Comments (3)
Here's how it looks like in Fiji (and we want to be somewhat compatible with that, at least the location of mean
and stddev
for normalization needs to be the same):
name: YOUR MODEL NAME HERE
description: YOUR DESCRIPTION HERE
cite:
text: |-
Buchholz, T. et al. - Content-aware image restoration for electron microscopy.
Methods in Cell Biology, Volume 152 p.277-289, ISSN 0091-679X (2019)
doi: https://doi.org/10.1016/bs.mch.2019.05.001
authors: [YOUR NAMES HERE]
documentation: README.md
test_input: ./test_input.tif
test_output: ./test_output.tif
covers: [./thumbnail.png]
tags: [denoising, unet2d, n2v]
license: BSD 3
format_version: 0.1.0
language: java
framework: tensorflow
source: de.csbdresden.n2v.train.N2VPrediction
inputs:
- name: raw
axes: byxc
data_type: float32
data_range: [-inf, inf]
shape:
min: [1, 4, 4, 1]
step: [1, 4, 4, 0]
outputs:
- name: denoised
axes: byxc
data_type: float32
data_range: [-inf, inf]
halo: [0, 32, 32, 0]
shape:
reference_input: raw
scale: [1, 1, 1, 1]
offset: [0, 0, 0, 0]
training:
source: de.csbdresden.n2v.train.N2VTraining
kwargs: {batchDimLength: 180, batchSize: 64, trainDimensions: 2, neighborhoodRadius: 5, numEpochs: 100,
numStepsPerEpoch: 300, patchDimLength: 60, stepsFinished: 30000}
prediction:
preprocess:
spec: de.csbdresden.n2v.predict.N2VPrediction::preprocess
kwargs: {mean: 41498.87, stdDev: 15007.021}
weights: {source: https://github.com/bioimage-io/fiji-bioimage-io/releases/download/v0.1.0/n2v-sem-demo.zip}
postprocess:
spec: de.csbdresden.n2v.predict.N2VPrediction::postprocess
kwargs: {mean: 41498.87, stdDev: 15007.021}
dependencies: ./dependencies.yaml
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Hi, are model exports according to the modelzoo specifications already supported in Fiji (or anywhere else)?
We talked about this a while ago, but haven't heard anything recently. It's a coincidence that I just saw this issue.
Best,
Uwe
from n2v.
@uschmidt83 yes, it's currently being implemented here and I recently added a reader and writer for the spec to imagej-modelzoo
(see howto). I just talked to @maweigert yesterday about having a meeting with you two after the NEUBIAS course next week to plan integrating this into CSBDeep as well.
from n2v.
Related Issues (20)
- Model export does not work for N2V2 HOT 1
- Add 3D support for N2V2
- M1 Mac: Graph execution error on 3D data HOT 4
- error in predicting model HOT 2
- Multi-channel tiff (YXC) file denoising problem HOT 7
- Config should not need X HOT 2
- N2V Fiji crashes HOT 2
- train HOT 2
- How to run through the code HOT 2
- tensor dimension input error when running 3D N2V HOT 7
- Updating N2V to N2V2 settings HOT 4
- Wrong shape in training data generation
- Peculiar behavior of N2V2 prediction HOT 6
- How to employ multiple GPUs during training HOT 1
- Poor performance HOT 5
- the filepath provided must end in `.weights.h5` HOT 2
- N2V for large datasets HOT 3
- save_tiff_imagej_compatible('pred_train.tif', pred_train, axes='YX') HOT 3
- "weights_best.h5" is not working HOT 4
- Running N2V prediction on a GPU cluster fails
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