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https://github.com/mviereck/microscopy-tools

Tools for microscopic captures and focus stackshots (beta)
https://github.com/mviereck/microscopy-tools

alignment arduino camera camera-configuration camera-control enfuse focus-stackshots fuse-stackshot-images imagemagick micrometer microscopy stacking stackshot stepper-motor tethered-shooting

Last synced: 7 months ago
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Tools for microscopic captures and focus stackshots (beta)

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README 

          
# microscopy-tools



Tools for microscopy and image focus stacking.



 - Tools already useful, in active development:

   - [`imfuse`](#imfuse): Fuse focus stackshot images with ImageMagick. (Terminal)

   - [`stackprepare`](#stackprepare): Batch processing of image stack for contrast, crop, gamma etc. 

 - Tools considered to be (mostly) stable and ready for use:

   - [`stackalign`](#stackalign): Align image stack with the help of [focus-stack]((https://github.com/PetteriAimonen/focus-stack)) and ImageMagick.

   - [`imgruler`](#imgruler): Draw a ruler or micrometer into an image. (Terminal)

 - Tools awaiting further development, currently less useful:

   - [`camcfg`](#camcfg): Terminal dialog frontend for camera configuration. (Terminal)

 - Deprecated, stored for partial code reuse:

   - [`stackfuser`](#stackfuser): Align, prepare and fuse focus stack images. (GUI)

   - [`stackshooter`](#stackshooter): Shoot focus stackshots with stepper motor and camera. (GUI)



`stackfuser` and `stackshooter` need some further development and documentation before they can be recommended for general use.

Especially they need a new GUI backend because the currently used `kaptain` GUI is outdated and does not run on up-to-date systems.



## imfuse



Combines focus stackshot images to an overall sharp image.



 - For all of (many) options see `imfuse --help`.

 - For an overview of imfuse workflow see [wiki: How imfuse works](https://github.com/mviereck/microscopy-tools/wiki/How-imfuse-works)

 - For some examples see [wiki: Examples](https://github.com/mviereck/microscopy-tools/wiki/Examples)



Dependencies:

 - `imagemagick` version 7 (command `magick`)

 - `geeqie` and `feh` (optional image viewers)

 - `exiftool` (optional to preserve exif meta data)

 - [`PetteriAimonen/focus-stack`](https://github.com/PetteriAimonen/focus-stack) (optional for option `--align`)

 - `enfuse` (optional, needed for some options)



Much thanks to the developers and supporters of ImageMagick!

 - Most image processing of imfuse is done by [`ImageMagick`](https://imagemagick.org).

 - imfuse contains code written by [Fred Weinhaus](http://www.fmwconcepts.com/imagemagick) with his friendly permission.

 - imfuse was inspired by [Alan Gibson](https://im.snibgo.com/)'s [focStack.bat](https://im.snibgo.com/focstack.htm).



## stackalign



Aligns image stack.



Dependencies:

 - [`PetteriAimonen/focus-stack`](https://github.com/PetteriAimonen/focus-stack)

 - `imagemagick`



The core work is done by `focus-stack`, this tool helps to crop the images to the usable common area.



## stackprepare



Batch processing of image stack for contrast, crop, gamma etc.



Dependencies:

 - `imagemagick`



## imgruler



Draws a ruler into an image.

Intended to draw micrometers into micoscopic captures.

Contains a calibration instruction in english and german.



Runs on Linux, macOS and (in Cygwin) on MS Windows.

Considered to be ready for general use.



Dependencies:

 - `imagemagick`

 

## camcfg

`dialog` frontend for `gphoto2` camera configuration. Reads possible configurations of a camera and provides a dialog in terminal to choose desired settings. Beta stage, already useable.

 - `camcfg` shows all available configurations.

 - `camcfg ENTRY` shows configuration of entry ENTRY. Example: `camcfg iso`

 

Dependencies:

 - `dialog`

 - `gphoto2`



## stackfuser



GUI frontend for image foto stacking with enfuse.



Deprecated, will be replaced by multiple single tools.



Provides:

 - Image preprocessing with `imagemagick` to enhance contrast and sharpness. 

 - Image alignment with `ffmpeg`/[vidstab](https://github.com/georgmartius/vid.stab) or `align_image_stack`.

 - Generating multiple overall sharp images from stackshot with `enfuse`. Further combining of these results with `imagemagick`.

 - Animated videos of focus stackshots.



Dependencies, most essentiell:

 - `align_image_stack` (hugin tools)

 - `enfuse`

 - `geeqie`

 - `imagemagick`

 - [`imfuse`](#imfuse)

 - [`kaptain`](https://github.com/mviereck/kaptain)

 - `viewnior`



Dependencies, also recommended:

 - `ffmpeg`

 - `exiftool`

 - [`imgruler`](#imgruler)

 - `ufraw`

 

## stackshooter

GUI for foto stacking with a stepper motor controlled by an Arduino and a camera connected on USB. 

Note: The user must be in group `dialout` to access the Arduino.



Deprecated, will be replaced.



Features:

 - Camera control with `gphoto2` for preview videos and tethered shooting.

 - Stepper motor control for focus adjustment.

 - Automated focus stackshots combining camera and stepper motor.

 

`pololu_a4988.ino` is my code to control my stepper motor driver with an Arduino. The control commands send by `stackshooter` to Arduino can be customized in `stackshooter` configuration dialog.



Dependencies:

 - `ffmpeg`

 - `geeqie`

 - `gphoto2`

 - `align_image_stack` (hugin tools)

 - [`kaptain`](https://github.com/mviereck/kaptain)

 - `xinput`

 - `xdotool`



## Example

Image of some flower pollen. Generated with `stackshooter` and `stackfuser`. 

Technic: Microscope from [Hund/Wetzlar](https://www.hund.de/en/) with a stepper motor and an arduino. 

Camera: Canon EOS 1000D. 

Stackshot result of 240 single captures with slightly different focus:



![screenshot](https://raw.githubusercontent.com/mviereck/microscopy-tools/images/example.jpg)



Iconified excerpt of source stackshot:



![screenshot](https://raw.githubusercontent.com/mviereck/microscopy-tools/images/sourcetable.jpg)



Animated video:



![screenshot](https://raw.githubusercontent.com/mviereck/microscopy-tools/images/animate.gif)



## Related tools



### Free and Open Source

 - [CombineZP](https://github.com/mviereck/CombineZP):

   Stacker for MS Windows. Works with wine on Linux, too. Good but unfortunately not maintained.

 - [`enfuse`](https://enblend.sourceforge.net/):

   Enfuse blends differently exposed images of the same scene into a nice output image.

   Command line tool, used by `stackfuser`.

 - [`Entangle`](https://entangle-photo.org/):

   Entangle provides a graphical interface for "tethered shooting", aka taking photographs with a digital camera completely controlled from the computer.

 - [`PetteriAimonen/focus-stack`](https://github.com/PetteriAimonen/focus-stack):

   A cross-platform tool for focus stacking images based on wavelet algorithms.

 - [`pulsar123/Macro-scripts`](https://github.com/pulsar123/Macro-scripts):

   A set of BASH scripts and C++ programs representing a complete workflow for processing macro focus stacking photographs.

 - [`gphoto2`](http://www.gphoto.org/):

   The gphoto2 library allows access and control of various digital camera models.

   Command line tool, used by `stackshooter` and `camcfg`.

 - [`hugin`](https://hugin.sourceforge.io/):

   Hugin is a panorama photo stitching program for several overlapping photos taken from the same location, transforming the photos to one larger image.

 - [`ImageMagick`](https://imagemagick.org):

   ImageMagick is a powerful software suite to create, edit, and compose bitmap images. 

   Command line tool, used by almost all tools in this repo.

 - [`mfkter`](https://github.com/hqhoang/mftker):

   GUI for enfuse. Replaces former MacroFusion.

 - [`RawTherapee`](https://www.rawtherapee.com/):

   RawTherapee is an advanced program for developing raw photos and for processing non-raw photos.

 - ImageMagick scripts:

   - [Snibgo's ImageMagick pages](https://im.snibgo.com/) (Windows batch scripts.)

   - [Fred's ImageMagick Scripts](http://www.fmwconcepts.com/imagemagick) (Linux bash scripts.)



### Closed Source freeware

 - [Picolay](http://www.picolay.de/):

   Stacker for MS Windows. Works with wine on Linux, too.

 - [stacky](https://www.bewie.de/stacky.php):

   Stacker for MS Windows. Works with wine on Linux, too.



### Closed Source commercial

 - [Helicon Focus](https://www.heliconsoft.com/heliconsoft-products/helicon-focus/):

   30 days trial version. Available for Mac and Windows.

 - [ZereneStacker](https://zerenesystems.com/cms/stacker):

   30 days trial version. Available for Linux, Mac and Windows.