by the nodes available in the package (SBEM data). In that context...
- [ ] include keras as external module (similar to `caffe`) - [ ] implement `keras.Train` - [ ] implement `keras.Process`
Greetings from the Mehta Lab and apologies in advance for the long post! I am attempting to use gunpowder as a dataloader for (float32) data in the ome-zarr format. I...
Below is a minimal example of what I'd like to do. Note that the request size (in voxels) is not a power of 2. The chunk size for the new...
Turns out that the default value for `max_shared_memory` https://github.com/funkey/gunpowder/blob/e523b49ca846a9fd46ab6fc0dd1040cc4a4d53b4/gunpowder/tensorflow/nodes/predict.py#L71 does not allocate 1GB of rather 4GB because the value type `ctypes.c_float` is used when for creating the `RawArray`. https://github.com/funkey/gunpowder/blob/e523b49ca846a9fd46ab6fc0dd1040cc4a4d53b4/gunpowder/tensorflow/nodes/predict.py#L90 With...
For prototyping it would be very useful to have a node that applies a user-provided mapping to the voxels of an array for a key/multiple keys (the shape of the...
As discussed in https://github.com/funkey/gunpowder/pull/29 z5py has a runtime dependency on some GCC-related libraries which are more recent than those available on conda and travis. More recent systems don't seem to...
- [x] `AddAffinities` - [x] `Chunk` - [ ] `DefectAugment` - [x] `DvidSource` - [x] `ElasticAugment` - [ ] `ExcludeLabels` - [ ] `GrowBoundary` - [x] `Hdf5Source` - [ ]...
