Calliope Setup Guide

[Radomskyi Oleksandr]

Hi devs,

Could you, please, provide guide for the Calliope since I am not familiar with typical calcium image analysis environment?

1. Environment
   a) Matlab<version>
   b) adodb_tools <version>?
   c) database itself, which one?
   d) What else shoud be installed?</version></version>

2. Environment Configuration
   a) What should be added to PATH?
   b) What should be stored locally, where?
   c) What files should be created manually?
   d) Are there any automation scripts (like folders or data generation, copying libraries etc.) that need to be run before using Calliope
   e) What else should be done to the environment?

3. Software Configuration
   a) What other programs should be started before running Calliope?
   b) What should be loaded into memory before running Calliope?
   c) How Calliope interract with it's environment?
   d) What else should be configured?

4. Entry points
   a) After starting all the software, what is the first script(method) to be run for loading the settings into memory(workspace)?
   b) After loading settings, what to call fo loading the dataset(having path and settings)?

   Environment:
   Win 10
   Matlab R2018b
   adodb_tools 1.1.0.0

   Dataset:
   .ach
   .lvd
   .bin
   .ini

   Thank you,
   Alex

[Radomskyi Oleksandr]

Hi,
File format specs for:

.lvd
.bin

/**
* ---------- FILE FORMAT ------------
* ------------- *.lvd ---------------
*
* ------------- HEADER --------------
* 
* double    Scanning rate
* double    Number of channels
* double    Timestamp
* double    Input range
* 
* -------------- DATA ---------------
*            ...
* double    Value
*            ...
* -----------------------------------
* ----------------EOF----------------
* 
* Notes:
* 
* <double>  double precision 64 bit,
*           IEEE® Standard 754 
*/

/**
* ---------- FILE FORMAT ------------
* ------------- *.bin ---------------
*
* ------------- HEADER --------------
*
* int16    X resolution
* int16    Y resolution
*
* -------------- DATA ---------------
*                                     --.
* ------------- FRAME 0 -------------   |
*                ROW  COLUMN            |
* int16    Value  0     0               |
* int16    Value  0     1               |
* ...            ...   ...              |
* int16    Value  0     X               |
*                                       |
*                                       |
* int16    Value  1     0               |
* int16    Value  1     1               |
* ...            ...   ...              |
* int16    Value  1     X               |
*                                       |
* ...                                   | Piezo Layer 0
*                                       |
* int16    Value  Y     0               |
* int16    Value  Y     1               |
* ...            ...   ...              |
* int16    Value  Y     X               |
* -----------------------------------   |
*                                       |
*                ...                    |
*                                       |
* ------------- FRAME N -------------   |
* ...                                   |
* -----------------------------------   |
*                                     --*
*                ...
*                                     --.
* ------------- FRAME 0 -------------   |
* ...                                   |
* -----------------------------------   |
*                                       |
*                ...                    | Piezo Layer M
*                                       |
* ------------- FRAME N -------------   |
* ...                                   |
* -----------------------------------   |
*                                     --*
* ----------------EOF----------------
*
* Notes:
*
* <int16>           16-bit signed integer
*
* Header size               H = sizeof(int16) + sizeof(int16) = 4 bytes
* Data size                 D = FileSize - H
* Frame size                F = X * Y * sizeof(int16)
* Frames total              T = D / F
* Number of Piezo Layers    M   should be defined explicitly
* Frames per layer          N = (D / F) / M
*/

Best,
Alex

[Radomskyi Oleksandr]

Hi,

Which Motion Correction algo is the latest and provides better results?