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# ScanImageStitching

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ScanImage tiles and z-scans stitching

## Fiji
ImageJ2
version: 2.3.0/1.53f

## Plugins
Grid/Collection Stiching version: 1.2

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issues: snake order argument has white space in it

```
^Right & Down                $
```

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## Running headless script

```
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/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --ij2 --headless --console --run ScanImageStitching.ijm
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```

## ScanImage issue

[issue](https://forum.image.sc/t/converting-16-bit-signed-tiffs-to-16-bit-unsigned/5847/3) signed vs unsigned 16 bit images

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## Microscopy Image Stitching Tool (MIST)
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[MIST](https://github.com/USNISTGOV/MIST/wiki/Install-Guide)

## Pipeline

* even stack = "right & down"
* odd stack = "right & up"
* alternate based on the stack number

## Run

```
Plugins > Macros > Run ... > ScanImageStitching.ijm
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```

## Snake Indexing

### Grid: snake by rows
* Right & Down
* Left & Down
* Right & Up
* Left & Up


### Even Grid

* Z = odd -> {Right & Down}

* Z = even && Grid = even -> {Right & Up}
* Z = even && Grid = odd -> {Left & Up}