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Open-weight model · Image segmentation

MicroStructFormer

by Nianqi Deng Dnq2025/MicroStructFormer

MicroStructFormer is an open-weight model for image segmentation from Nianqi Deng, released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0. It has 216M parameters. At 16-bit it needs about 0.5 GB of GPU memory, which fits on 1x MI300X from $1.85 an hour, at the lowest prices in the SAVRN Index. It draws 11 downloads a month.

MicroStructFormer is a high-capacity Mask2Former model built on a Swin-Large backbone, designed for the semantic segmentation of ultrastructures in Electron Microscopy (EM) images.

Parameters216M
Context—
Weights865.9 MB
Licensecc-by-nc-sa-4.0
AccessOpen weights
Monthly Downloads11

Runs On

What it takes to serve MicroStructFormer (216M parameters): the memory its weights need at each precision, and the cheapest way to rent enough data-center GPUs to hold them.

PrecisionWeightsMemory neededCheapest setupPer hourAlso fits
16-bit 0.4 GB 0.5 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00
8-bit 0.2 GB 0.3 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00
4-bit 0.1 GB 0.1 GB 1x MI300X (192 GB)
Vultr
$1.85 1x H100 $1.99 · 1x MI325X $2.00

Memory is the weights at that precision plus 20% for the runtime and a short context; a long context needs more. Prices are the lowest on-demand hourly rates in the SAVRN Index, read Oct 18, 2026.

MicroStructFormer on every accelerator the SAVRN Index prices, at every precision

Model Card

MicroStructFormer is a high-capacity Mask2Former model built on a Swin-Large backbone, designed for the semantic segmentation of ultrastructures in Electron Microscopy (EM) images. This model has been trained to accurately segment the following critical ultrastructural elements: Note: While the model architecture theoretically supports axon and myelin segmentation, this specific release is optimized and calibrated for the classes listed below due to dataset annotations. You can use this model easily via the transformers library. This Hugging Face model repository is associated with the following bioRxiv preprint: These model weights and associated architectures are provided for…

Excerpt from the card by Nianqi Deng, licensed cc-by-nc-sa-4.0.

Configuration

Architecture
Mask2FormerForUniversalSegmentation
Layers
10
Attention heads
8
Stored precision
float32
Model type
mask2former

Identity and Version

Repository
Dnq2025/MicroStructFormer
Publisher
Nianqi Deng
Task
Image segmentation
Modality
Image
Library
transformers
Parameters
216M parameters
Languages
en
Revision
905350fef32f5373f2a50a2092d4cda46e01c77a
First published
2026-05-26
Last updated
2026-10-09

Files and Weights

7 files, 897.4 MB in total. The weights are 1 file totalling 865.9 MB in safetensors.

Weights1 file · 865.9 MB
Configuration2 files · 76.1 KB
Documentation1 file · 4.6 KB
Other2 files · 31.4 MB
Repository1 file · 308 B
Every file
FileTypeSizeSHA-256
model.safetensorsWeights865.9 MB 47556111de44
config.jsonConfiguration75.6 KB —
preprocessor_config.jsonConfiguration520 B —
README.mdDocumentation4.6 KB —
sample/sample_image.pngOther16.7 MB 76ed844d056b
sample/sample_prediction.pngOther14.8 MB c72b11ae84ff
.gitattributesRepository308 B —

License and Download

License
cc-by-nc-sa-4.0
Access
Open weights, no gate
Download size
865.9 MB
Download from Nianqi Deng

Released by Nianqi Deng through its official repository on Hugging Face.

Built From

  • Derived from Dnq2025/swin-large-mask2former-finetuned-ER-Mito-LD8
  • Trained on (disclosed) Dnq2025/Mask2former_Finetune

Memory Requirements

PrecisionWeights in memory
As published865.9 MB
16-bit0.4 GB
8-bit0.2 GB
4-bit0.1 GB

Weights only, from the published parameter count; the key-value cache and runtime add to this.

Questions About MicroStructFormer

How much GPU memory does MicroStructFormer need?

About 0.5 GB at 16-bit and 0.1 GB at 4-bit: the weights (216M parameters) plus a working margin. A long context needs more.

What is the cheapest GPU to run MicroStructFormer on?

At 16-bit, 1x MI300X from $1.85 an hour; at 4-bit, 1x MI300X from $1.85 an hour, at the lowest on-demand prices the SAVRN Index lists.

Can I use MicroStructFormer commercially?

Not without separate permission. MicroStructFormer is released under Creative Commons Attribution-NonCommercial-ShareAlike 4.0. CC BY-NC-SA 4.0 permits non-commercial sharing and adapting with credit, and requires adaptations to use the same license. Commercial use needs separate permission.

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